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Lloyd D, House JS, Akhtari FS, Schmitt CP, Fargo DC, Scholl EH, Phillips J, Choksi S, Shah R, Hall JE, Motsinger-Reif AA. Interactive data sharing for multiple questionnaire-based exposome-wide association studies and exposome correlations in the Personalized Environment and Genes Study. Exposome 2024; 4:osae003. [PMID: 38425336 PMCID: PMC10899804 DOI: 10.1093/exposome/osae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/20/2023] [Accepted: 01/01/2024] [Indexed: 03/02/2024]
Abstract
The correlations among individual exposures in the exposome, which refers to all exposures an individual encounters throughout life, are important for understanding the landscape of how exposures co-occur, and how this impacts health and disease. Exposome-wide association studies (ExWAS), which are analogous to genome-wide association studies (GWAS), are increasingly being used to elucidate links between the exposome and disease. Despite increased interest in the exposome, tools and publications that characterize exposure correlations and their relationships with human disease are limited, and there is a lack of data and results sharing in resources like the GWAS catalog. To address these gaps, we developed the PEGS Explorer web application to explore exposure correlations in data from the diverse North Carolina-based Personalized Environment and Genes Study (PEGS) that were rigorously calculated to account for differing data types and previously published results from ExWAS. Through globe visualizations, PEGS Explorer allows users to explore correlations between exposures found to be associated with complex diseases. The exposome data used for analysis includes not only standard environmental exposures such as point source pollution and ozone levels but also exposures from diet, medication, lifestyle factors, stress, and occupation. The web application addresses the lack of accessible data and results sharing, a major challenge in the field, and enables users to put results in context, generate hypotheses, and, importantly, replicate findings in other cohorts. PEGS Explorer will be updated with additional results as they become available, ensuring it is an up-to-date resource in exposome science.
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Affiliation(s)
- Dillon Lloyd
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - John S House
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Farida S Akhtari
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Charles P Schmitt
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - David C Fargo
- Office of the Director, National Institute of Environmental Health Sciences, Durham, NC, USA
| | | | | | | | | | - Janet E Hall
- Clinical Research Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Alison A Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
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Lloyd D, House JS, Akhtari FS, Schmitt CP, Fargo DC, Scholl EH, Phillips J, Choksi S, Shah R, Hall JE, Motsinger-Reif AA. Questionnaire-based exposome-wide association studies for common diseases in the Personalized Environment and Genes Study. Exposome 2024; 4:osae002. [PMID: 38450326 PMCID: PMC10914401 DOI: 10.1093/exposome/osae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/01/2024] [Indexed: 03/08/2024]
Abstract
The exposome collectively refers to all exposures, beginning in utero and continuing throughout life, and comprises not only standard environmental exposures such as point source pollution and ozone levels but also exposures from diet, medication, lifestyle factors, stress, and occupation. The exposome interacts with individual genetic and epigenetic characteristics to affect human health and disease, but large-scale studies that characterize the exposome and its relationships with human disease are limited. To address this gap, we used extensive questionnaire data from the diverse North Carolina-based Personalized Environment and Genes Study (PEGS, n = 9, 429) to evaluate exposure associations in relation to common diseases. We performed an exposome-wide association study (ExWAS) to examine single exposure models and their associations with 11 common complex diseases, namely allergic rhinitis, asthma, bone loss, fibroids, high cholesterol, hypertension, iron-deficient anemia, ovarian cysts, lower GI polyps, migraines, and type 2 diabetes. Across diseases, we found associations with lifestyle factors and socioeconomic status as well as asbestos, various dust types, biohazardous material, and textile-related exposures. We also found disease-specific associations such as fishing with lead weights and migraines. To differentiate between a replicated result and a novel finding, we used an AI-based literature search and database tool that allowed us to examine the current literature. We found both replicated findings, especially for lifestyle factors such as sleep and smoking across diseases, and novel findings, especially for occupational exposures and multiple diseases.
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Affiliation(s)
- Dillon Lloyd
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - John S House
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Farida S Akhtari
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Charles P Schmitt
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - David C Fargo
- Office of the Director, National Institute of Environmental Health Sciences, Durham, NC, USA
| | | | | | | | | | - Janet E Hall
- Clinical Research Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Alison A Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
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3
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Chung MK, House JS, Akhtari FS, Makris KC, Langston MA, Islam KT, Holmes P, Chadeau-Hyam M, Smirnov AI, Du X, Thessen AE, Cui Y, Zhang K, Manrai AK, Motsinger-Reif A, Patel CJ. Decoding the exposome: data science methodologies and implications in exposome-wide association studies (ExWASs). Exposome 2024; 4:osae001. [PMID: 38344436 PMCID: PMC10857773 DOI: 10.1093/exposome/osae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 10/16/2023] [Accepted: 11/20/2023] [Indexed: 03/07/2024]
Abstract
This paper explores the exposome concept and its role in elucidating the interplay between environmental exposures and human health. We introduce two key concepts critical for exposomics research. Firstly, we discuss the joint impact of genetics and environment on phenotypes, emphasizing the variance attributable to shared and nonshared environmental factors, underscoring the complexity of quantifying the exposome's influence on health outcomes. Secondly, we introduce the importance of advanced data-driven methods in large cohort studies for exposomic measurements. Here, we introduce the exposome-wide association study (ExWAS), an approach designed for systematic discovery of relationships between phenotypes and various exposures, identifying significant associations while controlling for multiple comparisons. We advocate for the standardized use of the term "exposome-wide association study, ExWAS," to facilitate clear communication and literature retrieval in this field. The paper aims to guide future health researchers in understanding and evaluating exposomic studies. Our discussion extends to emerging topics, such as FAIR Data Principles, biobanked healthcare datasets, and the functional exposome, outlining the future directions in exposomic research. This abstract provides a succinct overview of our comprehensive approach to understanding the complex dynamics of the exposome and its significant implications for human health.
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Affiliation(s)
- Ming Kei Chung
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
- Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | - John S House
- Biostatistics and Computational Biology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Farida S Akhtari
- Biostatistics and Computational Biology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Konstantinos C Makris
- Cyprus International Institute for Environmental and Public Health, School of Health Sciences, Cyprus University of Technology, Limassol, Cyprus
| | - Michael A Langston
- Department of Electrical Engineering and Computer Science, University of TN, Knoxville, TN, USA
| | - Khandaker Talat Islam
- Department of Population and Public Health Sciences, Keck School of Medicine of the University of Southern CA, Los Angeles, CA, USA
| | - Philip Holmes
- Department of Physics, Villanova University, Villanova, Philadelphia, USA
| | - Marc Chadeau-Hyam
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Alex I Smirnov
- Department of Chemistry, NC State University, Raleigh, NC, USA
| | - Xiuxia Du
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of NC at Charlotte, Charlotte, NC, USA
| | - Anne E Thessen
- Department of Biomedical Informatics, University of CO Anschutz Medical Campus, Aurora, CO, USA
| | - Yuxia Cui
- Exposure, Response, and Technology Branch, Division of Extramural Research and Training, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Kai Zhang
- Department of Environmental Health Sciences, School of Public Health, University at Albany, State University of NY, Rensselaer, NY, USA
| | - Arjun K Manrai
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Chirag J Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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4
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Armstrong ND, Srinivasasainagendra V, Ammous F, Assimes TL, Beitelshees AL, Brody J, Cade BE, Ida Chen YD, Chen H, de Vries PS, Floyd JS, Franceschini N, Guo X, Hellwege JN, House JS, Hwu CM, Kardia SLR, Lange EM, Lange LA, McDonough CW, Montasser ME, O’Connell JR, Shuey MM, Sun X, Tanner RM, Wang Z, Zhao W, Carson AP, Edwards TL, Kelly TN, Kenny EE, Kooperberg C, Loos RJF, Morrison AC, Motsinger-Reif A, Psaty BM, Rao DC, Redline S, Rich SS, Rotter JI, Smith JA, Smith AV, Irvin MR, Arnett DK. Whole genome sequence analysis of apparent treatment resistant hypertension status in participants from the Trans-Omics for Precision Medicine program. Front Genet 2023; 14:1278215. [PMID: 38162683 PMCID: PMC10755672 DOI: 10.3389/fgene.2023.1278215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 11/24/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction: Apparent treatment-resistant hypertension (aTRH) is characterized by the use of four or more antihypertensive (AHT) classes to achieve blood pressure (BP) control. In the current study, we conducted single-variant and gene-based analyses of aTRH among individuals from 12 Trans-Omics for Precision Medicine cohorts with whole-genome sequencing data. Methods: Cases were defined as individuals treated for hypertension (HTN) taking three different AHT classes, with average systolic BP ≥ 140 or diastolic BP ≥ 90 mmHg, or four or more medications regardless of BP (n = 1,705). A normotensive control group was defined as individuals with BP < 140/90 mmHg (n = 22,079), not on AHT medication. A second control group comprised individuals who were treatment responsive on one AHT medication with BP < 140/ 90 mmHg (n = 5,424). Logistic regression with kinship adjustment using the Scalable and Accurate Implementation of Generalized mixed models (SAIGE) was performed, adjusting for age, sex, and genetic ancestry. We assessed variants using SKAT-O in rare-variant analyses. Single-variant and gene-based tests were conducted in a pooled multi-ethnicity stratum, as well as self-reported ethnic/racial strata (European and African American). Results: One variant in the known HTN locus, KCNK3, was a top finding in the multi-ethnic analysis (p = 8.23E-07) for the normotensive control group [rs12476527, odds ratio (95% confidence interval) = 0.80 (0.74-0.88)]. This variant was replicated in the Vanderbilt University Medical Center's DNA repository data. Aggregate gene-based signals included the genes AGTPBP, MYL4, PDCD4, BBS9, ERG, and IER3. Discussion: Additional work validating these loci in larger, more diverse populations, is warranted to determine whether these regions influence the pathobiology of aTRH.
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Affiliation(s)
- Nicole D. Armstrong
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | | | - Farah Ammous
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
- Survey Research Center, Institute for Social Research, Ann Arbor, MI, United States
| | - Themistocles L. Assimes
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Amber L. Beitelshees
- Division of Endocrinology, Diabetes, and Nutrition, Program for Personalized and Genomic Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Jennifer Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, United States
| | - Brian E. Cade
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States
| | - Han Chen
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Paul S. de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - James S. Floyd
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Epidemiology, University of Washington, Seattle, WA, United States
| | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, United States
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States
| | - Jacklyn N. Hellwege
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, United States
| | - John S. House
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Chii-Min Hwu
- Section of Endocrinology and Metabolism, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Sharon L. R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Ethan M. Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Leslie A. Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Caitrin W. McDonough
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - May E. Montasser
- Division of Endocrinology, Diabetes, and Nutrition, Program for Personalized and Genomic Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | | | - Megan M. Shuey
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Xiao Sun
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States
| | - Rikki M. Tanner
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
- Survey Research Center, Institute for Social Research, Ann Arbor, MI, United States
| | - April P. Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, United States
| | - Todd L. Edwards
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, United States
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Tanika N. Kelly
- Division of Nephrology, Department of Medicine, College of Medicine, University of Illinois Chicago, Chicago, IL, United States
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Ruth J. F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Alanna C. Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Epidemiology, University of Washington, Seattle, WA, United States
| | - Dabeeru C. Rao
- Division of Biostatistics, School of Medicine, Washington University in St. Louis, St. Louis, MO, United States
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Stephen S. Rich
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
- Survey Research Center, Institute for Social Research, Ann Arbor, MI, United States
| | - Albert V. Smith
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Marguerite R. Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Donna K. Arnett
- Office of the Provost, University of South Carolina, Columbia, SC, United States
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5
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Choudhary P, Monasso GS, Karhunen V, Ronkainen J, Mancano G, Howe CG, Niu Z, Zeng X, Guan W, Dou J, Feinberg JI, Mordaunt C, Pesce G, Baïz N, Alfano R, Martens DS, Wang C, Isaevska E, Keikkala E, Mustaniemi S, Thio CHL, Fraszczyk E, Tobi EW, Starling AP, Cosin-Tomas M, Urquiza J, Röder S, Hoang TT, Page C, Jima DD, House JS, Maguire RL, Ott R, Pawlow X, Sirignano L, Zillich L, Malmberg A, Rauschert S, Melton P, Gong T, Karlsson R, Fore R, Perng W, Laubach ZM, Czamara D, Sharp G, Breton CV, Schisterman E, Yeung E, Mumford SL, Fallin MD, LaSalle JM, Schmidt RJ, Bakulski KM, Annesi-Maesano I, Heude B, Nawrot TS, Plusquin M, Ghantous A, Herceg Z, Nisticò L, Vafeiadi M, Kogevinas M, Vääräsmäki M, Kajantie E, Snieder H, Corpeleijn E, Steegers-Theunissen RPM, Yang IV, Dabelea D, Fossati S, Zenclussen AC, Herberth G, Magnus M, Håberg SE, London SJ, Munthe-Kaas MC, Murphy SK, Hoyo C, Ziegler AG, Hummel S, Witt SH, Streit F, Frank J, Räikkönen K, Lahti J, Huang RC, Almqvist C, Hivert MF, Jaddoe VWV, Järvelin MR, Kantomaa M, Felix JF, Sebert S. Maternal educational attainment in pregnancy and epigenome-wide DNA methylation changes in the offspring from birth until adolescence. Mol Psychiatry 2023:10.1038/s41380-023-02331-5. [PMID: 38052982 DOI: 10.1038/s41380-023-02331-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/07/2023] [Accepted: 11/15/2023] [Indexed: 12/07/2023]
Abstract
Maternal educational attainment (MEA) shapes offspring health through multiple potential pathways. Differential DNA methylation may provide a mechanistic understanding of these long-term associations. We aimed to quantify the associations of MEA with offspring DNA methylation levels at birth, in childhood and in adolescence. Using 37 studies from high-income countries, we performed meta-analysis of epigenome-wide association studies (EWAS) to quantify the associations of completed years of MEA at the time of pregnancy with offspring DNA methylation levels at birth (n = 9 881), in childhood (n = 2 017), and adolescence (n = 2 740), adjusting for relevant covariates. MEA was found to be associated with DNA methylation at 473 cytosine-phosphate-guanine sites at birth, one in childhood, and four in adolescence. We observed enrichment for findings from previous EWAS on maternal folate, vitamin-B12 concentrations, maternal smoking, and pre-pregnancy BMI. The associations were directionally consistent with MEA being inversely associated with behaviours including smoking and BMI. Our findings form a bridge between socio-economic factors and biology and highlight potential pathways underlying effects of maternal education. The results broaden our understanding of bio-social associations linked to differential DNA methylation in multiple early stages of life. The data generated also offers an important resource to help a more precise understanding of the social determinants of health.
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Affiliation(s)
- Priyanka Choudhary
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, 90014, Oulu, Finland.
| | - Giulietta S Monasso
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Ville Karhunen
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, 90014, Oulu, Finland
- Research Unit of Mathematical Sciences, Faculty of Science, University of Oulu, Oulu, Finland
| | - Justiina Ronkainen
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, 90014, Oulu, Finland
| | - Giulia Mancano
- Medical Research Council Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol Medical School Population Health Sciences, University of Bristol, Bristol, UK
| | - Caitlin G Howe
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Zhongzheng Niu
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, 55455, USA
| | - John Dou
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jason I Feinberg
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MA, USA
| | - Charles Mordaunt
- Department of Medical Micriobiology and Immunology, University of California Davis, Davis, CA, USA
| | - Giancarlo Pesce
- Epidemiology of Allergic and Respiratory Diseases (EPAR) team, Faculté de Médecine Saint-Antoine, Institute Pierre Louis d'Epidemiologie et Sante Publique (IPLESP), Sorbonne Université and INSERM, Paris, France
- Paris-Saclay University, Paris-South University, UVSQ, Center for Research in Epidemiology and Population Health (CESP), INSERM, Villejuif, France
| | - Nour Baïz
- Institute Desbrest of Epidemiology and Public Health, University of Montpellier and INSERM, Montpellier, France
| | - Rossella Alfano
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Dries S Martens
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Congrong Wang
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Elena Isaevska
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin and CPO-Piemonte, Torino, Italy
| | - Elina Keikkala
- Department of Obstetrics and Gynaecology, Research Unit of Clinical Medicine, Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
- Finnish Institute for Health and Welfare, Population Health Unit, Public Health and Welfare, Helsinki and Oulu, Finland
| | - Sanna Mustaniemi
- Department of Obstetrics and Gynaecology, Research Unit of Clinical Medicine, Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
- Finnish Institute for Health and Welfare, Population Health Unit, Public Health and Welfare, Helsinki and Oulu, Finland
| | - Chris H L Thio
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Eliza Fraszczyk
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Elmar W Tobi
- Department of Obstetrics and Gynaecology, Division of Obstetrics and Prenatal Medicine, Erasmus MC, University Medical Center, 3000 CA, Rotterdam, the Netherlands
| | - Anne P Starling
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Marta Cosin-Tomas
- ISGlobal (Barcelona Institute for Global Health), Barcelona Biomedical Research Park (PRBB), Doctor Aiguader, 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Jose Urquiza
- ISGlobal (Barcelona Institute for Global Health), Barcelona Biomedical Research Park (PRBB), Doctor Aiguader, 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Stefan Röder
- Department for Environmental Immunology, Helmholtz Centre for Environmental Research, UFZ, Leipzig, Germany
| | - Thanh T Hoang
- Epidemiology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Christian Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Oslo Centre for Biostatistics and Epidemiology, Section for Research Support, Oslo University Hospital, Oslo, Norway
| | - Dereje D Jima
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27606, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27606, USA
| | - John S House
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27606, USA
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, Durham, NC, 27709, USA
| | - Rachel L Maguire
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, 27701, USA
| | - Raffael Ott
- Institute of Diabetes Research, Helmholtz Munich, German Research Center for Environmental Health, Munich, Germany
- Forschergruppe Diabetes eV, Neuherberg, Germany
| | - Xenia Pawlow
- Institute of Diabetes Research, Helmholtz Munich, German Research Center for Environmental Health, Munich, Germany
- Forschergruppe Diabetes eV, Neuherberg, Germany
| | - Lea Sirignano
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Lea Zillich
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Anni Malmberg
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | - Phillip Melton
- Menzies Institute of Medical Research, University of Tasmania, Hobart, TAS, Australia
- University of Western Australia, School of Population and Global Health, Perth, WA, Australia
| | - Tong Gong
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ruby Fore
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Wei Perng
- Department of Epidemiology and the Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Zachary M Laubach
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Darina Czamara
- Department Genes and Environment, Max Planck Institute for Psychiatry, Kraepelinstrasse 2+10, 80804, Munich, Germany
| | - Gemma Sharp
- Medical Research Council Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol Medical School Population Health Sciences, University of Bristol, Bristol, UK
- School of Psychology, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Carrie V Breton
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Enrique Schisterman
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Edwina Yeung
- Epidemiology Branch, Division of Population Health Research, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20817, USA
| | - Sunni L Mumford
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epidemiology Branch, Division of Population Health Research, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20817, USA
| | - M Daniele Fallin
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MA, USA
| | - Janine M LaSalle
- Department of Medical Micriobiology and Immunology, University of California Davis, Davis, CA, USA
| | - Rebecca J Schmidt
- Department of Public Health Sciences, School of Medicine, University of California Davis (UC Davis), Davis, CA, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Isabella Annesi-Maesano
- Institute Desbrest of Epidemiology and Public Health, University of Montpellier and INSERM, Montpellier, France
| | - Barbara Heude
- Université de Paris Cité, Inserm, INRAE, Centre of Research in Epidemiology and StatisticS (CRESS), F-75004, Paris, France
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Akram Ghantous
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| | - Lorenza Nisticò
- Centre for Behavioural Sciences and Mental Health, Istituto Superiore di Sanità, Viale Regina Elena, Rome, Italy
| | - Marina Vafeiadi
- Department of Social Medicine, School of Medicine, University of Crete, Heraklion, Crete, Greece
| | - Manolis Kogevinas
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Centro de Investigación Biomédicaen Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Marja Vääräsmäki
- Department of Obstetrics and Gynaecology, Research Unit of Clinical Medicine, Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
- Finnish Institute for Health and Welfare, Population Health Unit, Public Health and Welfare, Helsinki and Oulu, Finland
| | - Eero Kajantie
- Finnish Institute for Health and Welfare, Population Health Unit, Public Health and Welfare, Helsinki and Oulu, Finland
- Clinical Medicine Research Unit, Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Harold Snieder
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Eva Corpeleijn
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Regine P M Steegers-Theunissen
- Department of Obstetrics and Gynaecology, Division of Obstetrics and Prenatal Medicine, Erasmus MC, University Medical Center, 3000 CA, Rotterdam, the Netherlands
| | - Ivana V Yang
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Dana Dabelea
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Pediatrics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Serena Fossati
- ISGlobal (Barcelona Institute for Global Health), Barcelona Biomedical Research Park (PRBB), Doctor Aiguader, 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Ana C Zenclussen
- Department for Environmental Immunology, Helmholtz Centre for Environmental Research, UFZ, Leipzig, Germany
| | - Gunda Herberth
- Department for Environmental Immunology, Helmholtz Centre for Environmental Research, UFZ, Leipzig, Germany
| | - Maria Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Stephanie J London
- Epidemiology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Monica Cheng Munthe-Kaas
- Department of Pediatrics, Oncology and Hematology, Oslo University Hospital, Oslo, Norway
- Norwegian Institute of Public Health, Oslo, Norway
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, 27701, USA
| | - Cathrine Hoyo
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27606, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Anette-G Ziegler
- Institute of Diabetes Research, Helmholtz Munich, German Research Center for Environmental Health, Munich, Germany
- Forschergruppe Diabetes eV, Neuherberg, Germany
- Technical University Munich, School of Medicine, Forschergruppe Diabetes at Klinikum rechts der Isar, Munich, Germany
| | - Sandra Hummel
- Institute of Diabetes Research, Helmholtz Munich, German Research Center for Environmental Health, Munich, Germany
- Forschergruppe Diabetes eV, Neuherberg, Germany
- Technical University Munich, School of Medicine, Forschergruppe Diabetes at Klinikum rechts der Isar, Munich, Germany
| | - Stephanie H Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Innovative Psychiatric and Psychotherapeutic Research, Biobank, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Fabian Streit
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Josef Frank
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Katri Räikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Rae-Chi Huang
- Telethon Kids Institute, Perth, WA, Australia
- Edith Cowan University, School of Medicine and Health Sciences, Joondalup, WA, Australia
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pediatric Allergy and Pulmonology Unit at Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Marjo-Riitta Järvelin
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, 90014, Oulu, Finland
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, UK
| | - Marko Kantomaa
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, 90014, Oulu, Finland
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Sylvain Sebert
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, 90014, Oulu, Finland
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6
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Jackson TW, House JS, Henriquez AR, Schladweiler MC, Jackson KM, Fisher AA, Snow SJ, Alewel DI, Motsinger-Reif AA, Kodavanti UP. Multi-tissue transcriptomic and serum metabolomic assessment reveals systemic implications of acute ozone-induced stress response in male Wistar Kyoto rats. Metabolomics 2023; 19:81. [PMID: 37690105 DOI: 10.1007/s11306-023-02043-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/21/2023] [Indexed: 09/12/2023]
Abstract
Air pollutant exposures have been linked to systemic disease; however, the underlying mechanisms between responses of the target tissue and systemic effects are poorly understood. A prototypic inducer of stress, ozone causes respiratory and systemic multiorgan effects through activation of a neuroendocrine stress response. The goal of this study was to assess transcriptomic signatures of multiple tissues and serum metabolomics to understand how neuroendocrine and adrenal-derived stress hormones contribute to multiorgan health outcomes. Male Wistar Kyoto rats (12-13 weeks old) were exposed to filtered air or 0.8 ppm ozone for 4-hours, and blood/tissues were collected immediately post-exposure. Each tissue had distinct expression profiles at baseline. Ozone changed 1,640 genes in lung, 274 in hypothalamus, 2,516 in adrenals, 1,333 in liver, 1,242 in adipose, and 5,102 in muscle (adjusted p-value < 0.1, absolute fold-change > 50%). Serum metabolomic analysis identified 863 metabolites, of which 447 were significantly altered in ozone-exposed rats (adjusted p-value < 0.1, absolute fold change > 20%). A total of 6 genes were differentially expressed in all 6 tissues. Glucocorticoid signaling, hypoxia, and GPCR signaling were commonly changed, but ozone induced tissue-specific changes in oxidative stress, immune processes, and metabolic pathways. Genes upregulated by TNF-mediated NFkB signaling were differentially expressed in all ozone-exposed tissues, but those defining inflammatory response were tissue-specific. Upstream predictor analysis identified common mediators of effects including glucocorticoids, although the specific genes responsible for these predictors varied by tissue. Metabolomic analysis showed major changes in lipids, amino acids, and metabolites linked to the gut microbiome, concordant with transcriptional changes identified through pathway analysis within liver, muscle, and adipose tissues. The distribution of receptors and transcriptional mechanisms underlying the ozone-induced stress response are tissue-specific and involve induction of unique gene networks and metabolic phenotypes, but the shared initiating triggers converge into shared pathway-level responses. This multi-tissue transcriptomic analysis, combined with circulating metabolomic assessment, allows characterization of the systemic inhaled pollutant-induced stress response.
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Affiliation(s)
- Thomas W Jackson
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA.
- Oak Ridge Institute for Science and Education Research Participation Program, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA.
| | - John S House
- Division of Intramural Research, National Institute of Environmental Health Sciences, Department of Health and Human Services, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Andres R Henriquez
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Mette C Schladweiler
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
| | | | - Anna A Fisher
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
| | - Sam J Snow
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
- ICF, Durham, NC, USA
| | - Devin I Alewel
- Oak Ridge Institute for Science and Education Research Participation Program, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
| | - Allison A Motsinger-Reif
- Oak Ridge Institute for Science and Education Research Participation Program, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
| | - Urmila P Kodavanti
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
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7
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Lee EY, Choi W, Burkholder AB, Perera L, Mack JA, Miller FW, Fessler MB, Cook DN, Karmaus PWF, Nakano H, Garantziotis S, Madenspacher JH, House JS, Akhtari FS, Schmitt CS, Fargo DC, Hall JE, Motsinger-Reif AA. Race/ethnicity-stratified fine-mapping of the MHC locus reveals genetic variants associated with late-onset asthma. Front Genet 2023; 14:1173676. [PMID: 37415598 PMCID: PMC10321602 DOI: 10.3389/fgene.2023.1173676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 06/09/2023] [Indexed: 07/08/2023] Open
Abstract
Introduction: Asthma is a chronic disease of the airways that impairs normal breathing. The etiology of asthma is complex and involves multiple factors, including the environment and genetics, especially the distinct genetic architecture associated with ancestry. Compared to early-onset asthma, little is known about genetic predisposition to late-onset asthma. We investigated the race/ethnicity-specific relationship among genetic variants within the major histocompatibility complex (MHC) region and late-onset asthma in a North Carolina-based multiracial cohort of adults. Methods: We stratified all analyses by self-reported race (i.e., White and Black) and adjusted all regression models for age, sex, and ancestry. We conducted association tests within the MHC region and performed fine-mapping analyses conditioned on the race/ethnicity-specific lead variant using whole-genome sequencing (WGS) data. We applied computational methods to infer human leukocyte antigen (HLA) alleles and residues at amino acid positions. We replicated findings in the UK Biobank. Results: The lead signals, rs9265901 on the 5' end of HLA-B, rs55888430 on HLA-DOB, and rs117953947 on HCG17, were significantly associated with late-onset asthma in all, White, and Black participants, respectively (OR = 1.73, 95%CI: 1.31 to 2.14, p = 3.62 × 10-5; OR = 3.05, 95%CI: 1.86 to 4.98, p = 8.85 × 10-6; OR = 19.5, 95%CI: 4.37 to 87.2, p = 9.97 × 10-5, respectively). For the HLA analysis, HLA-B*40:02 and HLA-DRB1*04:05, HLA-B*40:02, HLA-C*04:01, and HLA-DRB1*04:05, and HLA-DRB1*03:01 and HLA-DQB1 were significantly associated with late-onset asthma in all, White, and Black participants. Conclusion: Multiple genetic variants within the MHC region were significantly associated with late-onset asthma, and the associations were significantly different by race/ethnicity group.
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Affiliation(s)
- Eunice Y. Lee
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Wonson Choi
- Genomics and Bioinformatics Laboratory, Seoul National University, Seoul, Republic of Korea
| | - Adam B. Burkholder
- National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Lalith Perera
- Genomic Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Jasmine A. Mack
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, United States
- Department of Obstetrics and Gynecology, University of Cambridge, Cambridge, United Kingdom
| | - Frederick W. Miller
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Michael B. Fessler
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Donald N. Cook
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, Durham, NC, United States
- Immunogenetics Group, National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Peer W. F. Karmaus
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Hideki Nakano
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Stavros Garantziotis
- Clinical Research Branch, National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Jennifer H. Madenspacher
- Clinical Research Branch, National Institute of Environmental Health Sciences, Durham, NC, United States
| | - John S. House
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Farida S. Akhtari
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, United States
- Clinical Research Branch, National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Charles S. Schmitt
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, Durham, NC, United States
| | - David C. Fargo
- National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Janet E. Hall
- Clinical Research Branch, National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Alison A. Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, United States
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8
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Tsai HHD, House JS, Wright FA, Chiu WA, Rusyn I. A tiered testing strategy based on in vitro phenotypic and transcriptomic data for selecting representative petroleum UVCBs for toxicity evaluation in vivo. Toxicol Sci 2023; 193:219-233. [PMID: 37079747 PMCID: PMC10230285 DOI: 10.1093/toxsci/kfad041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
Hazard evaluation of substances of "unknown or variable composition, complex reaction products and biological materials" (UVCBs) remains a major challenge in regulatory science because their chemical composition is difficult to ascertain. Petroleum substances are representative UVCBs and human cell-based data have been previously used to substantiate their groupings for regulatory submissions. We hypothesized that a combination of phenotypic and transcriptomic data could be integrated to make decisions as to selection of group-representative worst-case petroleum UVCBs for subsequent toxicity evaluation in vivo. We used data obtained from 141 substances from 16 manufacturing categories previously tested in 6 human cell types (induced pluripotent stem cell [iPSC]-derived hepatocytes, cardiomyocytes, neurons, and endothelial cells, and MCF7 and A375 cell lines). Benchmark doses for gene-substance combinations were calculated, and both transcriptomic and phenotype-derived points of departure (PODs) were obtained. Correlation analysis and machine learning were used to assess associations between phenotypic and transcriptional PODs and to determine the most informative cell types and assays, thus representing a cost-effective integrated testing strategy. We found that 2 cell types-iPSC-derived-hepatocytes and -cardiomyocytes-contributed the most informative and protective PODs and may be used to inform selection of representative petroleum UVCBs for further toxicity evaluation in vivo. Overall, although the use of new approach methodologies to prioritize UVCBs has not been widely adopted, our study proposes a tiered testing strategy based on iPSC-derived hepatocytes and cardiomyocytes to inform selection of representative worst-case petroleum UVCBs from each manufacturing category for further toxicity evaluation in vivo.
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Affiliation(s)
- Han-Hsuan Doris Tsai
- Interdisciplinary Faculty of Toxicology, College Station, Texas 77843, USA
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, USA
| | - John S House
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
| | - Fred A Wright
- Interdisciplinary Faculty of Toxicology, College Station, Texas 77843, USA
- Department of Statistics and Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27603, USA
- Department of Biological Sciences and Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27603, USA
| | - Weihsueh A Chiu
- Interdisciplinary Faculty of Toxicology, College Station, Texas 77843, USA
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, USA
| | - Ivan Rusyn
- Interdisciplinary Faculty of Toxicology, College Station, Texas 77843, USA
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, USA
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9
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House JS, Gray S, Owen JR, Jima DD, Smart RC, Hall JR. C/EBPβ deficiency enhances the keratinocyte innate immune response to direct activators of cytosolic pattern recognition receptors. Innate Immun 2023; 29:14-24. [PMID: 37094088 PMCID: PMC10164275 DOI: 10.1177/17534259231162192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/10/2023] [Accepted: 02/08/2023] [Indexed: 04/26/2023] Open
Abstract
The skin is the first line of defense to cutaneous microbes and viruses, and epidermal keratinocytes play a critical role in preventing infection by viruses and pathogens through activation of the type I interferon (IFN) response. Using RNAseq analysis, here we report that the conditional deletion of C/EBPβ transcription factor in mouse epidermis (CKOβ mice) resulted in the upregulation of IFNβ and numerous keratinocyte interferon-stimulated genes (ISGs). The expression of cytosolic pattern recognition receptors (cPRRs), that recognize viral RNA and DNA, were significantly increased, and enriched in the RNAseq data set. cPRRs stimulate a type I IFN response that can trigger cell death to eliminate infected cells. To determine if the observed increases in cPRRs had functional consequences, we transfected CKOβ primary keratinocytes with the pathogen and viral mimics poly(I:C) (dsRNA) or poly(dA:dT) (synthetic B-DNA) that directly activate PRRs. Transfected CKOβ primary keratinocytes displayed an amplified type I IFN response which was accompanied by increased activation of IRF3, enhanced ISG expression, enhanced activation of caspase-8, caspase-3 and increased apoptosis. Our results identify C/EBPβ as a critical repressor of the keratinocyte type I IFN response, and demonstrates that the loss of C/EBPβ primes keratinocytes to the activation of cytosolic PRRs by pathogen RNA and DNA to induce cell death mediated by caspase-8 and caspase-3.
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Affiliation(s)
- John S. House
- Center of Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA
- Toxicology Graduate Program, North Carolina State University, Raleigh, NC, 27695, USA
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, Durham, NC 27709, USA
| | - Sophia Gray
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Jennifer R. Owen
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Dereje D. Jima
- Center of Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Robert C. Smart
- Center of Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA
- Toxicology Graduate Program, North Carolina State University, Raleigh, NC, 27695, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Jonathan R. Hall
- Center of Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA
- Toxicology Graduate Program, North Carolina State University, Raleigh, NC, 27695, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
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10
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Henriquez AR, Snow SJ, Jackson TW, House JS, Alewel DI, Schladweiler MC, Valdez MC, Freeborn DL, Miller CN, Grindstaff R, Kodavanti PRS, Kodavanti UP. Social isolation exacerbates acute ozone inhalation induced pulmonary and systemic health outcomes. Toxicol Appl Pharmacol 2022; 457:116295. [PMID: 36341779 PMCID: PMC9722630 DOI: 10.1016/j.taap.2022.116295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022]
Abstract
Psychosocially-stressed individuals might have exacerbated responses to air pollution exposure. Acute ozone exposure activates the neuroendocrine stress response leading to systemic metabolic and lung inflammatory changes. We hypothesized chronic mild stress (CS) and/or social isolation (SI) would cause neuroendocrine, inflammatory, and metabolic phenotypes that would be exacerbated by an acute ozone exposure. Male 5-week-old Wistar-Kyoto rats were randomly assigned into 3 groups: no stress (NS) (pair-housed, regular-handling); SI (single-housed, minimal-handling); CS (single-housed, subjected to mild unpredicted-randomized stressors [restraint-1 h, tilted cage-1 h, shaking-1 h, intermittent noise-6 h, and predator odor-1 h], 1-stressor/day*5-days/week*8-weeks. All animals then 13-week-old were subsequently exposed to filtered-air or ozone (0.8-ppm) for 4 h and immediately necropsied. CS, but not SI animals had increased adrenal weights. However, relative to NS, both CS and SI had lower circulating luteinizing hormone, prolactin, and follicle-stimulating hormone regardless of exposure (SI > CS), and only CS demonstrated lower thyroid-stimulating hormone levels. SI caused more severe systemic inflammation than CS, as evidenced by higher circulating cytokines and cholesterol. Ozone exposure increased urine corticosterone and catecholamine metabolites with no significant stressor effect. Ozone-induced lung injury, and increases in lavage-fluid neutrophils and IL-6, were exacerbated by SI. Ozone severely lowered circulating thyroid-stimulating hormone, prolactin, and luteinizing hormone in all groups and exacerbated systemic inflammation in SI. Ozone-induced increases in serum glucose, leptin, and triglycerides were consistent across stressors; however, increases in cholesterol were exacerbated by SI. Collectively, psychosocial stressors, especially SI, affected the neuroendocrine system and induced adverse metabolic and inflammatory effects that were exacerbated by ozone exposure.
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Affiliation(s)
- Andres R Henriquez
- Oak Ridge Institute for Science and Education Research Participation Program, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | - Samantha J Snow
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | - Thomas W Jackson
- Oak Ridge Institute for Science and Education Research Participation Program, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | - John S House
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Devin I Alewel
- Oak Ridge Institute for Science and Education Research Participation Program, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | - Mette C Schladweiler
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | - Matthew C Valdez
- Oak Ridge Institute for Science and Education Research Participation Program, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | - Danielle L Freeborn
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | - Colette N Miller
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | - Rachel Grindstaff
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | - Prasada Rao S Kodavanti
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | - Urmila P Kodavanti
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
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Henriquez AR, Snow SJ, Jackson TW, House JS, Motsinger-Reif AA, Ward-Caviness CK, Schladweiler MC, Alewel DI, Miller CN, Farraj AK, Hazari MS, Grindstaff R, Diaz-Sanchez D, Ghio AJ, Kodavanti UP. Stress Drivers of Glucose Dynamics during Ozone Exposure Measured Using Radiotelemetry in Rats. Environ Health Perspect 2022; 130:127006. [PMID: 36542476 PMCID: PMC9770052 DOI: 10.1289/ehp11088] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND Inhaled irritant air pollutants may trigger stress-related metabolic dysfunction associated with altered circulating adrenal-derived hormones. OBJECTIVES We used implantable telemetry in rats to assess real-time changes in circulating glucose during and after exposure to ozone and mechanistically linked responses to neuroendocrine stress hormones. METHODS First, using a cross-over design, we monitored glucose during ozone exposures (0.0, 0.2, 0.4, and 0.8 ppm) and nonexposure periods in male Wistar Kyoto rats implanted with glucose telemeters. A second cohort of unimplanted rats was exposed to ozone (0.0, 0.4 or 0.8 ppm) for 30 min, 1 h, 2 h, or 4 h with hormones measured immediately post exposure. We assessed glucose metabolism in sham and adrenalectomized rats, with or without supplementation of adrenergic/glucocorticoid receptor agonists, and in a separate cohort, antagonists. RESULTS Ozone (0.8 ppm) was associated with significantly higher blood glucose and lower core body temperature beginning 90 min into exposure, with reversal of effects 4-6 h post exposure. Glucose monitoring during four daily 4-h ozone exposures revealed duration of glucose increases, adaptation, and diurnal variations. Ozone-induced glucose changes were preceded by higher levels of adrenocorticotropic hormone, corticosterone, and epinephrine but lower levels of thyroid-stimulating hormone, prolactin, and luteinizing hormones. Higher glucose and glucose intolerance were inhibited in rats that were adrenalectomized or treated with adrenergic plus glucocorticoid receptor antagonists but exacerbated by agonists. DISCUSSION We demonstrated the temporality of neuroendocrine-stress-mediated biological sequalae responsible for ozone-induced glucose metabolic dysfunction and mechanism in a rodent model. Stress hormones assessment with real-time glucose monitoring may be useful in identifying interactions among irritant pollutants and stress-related illnesses. https://doi.org/10.1289/EHP11088.
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Affiliation(s)
- Andres R. Henriquez
- Oak Ridge Institute for Science and Education Research Participation Program, U.S. Environmental Protection Agency (U.S. EPA), Research Triangle Park, North Carolina, USA
| | - Samantha J. Snow
- Center for Public Health and Environmental Assessment, U.S. EPA, Research Triangle Park, North Carolina, USA
| | - Thomas W. Jackson
- Oak Ridge Institute for Science and Education Research Participation Program, U.S. Environmental Protection Agency (U.S. EPA), Research Triangle Park, North Carolina, USA
| | - John S. House
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Alison A. Motsinger-Reif
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Cavin K. Ward-Caviness
- Center for Public Health and Environmental Assessment, U.S. EPA, Research Triangle Park, North Carolina, USA
| | - Mette C. Schladweiler
- Center for Public Health and Environmental Assessment, U.S. EPA, Research Triangle Park, North Carolina, USA
| | - Devin I. Alewel
- Oak Ridge Institute for Science and Education Research Participation Program, U.S. Environmental Protection Agency (U.S. EPA), Research Triangle Park, North Carolina, USA
| | - Colette N. Miller
- Center for Public Health and Environmental Assessment, U.S. EPA, Research Triangle Park, North Carolina, USA
| | - Aimen K. Farraj
- Center for Public Health and Environmental Assessment, U.S. EPA, Research Triangle Park, North Carolina, USA
| | - Mehdi S. Hazari
- Center for Public Health and Environmental Assessment, U.S. EPA, Research Triangle Park, North Carolina, USA
| | - Rachel Grindstaff
- Center for Public Health and Environmental Assessment, U.S. EPA, Research Triangle Park, North Carolina, USA
| | - David Diaz-Sanchez
- Center for Public Health and Environmental Assessment, U.S. EPA, Research Triangle Park, North Carolina, USA
| | - Andrew J. Ghio
- Center for Public Health and Environmental Assessment, U.S. EPA, Research Triangle Park, North Carolina, USA
| | - Urmila P. Kodavanti
- Center for Public Health and Environmental Assessment, U.S. EPA, Research Triangle Park, North Carolina, USA
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12
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Akhtari FS, Lloyd D, Burkholder A, Tong X, House JS, Lee EY, Buse J, Schurman SH, Fargo DC, Schmitt CP, Hall J, Motsinger-Reif AA. Questionnaire-Based Polyexposure Assessment Outperforms Polygenic Scores for Classification of Type 2 Diabetes in a Multiancestry Cohort. Diabetes Care 2022; 46:929-937. [PMID: 36383734 PMCID: PMC10154656 DOI: 10.2337/dc22-0295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 10/23/2022] [Indexed: 11/17/2022]
Abstract
OBJECTIVE Environmental exposures may have greater predictive power for type 2 diabetes than polygenic scores (PGS). Studies examining environmental risk factors, however, have included only individuals with European ancestry, limiting the applicability of results. We conducted an exposome-wide association study in the multiancestry Personalized Environment and Genes Study to assess the effects of environmental factors on type 2 diabetes. RESEARCH DESIGN AND METHODS Using logistic regression for single-exposure analysis, we identified exposures associated with type 2 diabetes, adjusting for age, BMI, household income, and self-reported sex and race. To compare cumulative genetic and environmental effects, we computed an overall clinical score (OCS) as a weighted sum of BMI and prediabetes, hypertension, and high cholesterol status and a polyexposure score (PXS) as a weighted sum of 13 environmental variables. Using UK Biobank data, we developed a multiancestry PGS and calculated it for participants. RESULTS We found 76 significant associations with type 2 diabetes, including novel associations of asbestos and coal dust exposure. OCS, PXS, and PGS were significantly associated with type 2 diabetes. PXS had moderate power to determine associations, with larger effect size and greater power and reclassification improvement than PGS. For all scores, the results differed by race. CONCLUSIONS Our findings in a multiancestry cohort elucidate how type 2 diabetes odds can be attributed to clinical, genetic, and environmental factors and emphasize the need for exposome data in disease-risk association studies. Race-based differences in predictive scores highlight the need for genetic and exposome-wide studies in diverse populations.
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Affiliation(s)
- Farida S Akhtari
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC.,Clinical Research Branch, National Institute of Environmental Health Sciences, Durham, NC
| | - Dillon Lloyd
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC
| | - Adam Burkholder
- Office of the Director, National Institute of Environmental Health Sciences, Durham, NC
| | - Xiaoran Tong
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC
| | - John S House
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC
| | - Eunice Y Lee
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC
| | - John Buse
- Department of Medicine, University of North Carolina, Chapel Hill, NC
| | - Shepherd H Schurman
- Clinical Research Branch, National Institute of Environmental Health Sciences, Durham, NC
| | - David C Fargo
- Office of the Director, National Institute of Environmental Health Sciences, Durham, NC
| | - Charles P Schmitt
- Office of Data Science, National Institute of Environmental Health Science, Durham, NC
| | - Janet Hall
- Clinical Research Branch, National Institute of Environmental Health Sciences, Durham, NC
| | - Alison A Motsinger-Reif
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC
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13
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Brown E, Shekhar S, Delaney A, Burkholder AB, Plummer L, Mericq V, Merino PM, Quinton R, Lewis KL, Shaw ND, Welt CK, Martin KA, Seminara SB, Biesecker LG, Motsinger-Reif A, House JS, Hall J. LBMON114 Enrichment Of Rare Sequence Variants In Genes That Communicate Metabolic Signals To The GnRH System In Hypothalamic Amenorrhea. J Endocr Soc 2022. [PMCID: PMC9627140 DOI: 10.1210/jendso/bvac150.970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Introduction Functional hypothalamic amenorrhea (HA) is commonly associated with increased exercise or decreased caloric intake and often with stress. We have previously demonstrated an increased burden of rare sequence variants (RSVs) in genes involved in GnRH ontogeny and upstream regulation in women with HA, but the role of metabolic and stress signaling to the GnRH neuronal system is poorly defined in this population. Methods The study included 100 women with a confirmed diagnosis of HA. The control cohort consisted of 468 women (aged 45-65 years) drawn from the NIH ClinSeq® Project. Exome sequencing was performed on peripheral blood genomic DNA. A subset of 72 genes was analyzed that have been shown to: 1) link metabolic or stress with reproductive phenotypes or 2) integrate metabolic and stress pathways with control of GnRH secretion. Joint genotyping of case and control samples was performed using the GATK GenotypeGVCFs function, locus-filtering using the VariantRecalibrator function, and genotype refinement using CalculateGenotypePosteriors with computation of median depths. Median depth positions <10, positions failing GATK VQSR or GATK genotype quality scores <20 were excluded. RSVs were identified by < 1% frequency in any subpopulation in gnomeAD for all-subjects (AS) and < 1% frequency in non-Finnish Europeans for Caucasians (CS). Data were analyzed for AS and for CS using a one-sided Fisher exact test for metabolism genes and stress genes. An additional regression analysis was conducted on the number of RSVs in a given gene as a predictor of HA vs. control. Comparisons with a p-value of < 0.1 are reported. Results HA patients exhibited an increased burden of RSVs in metabolism genes vs. controls (AS p=0. 043; CS p=0.105). The total number of RSVs per gene highlighted differences between HA and controls for the following genes: ADAMTSL1, GRINA, GRIN1, HCRTR1, TENM3, and NOS1 (AS p<0. 001, p=0. 032, p=0. 057, p=0. 082, p=0. 091, p=0. 095; CS p=0. 024, p=0. 044, p=0. 044, p NS, p=0. 086, p NS). Interestingly, RSVs in NOS1 and TENM3 appeared to be protective for HA (odds ratio <1 for both). In contrast, candidate stress genes were not significant in either the AS or CS (p=0.788, p=0.910). Conclusions These data suggest that RSVs in genes involved in phenotypes or signaling pathways that link metabolism to GnRH secretion may predispose to development of HA in the setting of decreased energy balance, but not for stress-related genes. GRINA and GRIN1 are important components of glutamate signaling that facilitate both appetite and GnRH secretion either directly or through kisspeptin. HCRTR1 plays a similar role in linking appetite and GnRH secretion while NOS1, which facilitates kisspeptin signaling, may be protective. This work highlights the need for further studies to understand the potential roles of ADAMTSL1 and TENM3 as risk factors for HA. Presentation: Monday, June 13, 2022 12:30 p.m. - 2:30 p.m.
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Gonzalez-Nahm S, Marchesoni J, Maity A, Maguire RL, House JS, Tucker R, Atkinson T, Murphy SK, Hoyo C. Maternal Mediterranean Diet Adherence and Its Associations with Maternal Prenatal Stressors and Child Growth. Curr Dev Nutr 2022; 6:nzac146. [PMID: 36406812 PMCID: PMC9665863 DOI: 10.1093/cdn/nzac146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 08/19/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
Background Psychosocial and physiologic stressors, such as depression and obesity, during pregnancy can have negative consequences, such as increased systemic inflammation, contributing to chronic disease for both mothers and their unborn children. These conditions disproportionately affect racial/ethnic minorities. The effects of recommended dietary patterns in mitigating the effects of these stressors remain understudied. Objectives We aimed to evaluate the relations between maternal Mediterranean diet adherence (MDA) and maternal and offspring outcomes during the first decade of life in African Americans, Hispanics, and Whites. Methods This study included 929 mother-child dyads from the NEST (Newborn Epigenetics STudy), a prospective cohort study. FFQs were used to estimate MDA in pregnant women. Weight and height were measured in children between birth and age 8 y. Multivariable linear regression models were used to examine associations between maternal MDA, inflammatory cytokines, and pregnancy and postnatal outcomes. Results More than 55% of White women reported high MDA during the periconceptional period compared with 22% of Hispanic and 18% of African American women (P < 0.05). Higher MDA was associated with lower likelihood of depressive mood (β = -0.45; 95% CI: -0.90, -0.18; P = 0.02) and prepregnancy obesity (β = -0.29; 95% CI: -0.57, -0.0002; P = 0.05). Higher MDA was also associated with lower body size at birth, which was maintained to ages 3-5 and 6-8 y-this association was most apparent in White children (3-5 y: β = -2.9, P = 0.02; 6-8 y: β = -3.99, P = 0.01). Conclusions If replicated in larger studies, our data suggest that MDA provides a potent avenue by which effects of prenatal stressors on maternal and fetal outcomes can be mitigated to reduce ethnic disparities in childhood obesity.
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Affiliation(s)
- Sarah Gonzalez-Nahm
- Department of Nutrition, University of Massachusetts Amherst, Amherst, MA, USA
| | - Joddy Marchesoni
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Arnab Maity
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - Rachel L Maguire
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - John S House
- National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Rachel Tucker
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Tamara Atkinson
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University, Durham, NC, USA
| | - Cathrine Hoyo
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
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15
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Shive HR, House JS, Ferguson JL, Jima DD, Selmek AA, Lloyd DT. Abstract PR011: Characterization of the precancerous and cancer microenvironment in a zebrafish sarcoma model. Clin Cancer Res 2022. [DOI: 10.1158/1557-3265.sarcomas22-pr011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Contributions of the microenvironment to soft tissue sarcoma progression are relatively undefined, representing a major impediment to identifying essential regulatory networks in sarcomagenesis. Furthermore, genetic and molecular characteristics that distinguish precancerous versus cancerous microenvironments are not well known across human cancer types. While animal models have the potential to reveal these complex processes, significant impediments to such inquiries include (1) the difficulty in distinguishing microenvironmental cells from precancerous or cancer cells in tissue specimens; and (2) the challenge in defining a discrete tissue with known cancer predilection that represents a precancerous microenvironment. We developed a unique zebrafish model that allows segregation of microenvironmental, precancerous, and cancerous cell populations by fluorescence-activated cell sorting. This model exhibits high predilection for malignant peripheral nerve sheath tumor (MPNST), a type of soft tissue sarcoma with a particularly poor prognosis due to aggressive growth, limited response to conventional treatment, and ineffective targeted therapy options. Using RNA-seq, we profiled the transcriptomes of microenvironmental cells from our zebrafish MPNST model and determined that the precancerous and cancerous microenvironments exhibit broad activation of inflammatory and immune-associated signaling networks. Markers for both M1 and M2 macrophage polarization were upregulated in precancerous and cancerous microenvironments, suggesting the presence of a mixed macrophage population during sarcomagenesis. Patterns of ligand and receptor expression based on a previously defined human ligand-receptor network identified significant upregulation of multiple tumor-promoting ligands in both precancerous and cancerous microenvironments. We also identified specific ligand-receptor pairs that may mediate key signaling events during sarcoma initiation and progression. Together this work provide new insight into distinguishing characteristics of the cancer-prone cellular microenvironment that may promote MPNST initiation and progression in vertebrates.
Citation Format: Heather R. Shive, John S. House, Jordan L. Ferguson, Dereje D. Jima, Aubrie A. Selmek, Dillon T. Lloyd. Characterization of the precancerous and cancer microenvironment in a zebrafish sarcoma model [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr PR011.
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Affiliation(s)
| | - John S. House
- 1National Institute of Environmental Health Sciences, NIH, Durham, NC,
| | | | | | | | - Dillon T. Lloyd
- 4North Carolina State University; National Institute of Environmental Health Sciences, NIH, Raleigh, NC
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16
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Lloyd DT, Skinner HG, Maguire R, Murphy SK, Motsinger-Reif AA, Hoyo C, House JS. Clomifene and Assisted Reproductive Technology in Humans Are Associated with Sex-Specific Offspring Epigenetic Alterations in Imprinted Control Regions. Int J Mol Sci 2022; 23:10450. [PMID: 36142363 PMCID: PMC9499479 DOI: 10.3390/ijms231810450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/02/2022] [Accepted: 09/07/2022] [Indexed: 12/04/2022] Open
Abstract
Children conceived with assisted reproductive technology (ART) have an increased risk of adverse outcomes, including congenital malformations and imprinted gene disorders. In a retrospective North Carolina-based-birth-cohort, we examined the effect of ovulation drugs and ART on CpG methylation in differentially methylated CpGs in known imprint control regions (ICRs). Nine ICRs containing 48 CpGs were assessed for methylation status by pyrosequencing in mixed leukocytes from cord blood. After restricting to non-smoking, college-educated participants who agreed to follow-up, ART-exposed (n = 27), clomifene-only-exposed (n = 22), and non-exposed (n = 516) groups were defined. Associations of clomifene and ART with ICR CpG methylation were assessed with linear regression and stratifying by offspring sex. In males, ART was associated with hypomethylation of the PEG3 ICR [β(95% CI) = -1.46 (-2.81, -0.12)] and hypermethylation of the MEG3 ICR [3.71 (0.01, 7.40)]; clomifene-only was associated with hypomethylation of the NNAT ICR [-5.25 (-10.12, -0.38)]. In female offspring, ART was associated with hypomethylation of the IGF2 ICR [-3.67 (-6.79, -0.55)]. Aberrant methylation of these ICRs has been associated with cardiovascular disease and metabolic and behavioral outcomes in children. The results suggest that the increased risk of adverse outcomes in offspring conceived through ART may be due in part to altered methylation of ICRs. Larger studies utilizing epigenome-wide interrogation are warranted.
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Affiliation(s)
- Dillon T. Lloyd
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27606, USA
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27607, USA
| | - Harlyn G. Skinner
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27606, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27607, USA
| | - Rachel Maguire
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27606, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27607, USA
| | - Susan K. Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Duke University, Durham, NC 27701, USA
| | - Alison A. Motsinger-Reif
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Cathrine Hoyo
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27606, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27607, USA
| | - John S. House
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27606, USA
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27607, USA
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17
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Lee EY, Akhtari F, House JS, Simpson RJ, Schmitt CP, Fargo DC, Schurman SH, Hall JE, Motsinger-Reif AA. Questionnaire-based exposome-wide association studies (ExWAS) reveal expected and novel risk factors associated with cardiovascular outcomes in the Personalized Environment and Genes Study. Environ Res 2022; 212:113463. [PMID: 35605674 DOI: 10.1016/j.envres.2022.113463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 04/01/2022] [Accepted: 05/07/2022] [Indexed: 06/15/2023]
Abstract
While multiple factors are associated with cardiovascular disease (CVD), many environmental exposures that may contribute to CVD have not been examined. To understand environmental effects on cardiovascular health, we performed an exposome-wide association study (ExWAS), a hypothesis-free approach, using survey data on endogenous and exogenous exposures at home and work and data from health and medical histories from the North Carolina-based Personalized Environment and Genes Study (PEGS) (n = 5015). We performed ExWAS analyses separately on six cardiovascular outcomes (cardiac arrhythmia, congestive heart failure, coronary artery disease, heart attack, stroke, and a combined atherogenic-related outcome comprising angina, angioplasty, atherosclerosis, coronary artery disease, heart attack, and stroke) using logistic regression and a false discovery rate of 5%. For each CVD outcome, we tested 502 single exposures and built multi-exposure models using the deletion-substitution-addition (DSA) algorithm. To evaluate complex nonlinear relationships, we employed the knockoff boosted tree (KOBT) algorithm. We adjusted all analyses for age, sex, race, BMI, and annual household income. ExWAS analyses revealed novel associations that include blood type A (Rh-) with heart attack (OR[95%CI] = 8.2[2.2:29.7]); paint exposures with stroke (paint related chemicals: 6.1[2.2:16.0], acrylic paint: 8.1[2.6:22.9], primer: 6.7[2.2:18.6]); biohazardous materials exposure with arrhythmia (1.8[1.5:2.3]); and higher paternal education level with reduced risk of multiple CVD outcomes (stroke, heart attack, coronary artery disease, and combined atherogenic outcome). In multi-exposure models, trouble sleeping and smoking remained important risk factors. KOBT identified significant nonlinear effects of sleep disorder, regular intake of grapefruit, and a family history of blood clotting problems for multiple CVD outcomes (combined atherogenic outcome, congestive heart failure, and coronary artery disease). In conclusion, using statistics and machine learning, these findings identify novel potential risk factors for CVD, enable hypothesis generation, provide insights into the complex relationships between risk factors and CVD, and highlight the importance of considering multiple exposures when examining CVD outcomes.
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Affiliation(s)
- Eunice Y Lee
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Farida Akhtari
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA; Clinical Research Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - John S House
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Ross J Simpson
- Department of Epidemiology, Gillings School of Public Health and Department of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Charles P Schmitt
- National Toxicology Program, National Institute of Health, Durham, NC, USA
| | - David C Fargo
- Office of the Director, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Shepherd H Schurman
- Clinical Research Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Janet E Hall
- Clinical Research Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Alison A Motsinger-Reif
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA.
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House JS, Grimm FA, Klaren WD, Dalzell A, Kuchi S, Zhang SD, Lenz K, Boogaard PJ, Ketelslegers HB, Gant TW, Rusyn I, Wright FA. Grouping of UVCB substances with dose-response transcriptomics data from human cell-based assays. ALTEX 2022; 39:388–404. [PMID: 35288757 PMCID: PMC9344966 DOI: 10.14573/altex.2107051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 02/22/2022] [Indexed: 12/18/2022]
Abstract
The application of in vitro biological assays as new approach methodologies (NAMs) to support grouping of UVCB (unknown or variable composition, complex reaction products, and biological materials) substances has recently been demonstrated. In addition to cell-based phenotyping as NAMs, in vitro transcriptomic profiling is used to gain deeper mechanistic understanding of biological responses to chemicals and to support grouping and read-across. However, the value of gene expression profiling for characterizing complex substances like UVCBs has not been explored. Using 141 petroleum substance extracts, we performed dose-response transcriptomic profiling in human induced pluripotent stem cell (iPSC)-derived hepatocytes, cardiomyocytes, neurons, and endothelial cells, as well as cell lines MCF7 and A375. The goal was to determine whether transcriptomic data can be used to group these UVCBs and to further characterize the molecular basis for in vitro biological responses. We found distinct transcriptional responses for petroleum substances by manufacturing class. Pathway enrichment informed interpretation of effects of substances and UVCB petroleum-class. Transcriptional activity was strongly correlated with concentration of polycyclic aromatic compounds (PAC), especially in iPSC-derived hepatocytes. Supervised analysis using transcriptomics, alone or in combination with bioactivity data collected on these same substances/cells, suggest that transcriptomics data provide useful mechanistic information, but only modest additional value for grouping. Overall, these results further demonstrate the value of NAMs for grouping of UVCBs, identify informative cell lines, and provide data that could be used for justifying selection of substances for further testing that may be required for registration.
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Affiliation(s)
- John S House
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.,Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, RTP, NC, USA
| | - Fabian A Grimm
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - William D Klaren
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.,current address: ToxStrategies, Inc., Asheville, NC, USA
| | - Abigail Dalzell
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Harwell Science Campus, Oxon, UK
| | - Srikeerthana Kuchi
- Northern Ireland Centre for Stratified Medicine, Ulster University, L/Derry, Northern Ireland, UK.,current address: MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
| | - Shu-Dong Zhang
- Northern Ireland Centre for Stratified Medicine, Ulster University, L/Derry, Northern Ireland, UK
| | - Klaus Lenz
- SYNCOM Forschungs und Entwicklungsberatung GmbH, Ganderkesee, Germany
| | | | | | - Timothy W Gant
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Harwell Science Campus, Oxon, UK
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Fred A Wright
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
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Wolkin A, Collier S, House JS, Reif D, Motsinger-Reif A, Duca L, Sharpe JD. Comparison of National Vulnerability Indices Used by the Centers for Disease Control and Prevention for the COVID-19 Response. Public Health Rep 2022; 137:803-812. [PMID: 35514159 PMCID: PMC9257512 DOI: 10.1177/00333549221090262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVE Vulnerability indices use quantitative indicators and geospatial data to examine the level of vulnerability to morbidity in a community. The Centers for Disease Control and Prevention (CDC) uses 3 indices for the COVID-19 response: the CDC Social Vulnerability Index (CDC-SVI), the US COVID-19 Community Vulnerability Index (CCVI), and the Pandemic Vulnerability Index (PVI). The objective of this review was to describe these tools and explain the similarities and differences between them. METHODS We described the 3 indices, outlined the underlying data sources and metrics for each, and discussed their use by CDC for the COVID-19 response. We compared the percentile score for each county for each index by calculating Spearman correlation coefficients (Spearman ρ). RESULTS These indices have some, but not all, component metrics in common. The CDC-SVI is a validated metric that estimates social vulnerability, which comprises the underlying population-level characteristics that influence differences in health risk among communities. To address risk specific to the COVID-19 pandemic, the CCVI and PVI build on the CDC-SVI and include additional variables. The 3 indices were highly correlated. Spearman ρ for comparisons between the CDC-SVI score and the CCVI and between the CCVI and the PVI score was 0.83. Spearman ρ for the comparison between the CDC-SVI score and PVI score was 0.73. CONCLUSION The indices can empower local and state public health officials with additional information to focus resources and interventions on disproportionately affected populations to combat the ongoing pandemic and plan for future pandemics.
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Affiliation(s)
- Amy Wolkin
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sarah Collier
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John S. House
- Biostatistics and Computational Biology Branch, National Institute for Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - David Reif
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute for Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Lindsey Duca
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - J. Danielle Sharpe
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, GA, USA
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20
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Jackson TW, Henriquez AR, Snow SJ, Schladweiler MC, Fisher AA, Alewel DI, House JS, Kodavanti UP. Adrenal stress hormone regulation of hepatic homeostatic function after an acute ozone exposure in Wistar-Kyoto male rats. Toxicol Sci 2022; 189:73-90. [PMID: 35737395 DOI: 10.1093/toxsci/kfac065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ozone-induced lung injury and inflammation and pulmonary/hypothalamus gene expression changes are diminished in adrenalectomized (AD) rats. Acute ozone exposure induces metabolic alterations concomitant with increases in epinephrine and corticosterone. We hypothesized that adrenal hormones are responsible for observed hepatic ozone effects, and in AD rats, these changes would be diminished. 5-7 days after sham (SH) or AD surgeries, male Wistar-Kyoto rats were exposed to air or 0.8-ppm ozone for 4-hrs. Serum samples were analyzed for metabolites and liver for transcriptional changes immediately post-exposure. Ozone increased circulating triglycerides, cholesterol, free fatty-acids, and leptin in SH but not AD rats. Ozone-induced inhibition of glucose-mediated insulin release was absent in AD rats. Unlike diminution of ozone-induced hypothalamus and lung mRNA expression changes, AD in air-exposed rats (AD-air/SH-air) caused differential hepatic expression of ∼1000 genes. Likewise, ozone in AD rats caused differential expression of ∼1000 genes (AD-ozone/AD-air). Ozone-induced hepatic changes in SH rats reflected enrichment for pathways involving metabolic processes, including acetyl-CoA biosynthesis, TCA cycle, and sirtuins. Upstream predictor analysis identified similarity to responses produced by glucocorticoids and pathways involving forskolin. These changes were absent in AD rats exposed to ozone. However, ozone caused unique changes in AD liver mRNA reflecting activation of synaptogenesis, neurovascular coupling, neuroinflammation, and insulin signaling with inhibition of senescence pathways. In these rats, upstream predictor analysis identified numerous microRNAs involved in glucocorticoid insufficiency. These data demonstrate the critical role of adrenal stress hormones in ozone-induced hepatic homeostasis and necessitate further research elucidating their role in propagating environmentally driven diseases.
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Affiliation(s)
- Thomas W Jackson
- Oak Ridge Institute for Science and Education Research Participation Program, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
| | - Andres R Henriquez
- Oak Ridge Institute for Science and Education Research Participation Program, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
| | - Samantha J Snow
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
| | - Mette C Schladweiler
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
| | - Anna A Fisher
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
| | - Devin I Alewel
- Oak Ridge Institute for Science and Education Research Participation Program, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
| | - John S House
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Urmila P Kodavanti
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
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21
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Alick CL, Maguire RL, Murphy SK, Fuemmeler BF, Hoyo C, House JS. Periconceptional Maternal Diet Characterized by High Glycemic Loading Is Associated with Offspring Behavior in NEST. Nutrients 2021; 13:nu13093180. [PMID: 34579057 PMCID: PMC8469715 DOI: 10.3390/nu13093180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/07/2021] [Accepted: 09/09/2021] [Indexed: 01/08/2023] Open
Abstract
Maternal periconceptional diets have known associations with proper offspring neurodevelopment. Mechanisms for such associations include improper energy/nutrient balances between mother and fetus, as well as altered offspring epigenetics during development due to maternal nutrient and inflammatory status. Using a comprehensive food frequency questionnaire and assessing offspring temperament with the Infant-Toddler Social and Emotional Assessment (n = 325, mean age = 13.9 months), we sought to test whether a maternal periconceptional diet characterized by high glycemic loading (MGL) would affect offspring temperament using adjusted ordinal regression. After limiting false discovery to 10%, offspring born to mothers in tertile 3 of glycemic loading (referent = tertile 1) were more likely to be in the next tertile of anxiety [OR (95% CI) = 4.51 (1.88-11.07)] and inhibition-related behaviors [OR (95% CI) = 3.42 (1.49-7.96)]. Male offspring were more likely to exhibit impulsive [OR (95% CI) = 5.55 (1.76-18.33)], anxiety [OR (95% CI) = 4.41 (1.33-15.30)], sleep dysregulation [OR (95% CI) = 4.14 (1.34-13.16)], empathy [6.68 (1.95-24.40)], and maladaptive behaviors [OR (95% CI) = 9.86 (2.81-37.18)], while females were more likely to exhibit increased anxiety-related behaviors [OR (95% CI) = 15.02 (3.14-84.27)]. These associations persisted when concurrently modeled with the maternal-Mediterranean dietary pattern. In a subset (n = 142), we also found MGL associated with increased mean methylation of the imprint control region of SGCE/PEG10. In conclusion, these findings highlight the importance of maternal dietary patterns on offspring neurodevelopment, offering avenues for prevention options for mothers.
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Affiliation(s)
- Candice L. Alick
- Center for Health Promotion and Disease Prevention, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA;
| | - Rachel L. Maguire
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA; (R.L.M.); (C.H.)
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC 27701, USA;
| | - Susan K. Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC 27701, USA;
| | - Bernard F. Fuemmeler
- Department of Health Behavior and Policy, Virginia Commonwealth University, Richmond, VA 23219, USA;
| | - Cathrine Hoyo
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA; (R.L.M.); (C.H.)
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - John S. House
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA; (R.L.M.); (C.H.)
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, Durham, NC 27709, USA
- Correspondence:
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22
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Colonna CH, Henriquez AR, House JS, Motsinger-Reif AA, Alewel DI, Fisher A, Ren H, Snow SJ, Schladweiler MC, Miller DB, Miller CN, Kodavanti PRS, Kodavanti UP. The Role of Hepatic Vagal Tone in Ozone-Induced Metabolic Dysfunction in the Liver. Toxicol Sci 2021; 181:229-245. [PMID: 33662111 DOI: 10.1093/toxsci/kfab025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Air pollution has been associated with metabolic diseases and hepatic steatosis-like changes. We have shown that ozone alters liver gene expression for metabolic processes through neuroendocrine activation. This study aimed to further characterize ozone-induced changes and to determine the impact of hepatic vagotomy (HV) which reduces parasympathetic influence. Twelve-week-old male Wistar-Kyoto rats underwent HV or sham surgery 5-6 days before air or ozone exposure (0 or 1 ppm; 4 h/day for 1 or 2 days). Ozone-induced lung injury, hyperglycemia, glucose intolerance, and increases in circulating cholesterol, triglycerides, and leptin were similar in rats with HV and sham surgery. However, decreases in circulating insulin and increased HDL and LDL were observed only in ozone-exposed HV rats. Ozone exposure resulted in changed liver gene expression in both sham and HV rats (sham > HV), however, HV did not change expression in air-exposed rats. Upstream target analysis revealed that ozone-induced transcriptomic changes were similar to responses induced by glucocorticoid-mediated processes in both sham and HV rats. The directionality of ozone-induced changes reflecting cellular response to stress, metabolic pathways, and immune surveillance was similar in sham and HV rats. However, pathways regulating cell-cycle, regeneration, proliferation, cell growth, and survival were enriched by ozone in a directionally opposing manner between sham and HV rats. In conclusion, parasympathetic innervation modulated ozone-induced liver transcriptional responses for cell growth and regeneration without affecting stress-mediated metabolic changes. Thus, impaired neuroendocrine axes and parasympathetic innervation could collectively contribute to adverse effects of air pollutants on the liver.
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Affiliation(s)
- Catherine H Colonna
- Oak Ridge Institute for Science and Education Research Participation Program, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, 27711
| | - Andres R Henriquez
- Oak Ridge Institute for Science and Education Research Participation Program, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, 27711
| | - John S House
- Division of Intramural Research, Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Alison A Motsinger-Reif
- Division of Intramural Research, Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Devin I Alewel
- Oak Ridge Institute for Science and Education Research Participation Program, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, 27711
| | - Anna Fisher
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711
| | - Hongzu Ren
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711
| | - Samantha J Snow
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711
| | - Mette C Schladweiler
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711
| | - Desinia B Miller
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Colette N Miller
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711
| | - Prasada Rao S Kodavanti
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711
| | - Urmila P Kodavanti
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711
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23
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McDonough CW, Warren HR, Jack JR, Motsinger-Reif AA, Armstrong ND, Bis JC, House JS, Singh S, El Rouby NM, Gong Y, Mychaleckyj JC, Rotroff DM, Benavente OR, Caulfield MJ, Doria A, Pepine CJ, Psaty BM, Glorioso V, Glorioso N, Hiltunen TP, Kontula KK, Arnett DK, Buse JB, Irvin MR, Johnson JA, Munroe PB, Wagner MJ, Cooper-DeHoff RM. Adverse Cardiovascular Outcomes and Antihypertensive Treatment: A Genome-Wide Interaction Meta-Analysis in the International Consortium for Antihypertensive Pharmacogenomics Studies. Clin Pharmacol Ther 2021; 110:723-732. [PMID: 34231218 DOI: 10.1002/cpt.2355] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 06/11/2021] [Indexed: 01/01/2023]
Abstract
We sought to identify genome-wide variants influencing antihypertensive drug response and adverse cardiovascular outcomes, utilizing data from four randomized controlled trials in the International Consortium for Antihypertensive Pharmacogenomics Studies (ICAPS). Genome-wide antihypertensive drug-single nucleotide polymorphism (SNP) interaction tests for four drug classes (β-blockers, n = 9,195; calcium channel blockers (CCBs), n = 10,511; thiazide/thiazide-like diuretics, n = 3,516; ACE-inhibitors/ARBs, n = 2,559) and cardiovascular outcomes (incident myocardial infarction, stroke, or death) were analyzed among patients with hypertension of European ancestry. Top SNPs from the meta-analyses were tested for replication of cardiovascular outcomes in an independent Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) study (n = 21,267), blood pressure (BP) response in independent ICAPS studies (n = 1,552), and ethnic validation in African Americans from the Genetics of Hypertension Associated Treatment study (GenHAT; n = 5,115). One signal reached genome-wide significance in the β-blocker-SNP interaction analysis (rs139945292, Interaction P = 1.56 × 10-8 ). rs139945292 was validated through BP response to β-blockers, with the T-allele associated with less BP reduction (systolic BP response P = 6 × 10-4 , Beta = 3.09, diastolic BP response P = 5 × 10-3 , Beta = 1.53). The T-allele was also associated with increased adverse cardiovascular risk within the β-blocker treated patients' subgroup (P = 2.35 × 10-4 , odds ratio = 1.57, 95% confidence interval = 1.23-1.99). The locus showed nominal replication in CHARGE, and consistent directional trends in β-blocker treated African Americans. rs139945292 is an expression quantitative trait locus for the 50 kb upstream gene NTM (neurotrimin). No SNPs attained genome-wide significance for any other drugs classes. Top SNPs were located near CALB1 (CCB), FLJ367777 (ACE-inhibitor), and CES5AP1 (thiazide). The NTM region is associated with increased risk for adverse cardiovascular outcomes and less BP reduction in β-blocker treated patients. Further investigation into this region is warranted.
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Affiliation(s)
- Caitrin W McDonough
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Helen R Warren
- Clinical Pharmacology Department, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.,NIHR Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - John R Jack
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, North Carolina, USA
| | - Alison A Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Nicole D Armstrong
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - John S House
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Sonal Singh
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Nihal M El Rouby
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Yan Gong
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Joesyf C Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Daniel M Rotroff
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, North Carolina, USA
| | - Oscar R Benavente
- Department of Neurology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mark J Caulfield
- National Institute for Health Research, Barts Cardiovascular Biomedical Research Center, Queen Mary University of London, London, UK
| | - Alessandrio Doria
- Research Division, Joslin Diabetes Center; and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Carl J Pepine
- Division of Cardiovascular Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington, USA.,Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Valeria Glorioso
- Department of Statistics and Quantitative Methods, University of Milano-Bicocca, Milano, Italy
| | - Nicola Glorioso
- Department of Clinical, Surgical and Experimental Science, University of Sassari, Medical School, Sassari, Italy
| | - Timo P Hiltunen
- Department of Medicine and Research Program for Clinical and Molecular Metabolism, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kimmo K Kontula
- Department of Medicine and Research Program for Clinical and Molecular Metabolism, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Donna K Arnett
- College of Public Health, Dean's Office, University of Kentucky, Lexington, Kentucky, USA
| | - John B Buse
- Division of Endocrinology, Department of Medicine, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Julie A Johnson
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA.,Division of Cardiovascular Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Patricia B Munroe
- Clinical Pharmacology Department, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.,NIHR Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Michael J Wagner
- Center for Pharmacogenomics and Individualized Therapy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Rhonda M Cooper-DeHoff
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA.,Division of Cardiovascular Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
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24
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Maguire RL, House JS, Lloyd DT, Skinner HG, Allen TK, Raffi AM, Skaar DA, Park SS, McCullough LE, Kollins SH, Bilbo SD, Collier DN, Murphy SK, Fuemmeler BF, Gowdy KM, Hoyo C. Associations between maternal obesity, gestational cytokine levels and child obesity in the NEST cohort. Pediatr Obes 2021; 16:e12763. [PMID: 33381912 PMCID: PMC8178180 DOI: 10.1111/ijpo.12763] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 11/25/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND Although maternal systemic inflammation is hypothesized to link maternal pre-pregnancy obesity to offspring metabolic dysfunction, patient empirical data are limited. OBJECTIVES In this study, we hypothesized that pre-pregnancy obesity alters systemic chemo/cytokines concentrations in pregnancy, and this alteration contributes to obesity in children. METHODS In a multi-ethnic cohort of 361 mother-child pairs, we measured prenatal concentrations of plasma TNF-α, IL-6, IL-8, IL-1β, IL-4, IFN-γ, IL-12 p70 subunit, and IL-17A using a multiplex ELISA and examined associations of pre-pregnancy obesity on maternal chemo/cytokine levels, and associations of these cytokine levels with offspring body mass index z score (BMI-z) at age 2-6 years using linear regression. RESULTS After adjusting for maternal smoking, ethnicity, age, and education, pre-pregnancy obesity was associated with increased concentrations of TNF-α (P = .026) and IFN-γ (P = .06). While we found no evidence for associations between TNF-α concentrations and offspring BMI-z, increased IFN-γ concentrations were associated with decreased BMI-z (P = .0002), primarily in Whites (P = .0011). In addition, increased maternal IL-17A concentrations were associated with increased BMI-z in offspring (P = .0005) with stronger associations in African Americans (P = .0042) than Whites (P = .24). CONCLUSIONS Data from this study are consistent with maternal obesity-related inflammation during pregnancy, increasing the risk of childhood obesity in an ethnic-specific manner.
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Affiliation(s)
- Rachel L. Maguire
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA,Department of Obstetrics and Gynecology, Duke University, Durham, NC, USA
| | - John S. House
- 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,Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Dillon T. Lloyd
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Harlyn G. Skinner
- 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
| | | | - Asifa Mohamed Raffi
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - David A. Skaar
- 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
| | - Sarah S. Park
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | | | - Scott H. Kollins
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA
| | - Staci D. Bilbo
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
| | - David N. Collier
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA,Department of Pediatrics, Brody School of Medicine, East Carolina University, Greenville, NC, USA,East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC, USA
| | - Susan K. Murphy
- Department of Obstetrics and Gynecology, Duke University, Durham, NC, USA
| | - Bernard F. Fuemmeler
- Department of Health Behavior and Policy, Virginia Commonwealth University, Richmond, VA, USA
| | - Kymberly M. Gowdy
- Pulmonary, Critical Care and Sleep Medicine, The Ohio State University Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, Ohio, 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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25
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Sakolish C, House JS, Chramiec A, Liu Y, Chen Z, Halligan SP, Vunjak-Novakovic G, Rusyn I. Tissue-Engineered Bone Tumor as a Reproducible Human in Vitro Model for Studies of Anticancer Drugs. Toxicol Sci 2021; 173:65-76. [PMID: 31626302 DOI: 10.1093/toxsci/kfz220] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Studies of anticancer therapies in traditional cell culture models can demonstrate efficacy of direct-acting compounds but lack the 3-dimensional arrangement of the tumor cells and their tissue-specific microenvironments, both of which are important modulators of treatment effects in vivo. Bone cells reside in complex environments that regulate their fate and function. A bioengineered human bone-tumor model has been shown to provide a microphysiological niche for studies of cancer cell behavior. Here, we demonstrate successful transfer between 2 laboratories and utility of this model in efficacy studies using well-established chemotherapeutic agents. The bioengineered human bone-tumor model consisted of Ewing sarcoma (RD-ES) cancer cell aggregates infused into tissue-engineered bone that was grown from human mesenchymal stem cell-derived differentiated into osteoblasts within mineralized bone scaffolds. The tumor model was maintained in culture for over 5 weeks and subjected to clinically relevant doses of linsitinib, doxorubicin, cisplatin, methotrexate, vincristine, dexamethasone, or MAP (methotrexate, doxorubicin, and cisplatin combination). Drug administration cycles were designed to mimic clinical treatment regimens. The bioengineered tumors were evaluated days to weeks after the cessation of treatment to monitor the potential for relapse, using bioengineered bone and ES cell monolayers as controls. Drug binding to the scaffolds and media proteins and gene expression were also evaluated. We show that a bioengineered human bone tumor can be used as a microphysiological model for preclinical studies of anticancer drugs. We found that anticancer efficacy was achieved at concentrations approximating the human Cmax, in contrast to traditional ES cell monolayers. These studies show that the bone-tumor model can be successfully transferred between laboratories and has predictive power in preclinical studies. The effects of drugs on the bone tumors and healthy bone were studied in parallel, in support of the utility of this model for identification of new therapeutic targets.
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Affiliation(s)
- Courtney Sakolish
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843
| | - John S House
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27695
| | - Alan Chramiec
- Department of Biomedical Engineering, Columbia University, New York, New York 10032
| | - Yizhong Liu
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843
| | - Zunwei Chen
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843
| | - Susan P Halligan
- Department of Biomedical Engineering, Columbia University, New York, New York 10032
| | | | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843
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26
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Nichols CE, House JS, Li H, Ward JM, Wyss A, Williams JG, Deterding LJ, Bradbury JA, Miller L, Zeldin DC, London SJ. Lrp1 Regulation of Pulmonary Function. Follow-Up of Human GWAS in Mice. Am J Respir Cell Mol Biol 2021; 64:368-378. [PMID: 33290178 DOI: 10.1165/rcmb.2019-0444oc] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Human genome-wide association studies (GWASs) have identified more than 270 loci associated with pulmonary function; however, follow-up studies to determine causal genes at these loci are few. SNPs in low-density lipoprotein receptor-related protein 1 (LRP1) are associated with human pulmonary function in GWASs. Using murine models, we investigated the effect of genetic disruption of the Lrp1 gene in smooth muscle cells on pulmonary function in naive animals and after exposure to bacterial LPS or house dust mite extract. Disruption of Lrp1 in smooth muscle cells leads to an increase in tissue resistance, elastance, and tissue elastance at baseline. Furthermore, disruption of Lrp1 in smooth muscle increases airway responsiveness as measured by increased total lung resistance and airway resistance after methacholine. Immune cell counts in BAL fluid were increased in animals with Lrp1 disruption. The difference in airway responsiveness by genotype observed in naive animals was not observed after LPS or house dust mite extract exposure. To further explore the mechanisms contributing to changes in pulmonary function, we identified several ligands dysregulated with Lrp1 disruption in smooth muscle cells. These data suggest that dysregulation of LRP1 in smooth muscle cells affects baseline pulmonary function and airway responsiveness and helps establish LRP1 as the causal gene at this GWAS locus.
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Affiliation(s)
| | | | - Huiling Li
- Immunity, Inflammation, and Disease Laboratory
| | | | | | - Jason G Williams
- Mass Spectrometry Research and Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina
| | - Leesa J Deterding
- Mass Spectrometry Research and Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina
| | | | | | | | - Stephanie J London
- Immunity, Inflammation, and Disease Laboratory.,Epidemiology Branch, and
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Snow SJ, Henriquez AR, Fisher A, Vallanat B, House JS, Schladweiler MC, Wood CE, Kodavanti UP. Peripheral metabolic effects of ozone exposure in healthy and diabetic rats on normal or high-cholesterol diet. Toxicol Appl Pharmacol 2021; 415:115427. [PMID: 33524448 PMCID: PMC8086744 DOI: 10.1016/j.taap.2021.115427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 12/21/2022]
Abstract
Epidemiological studies show that individuals with underlying diabetes and diet-associated ailments are more susceptible than healthy individuals to adverse health effects of air pollution. Exposure to air pollutants can induce metabolic stress and increase cardiometabolic disease risk. Using male Wistar and Wistar-derived Goto-Kakizaki (GK) rats, which exhibit a non-obese type-2 diabetes phenotype, we investigated whether two key metabolic stressors, type-2 diabetes and a high-cholesterol atherogenic diet, exacerbate ozone-induced metabolic effects. Rats were fed a normal control diet (ND) or high-cholesterol diet (HCD) for 12 weeks and then exposed to filtered air or 1.0-ppm ozone (6 h/day) for 1 or 2 days. Metabolic responses were analyzed at the end of each day and after an 18-h recovery period following the 2-day exposure. In GK rats, baseline hyperglycemia and glucose intolerance were exacerbated by HCD vs. ND and by ozone vs. air. HCD also resulted in higher insulin in ozone-exposed GK rats and circulating lipase, aspartate transaminase, and alanine transaminase in all groups (Wistar>GK). Histopathological effects induced by HCD in the liver, which included macrovesicular vacuolation and hepatocellular necrosis, were more severe in Wistar vs. GK rats. Liver gene expression in Wistar and GK rats fed ND showed numerous strain differences, including evidence of increased lipid metabolizing activity and ozone-induced alterations in glucose and lipid transporters, specifically in GK rats. Collectively, these findings indicate that peripheral metabolic alterations induced by diabetes and high-cholesterol diet can enhance susceptibility to the metabolic effects of inhaled pollutants.
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MESH Headings
- Adipose Tissue, White/drug effects
- Adipose Tissue, White/metabolism
- Adipose Tissue, White/pathology
- Air Pollutants/toxicity
- Animals
- Biomarkers/blood
- Blood Glucose/drug effects
- Blood Glucose/metabolism
- Body Composition/drug effects
- Cholesterol, Dietary/metabolism
- Cholesterol, Dietary/toxicity
- Diabetes Mellitus, Type 2/blood
- Diabetes Mellitus, Type 2/complications
- Diabetes Mellitus, Type 2/genetics
- Diet, High-Fat/adverse effects
- Disease Models, Animal
- Energy Metabolism/drug effects
- Gene Expression Regulation
- Inhalation Exposure
- Insulin/blood
- Lipids/blood
- Liver/drug effects
- Liver/metabolism
- Liver/pathology
- Male
- Ozone/toxicity
- Rats, Wistar
- Species Specificity
- Rats
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Affiliation(s)
- Samantha J Snow
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States
| | - Andres R Henriquez
- Oak Ridge Institute for Science and Education Research Participation Program, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States
| | - Anna Fisher
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States
| | - Beena Vallanat
- Biomolecular and Computational Toxicology Division, Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States
| | - John S House
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, United States
| | - Mette C Schladweiler
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States
| | - Charles E Wood
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States
| | - Urmila P Kodavanti
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States; Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, United States.
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28
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Marvel SW, House JS, Wheeler M, Song K, Zhou YH, Wright FA, Chiu WA, Rusyn I, Motsinger-Reif A, Reif DM. The COVID-19 Pandemic Vulnerability Index (PVI) Dashboard: Monitoring County-Level Vulnerability Using Visualization, Statistical Modeling, and Machine Learning. Environ Health Perspect 2021; 129:17701. [PMID: 33400596 PMCID: PMC7785295 DOI: 10.1289/ehp8690] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/14/2020] [Accepted: 12/21/2020] [Indexed: 05/10/2023]
Affiliation(s)
- Skylar W. Marvel
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University (NCSU), Raleigh, North Carolina, USA
| | - John S. House
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Matthew Wheeler
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Kuncheng Song
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University (NCSU), Raleigh, North Carolina, USA
| | - Yi-Hui Zhou
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University (NCSU), Raleigh, North Carolina, USA
| | - Fred A. Wright
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University (NCSU), Raleigh, North Carolina, USA
- Department of Statistics, NCSU, Raleigh, North Carolina, USA
| | - Weihsueh A. Chiu
- Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Ivan Rusyn
- Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - David M. Reif
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University (NCSU), Raleigh, North Carolina, USA
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29
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Gonzalez-Nahm S, Nihlani K, S. House J, L. Maguire R, G. Skinner H, Hoyo C. Associations between Maternal Cadmium Exposure with Risk of Preterm Birth and Low after Birth Weight Effect of Mediterranean Diet Adherence on Affected Prenatal Outcomes. Toxics 2020; 8:toxics8040090. [PMID: 33092103 PMCID: PMC7712046 DOI: 10.3390/toxics8040090] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 12/15/2022]
Abstract
Prenatal cadmium exposure at non-occupational levels has been associated with poor birth outcomes. The intake of essential metals, such as iron and selenium, may mitigate cadmium exposure effects. However, at high levels, these metals can be toxic. The role of dietary patterns rich in these metals is less studied. We used a linear and logistic regression in a cohort of 185 mother-infant pairs to assess if a Mediterranean diet pattern during pregnancy modified the associations between prenatal cadmium exposure and (1) birth weight and (2) preterm birth. We found that increased cadmium exposure during pregnancy was associated with lower birth weight (β = -210.4; 95% CI: -332.0, -88.8; p = 0.008) and preterm birth (OR = 0.11; 95% CI: 0.01, 0.72; p = 0.04); however, these associations were comparable in offspring born to women reporting high adherence to a Mediterranean diet (β = -274.95; 95% CI: -701.17, 151.26; p = 0.20) and those with low adherence (β = -64.76; 95% CI: -359.90, 230.37; p = 0.66). While the small sample size limits inference, our findings suggest that adherence to a Mediterranean dietary pattern may not mitigate cadmium exposure effects. Given the multiple organs targeted by cadmium and its slow excretion rate, larger studies are required to clarify these findings.
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Affiliation(s)
- Sarah Gonzalez-Nahm
- Department of Nutrition, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Correspondence:
| | - Kiran Nihlani
- Department of Statistics, University of Pittsburgh, Pittsburgh, PA 15260, USA;
| | - John S. House
- National Institute of Environmental Health Sciences, Durham, NC 27709, USA;
| | - Rachel L. Maguire
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27606, USA; (R.L.M.); (H.G.S.); (C.H.)
| | - Harlyn G. Skinner
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27606, USA; (R.L.M.); (H.G.S.); (C.H.)
| | - Cathrine Hoyo
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27606, USA; (R.L.M.); (H.G.S.); (C.H.)
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30
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House JS, Grimm FA, Klaren WD, Dalzell A, Kuchi S, Zhang SD, Lenz K, Boogaard PJ, Ketelslegers HB, Gant TW, Wright FA, Rusyn I. Grouping of UVCB substances with new approach methodologies (NAMs) data. ALTEX 2020; 38:123-137. [PMID: 33086383 PMCID: PMC7900923 DOI: 10.14573/altex.2006262] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/07/2020] [Indexed: 11/23/2022]
Abstract
One of the most challenging areas in regulatory science is assessment of the substances known as UVCB (unknown or variable composition, complex reaction products and biological materials). Because the inherent complexity and variability of UVCBs present considerable challenges for establishing sufficient substance similarity based on chemical characteristics or other data, we hypothesized that new approach methodologies (NAMs), including in vitro test-derived biological activity signatures to characterize substance similarity, could be used to support grouping of UVCBs. We tested 141 petroleum substances as representative UVCBs in a compendium of 15 human cell types representing a variety of tissues. Petroleum substances were assayed in dilution series to derive point of departure estimates for each cell type and phenotype. Extensive quality control measures were taken to ensure that only high-confidence in vitro data were used to determine whether current groupings of these petroleum substances, based largely on the manufacturing process and physico-chemical properties, are justifiable. We found that bioactivity data-based groupings of petroleum substances were generally consistent with the manufacturing class-based categories. We also showed that these data, especially bioactivity from human induced pluripotent stem cell (iPSC)-derived and primary cells, can be used to rank substances in a manner highly concordant with their expected in vivo hazard potential based on their chemical compositional profile. Overall, this study demonstrates that NAMs can be used to inform groupings of UVCBs, to assist in identification of representative substances in each group for testing when needed, and to fill data gaps by read-across.
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Affiliation(s)
- John S House
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.,current address: Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, RTP, NC, USA
| | - Fabian A Grimm
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.,current address: ExxonMobil Biomedical Sciences Inc., Annandale, NJ, USA
| | - William D Klaren
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.,current address: S.C. Johnson and Son, Inc., Racine, WI, USA
| | - Abigail Dalzell
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Harwell Science Campus, Oxon, UK
| | - Srikeerthana Kuchi
- Northern Ireland Centre for Stratified Medicine, Ulster University, L/Derry, Northern Ireland, UK.,current address: MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
| | - Shu-Dong Zhang
- Northern Ireland Centre for Stratified Medicine, Ulster University, L/Derry, Northern Ireland, UK
| | - Klaus Lenz
- SYNCOM Forschungs- und Entwicklungsberatung GmbH, Ganderkesee, Germany
| | - Peter J Boogaard
- SHELL International BV, The Hague, Netherlands.,Concawe, Brussels, Belgium
| | | | - Timothy W Gant
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Harwell Science Campus, Oxon, UK
| | - Fred A Wright
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
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31
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Marvel SW, House JS, Wheeler M, Song K, Zhou Y, Wright FA, Chiu WA, Rusyn I, Motsinger-Reif A, Reif DM. The COVID-19 Pandemic Vulnerability Index (PVI) Dashboard: Monitoring county-level vulnerability using visualization, statistical modeling, and machine learning. medRxiv 2020:2020.08.10.20169649. [PMID: 32817964 PMCID: PMC7430608 DOI: 10.1101/2020.08.10.20169649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BACKGROUND While the COVID-19 pandemic presents a global challenge, the U.S. response places substantial responsibility for both decision-making and communication on local health authorities, necessitating tools to support decision-making at the community level. OBJECTIVES We created a Pandemic Vulnerability Index (PVI) to support counties and municipalities by integrating baseline data on relevant community vulnerabilities with dynamic data on local infection rates and interventions. The PVI visually synthesizes county-level vulnerability indicators, enabling their comparison in regional, state, and nationwide contexts. METHODS We describe the data streams used and how these are combined to calculate the PVI, detail the supporting epidemiological modeling and machine-learning forecasts, and outline the deployment of an interactive web Dashboard. Finally, we describe the practical application of the PVI for real-world decision-making. RESULTS Considering an outlook horizon from 1 to 28 days, the overall PVI scores are significantly associated with key vulnerability-related outcome metrics of cumulative deaths, population adjusted cumulative deaths, and the proportion of deaths from cases. The modeling results indicate the most significant predictors of case counts are population size, proportion of black residents, and mean PM2.5. The machine learning forecast results were strongly predictive of observed cases and deaths up to 14 days ahead. The modeling reinforces an integrated concept of vulnerability that accounts for both dynamic and static data streams and highlights the drivers of inequities in COVID-19 cases and deaths. These results also indicate that local areas with a highly ranked PVI should take near-term action to mitigate vulnerability. DISCUSSION The COVID-19 PVI Dashboard monitors multiple data streams to communicate county-level trends and vulnerabilities and facilitates decision-making and communication among government officials, scientists, community leaders, and the public to enable effective and coordinated action to combat the pandemic.
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Affiliation(s)
- Skylar W. Marvel
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - John S. House
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Matthew Wheeler
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Kuncheng Song
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Yihui Zhou
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Fred A. Wright
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
- Department of Statistics, North Carolina State University, Raleigh, NC 27695, USA
| | - Weihsueh A. Chiu
- Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77845, USA
| | - Ivan Rusyn
- Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77845, USA
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - David M. Reif
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
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House JS, Bouzos E, Fahy KM, Francisco VM, Lloyd DT, Wright FA, Motsinger-Reif AA, Asuri P, Wheeler KE. Low-Dose Silver Nanoparticle Surface Chemistry and Temporal Effects on Gene Expression in Human Liver Cells. Small 2020; 16:e2000299. [PMID: 32227433 PMCID: PMC7446734 DOI: 10.1002/smll.202000299] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/29/2020] [Accepted: 03/02/2020] [Indexed: 05/31/2023]
Abstract
Silver nanoparticles (AgNPs) are widely incorporated into consumer and biomedical products for their antimicrobial and plasmonic properties with limited risk assessment of low-dose cumulative exposure in humans. To evaluate cellular responses to low-dose AgNP exposures across time, human liver cells (HepG2) are exposed to AgNPs with three different surface charges (1.2 µg mL-1 ) and complete gene expression is monitored across a 24 h period. Time and AgNP surface chemistry mediate gene expression. In addition, since cells are fed, time has marked effects on gene expression that should be considered. Surface chemistry of AgNPs alters gene transcription in a time-dependent manner, with the most dramatic effects in cationic AgNPs. Universal to all surface coatings, AgNP-treated cells responded by inactivating proliferation and enabling cell cycle checkpoints. Further analysis of these universal features of AgNP cellular response, as well as more detailed analysis of specific AgNP treatments, time points, or specific genes, is facilitated with an accompanying application. Taken together, these results provide a foundation for understanding hepatic response to low-dose AgNPs for future risk assessment.
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Affiliation(s)
- John S House
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Evangelia Bouzos
- Department of Bioengineering, Santa Clara University, Santa Clara, CA, 95053, USA
- Department of Chemistry and Biochemistry, Santa Clara University, Santa Clara, CA, 95053, USA
| | - Kira M Fahy
- Department of Chemistry and Biochemistry, Santa Clara University, Santa Clara, CA, 95053, USA
| | | | - Dillon T Lloyd
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Fred A Wright
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Alison A Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Prashanth Asuri
- Department of Bioengineering, Santa Clara University, Santa Clara, CA, 95053, USA
| | - Korin E Wheeler
- Department of Chemistry and Biochemistry, Santa Clara University, Santa Clara, CA, 95053, USA
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Abstract
Fibrates are a medication class prescribed for decades as 'broad-spectrum' lipid-modifying agents used to lower blood triglyceride levels and raise high-density lipoprotein cholesterol levels. Such lipid changes are associated with a decrease in cardiovascular disease, and fibrates are commonly used to reduce risk of dangerous cardiovascular outcomes. As with most drugs, it is well established that response to fibrate treatment is variable, and this variation is heritable. This has motivated the investigation of pharmacogenomic determinants of response, and multiple studies have discovered a number of genes associated with fibrate response. Similar to other complex traits, the interrogation of single nucleotide polymorphisms using candidate gene or genome-wide approaches has not revealed a substantial portion of response variation. However, recent innovations in technological platforms and advances in statistical methodologies are revolutionizing the use and integration of other 'omes' in pharmacogenomics studies. Here, we detail successes, challenges, and recent advances in fibrate pharmacogenomics.
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Affiliation(s)
- John S House
- Division of Intramural Research, National Institute of Environmental Health Sciences, NIH, Department of Health & Human Services, Research Triangle Park, NC 27709, USA
| | - Alison A Motsinger-Reif
- Division of Intramural Research, National Institute of Environmental Health Sciences, NIH, Department of Health & Human Services, Research Triangle Park, NC 27709, USA
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Burnett SD, Blanchette AD, Grimm FA, House JS, Reif DM, Wright FA, Chiu WA, Rusyn I. Population-based toxicity screening in human induced pluripotent stem cell-derived cardiomyocytes. Toxicol Appl Pharmacol 2019; 381:114711. [PMID: 31425687 PMCID: PMC6745256 DOI: 10.1016/j.taap.2019.114711] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/06/2019] [Accepted: 08/14/2019] [Indexed: 11/23/2022]
Abstract
The potential for cardiotoxicity is carefully evaluated for pharmaceuticals, as it is a major safety liability. However, environmental chemicals are seldom tested for their cardiotoxic potential. Moreover, there is a large variability in both baseline and drug-induced cardiovascular risk in humans, but data are lacking on the degree to which susceptibility to chemically-induced cardiotoxicity may also vary. Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes have become an important in vitro model for drug screening. Thus, we hypothesized that a population-based model of iPSC-derived cardiomyocytes from a diverse set of individuals can be used to assess potential hazard and inter-individual variability in chemical effects on these cells. We conducted concentration-response screening of 134 chemicals (pharmaceuticals, industrial and environmental chemicals and food constituents) in iPSC-derived cardiomyocytes from 43 individuals, comprising both sexes and diverse ancestry. We measured kinetic calcium flux and conducted high-content imaging following chemical exposure, and utilized a panel of functional and cytotoxicity parameters in concentration-response for each chemical and donor. We show reproducible inter-individual variability in both baseline and chemical-induced effects on iPSC-derived cardiomyocytes. Further, chemical-specific variability in potency and degree of population variability were quantified. This study shows the feasibility of using an organotypic population-based human in vitro model to quantitatively assess chemicals for which little cardiotoxicity information is available. Ultimately, these results advance in vitro toxicity testing methodologies by providing an innovative tool for population-based cardiotoxicity screening, contributing to the paradigm shift from traditional animal models of toxicity to in vitro toxicity testing methods.
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Affiliation(s)
- Sarah D Burnett
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843-4458, USA.
| | - Alexander D Blanchette
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843-4458, USA.
| | - Fabian A Grimm
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843-4458, USA.
| | - John S House
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA.
| | - David M Reif
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA; Department of Statistics, North Carolina State University, Raleigh, NC 27695, USA
| | - Fred A Wright
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA; Department of Statistics, North Carolina State University, Raleigh, NC 27695, USA.
| | - Weihsueh A Chiu
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843-4458, USA.
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843-4458, USA.
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35
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Onel M, Beykal B, Ferguson K, Chiu WA, McDonald TJ, Zhou L, House JS, Wright FA, Sheen DA, Rusyn I, Pistikopoulos EN. Grouping of complex substances using analytical chemistry data: A framework for quantitative evaluation and visualization. PLoS One 2019; 14:e0223517. [PMID: 31600275 PMCID: PMC6786635 DOI: 10.1371/journal.pone.0223517] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 09/23/2019] [Indexed: 02/01/2023] Open
Abstract
A detailed characterization of the chemical composition of complex substances, such as products of petroleum refining and environmental mixtures, is greatly needed in exposure assessment and manufacturing. The inherent complexity and variability in the composition of complex substances obfuscate the choices for their detailed analytical characterization. Yet, in lieu of exact chemical composition of complex substances, evaluation of the degree of similarity is a sensible path toward decision-making in environmental health regulations. Grouping of similar complex substances is a challenge that can be addressed via advanced analytical methods and streamlined data analysis and visualization techniques. Here, we propose a framework with unsupervised and supervised analyses to optimally group complex substances based on their analytical features. We test two data sets of complex oil-derived substances. The first data set is from gas chromatography-mass spectrometry (GC-MS) analysis of 20 Standard Reference Materials representing crude oils and oil refining products. The second data set consists of 15 samples of various gas oils analyzed using three analytical techniques: GC-MS, GC×GC-flame ionization detection (FID), and ion mobility spectrometry-mass spectrometry (IM-MS). We use hierarchical clustering using Pearson correlation as a similarity metric for the unsupervised analysis and build classification models using the Random Forest algorithm for the supervised analysis. We present a quantitative comparative assessment of clustering results via Fowlkes-Mallows index, and classification results via model accuracies in predicting the group of an unknown complex substance. We demonstrate the effect of (i) different grouping methodologies, (ii) data set size, and (iii) dimensionality reduction on the grouping quality, and (iv) different analytical techniques on the characterization of the complex substances. While the complexity and variability in chemical composition are an inherent feature of complex substances, we demonstrate how the choices of the data analysis and visualization methods can impact the communication of their characteristics to delineate sufficient similarity.
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Affiliation(s)
- Melis Onel
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States of America
- Texas A&M Energy Institute, Texas A&M University, College Station, TX, United States of America
| | - Burcu Beykal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States of America
- Texas A&M Energy Institute, Texas A&M University, College Station, TX, United States of America
| | - Kyle Ferguson
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States of America
| | - Weihsueh A. Chiu
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States of America
| | - Thomas J. McDonald
- Department of Environmental and Occupational Health, Texas A&M University, College Station, TX, United States of America
| | - Lan Zhou
- Department of Statistics, Texas A&M University, College Station, TX, United States of America
| | - John S. House
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States of America
| | - Fred A. Wright
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States of America
- Departments of Statistics and Biological Sciences, North Carolina State University, Raleigh, NC, United States of America
| | - David A. Sheen
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, MD, United States of America
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States of America
| | - Efstratios N. Pistikopoulos
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States of America
- Texas A&M Energy Institute, Texas A&M University, College Station, TX, United States of America
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Tam HW, Hall JR, Messenger ZJ, Jima DD, House JS, Linder K, Smart RC. C/EBPβ suppresses keratinocyte autonomous type 1 IFN response and p53 to increase cell survival and susceptibility to UVB-induced skin cancer. Carcinogenesis 2019; 40:1099-1109. [PMID: 30698678 PMCID: PMC10893916 DOI: 10.1093/carcin/bgz012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 01/04/2019] [Accepted: 01/22/2019] [Indexed: 12/14/2022] Open
Abstract
p53 is activated by DNA damage and oncogenic stimuli to regulate senescence, apoptosis and cell-cycle arrest, which are essential to prevent cancer. Here, we utilized UVB radiation, a potent inducer of DNA damage, p53, apoptosis and skin cancer to investigate the mechanism of CCAAT/enhancer binding protein-β (C/EBPβ) in regulating p53-mediated apoptosis in keratinocytes and to test whether the deletion of C/EBPβ in epidermis can protect mice from UVB-induced skin cancer. UVB-treatment of C/EBPβ skin conditional knockout (CKOβ) mice increased p53 protein levels in epidermis and enhanced p53-dependent apoptotic activity 3-fold compared with UVB-treated control mice. UVB increased C/EBPβ levels through a p53-dependent pathway and stimulated the formation of a C/EBPβ-p53 protein complex; knockdown of C/EBPβ increased p53 protein stability in keratinocytes. These results suggest a p53-C/EBPβ feedback loop, whereby C/EBPβ, a transcriptional target of a p53 pathway, functions as a survival factor by negatively regulating p53 apoptotic activity in response to DNA damage. RNAseq analysis of UVB-treated CKOβ epidermis unexpectedly revealed that type 1 interferon (IFN) pathway was the most highly enriched pathway. Numerous pro-apoptotic interferon stimulated genes were upregulated including some known to enhance p53 apoptosis. Our results indicate that p53 and IFN pathways function together in response to DNA damage to result in the activation of extrinsic apoptosis pathways and caspase 8 cleavage. Last, we observed CKOβ mice were resistant to UVB-induced skin cancer. Our results suggest that C/EBPβ represses apoptosis through keratinocyte autonomous suppression of the type 1 IFN response and p53 to increase cell survival and susceptibility to UVB-induced skin cancer.
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Affiliation(s)
- Hann W Tam
- Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Jonathan R Hall
- Toxicology Program, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | | | - Dereje D Jima
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - John S House
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Keith Linder
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC, USA
| | - Robert C Smart
- Toxicology Program, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
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37
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Henriquez AR, House JS, Snow SJ, Miller CN, Schladweiler MC, Fisher A, Ren H, Valdez M, Kodavanti PR, Kodavanti UP. Ozone-induced dysregulation of neuroendocrine axes requires adrenal-derived stress hormones. Toxicol Sci 2019; 172:38-50. [PMID: 31397875 PMCID: PMC9344225 DOI: 10.1093/toxsci/kfz182] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/02/2019] [Accepted: 07/18/2019] [Indexed: 12/14/2022] Open
Abstract
Acute ozone inhalation increases circulating stress hormones through activation of the sympathetic-adrenal-medullary and hypothalamic-pituitary-adrenal axes. Adrenalectomized (AD) rats have attenuated ozone-induced lung responses. We hypothesized that ozone exposure will induce changes in circulating pituitary-derived hormones and global gene expression in the brainstem and hypothalamus, and that AD will ameliorate these effects. Male Wistar-Kyoto rats (13-weeks) that underwent sham-surgery (SHAM) or AD were exposed to ozone (0.8-ppm) or filtered-air for 4-hours. In SHAM rats, ozone exposure decreased circulating thyroid-stimulating hormone (TSH), prolactin (PRL), and luteinizing hormone (LH). AD prevented reductions in TSH and PRL, but not LH. AD increased ACTH ∼5-fold in both air and ozone-exposed rats. AD in air-exposed rats resulted in few significant transcriptional differences in the brainstem and hypothalamus (∼20 genes per tissue). By contrast, ozone-exposure in SHAM rats resulted in increases and decreases in expression of hundreds of genes in brainstem and hypothalamus relative to air-exposed SHAM rats (303 and 568 genes, respectively). Differentially expressed genes from ozone exposure were enriched for pathways involving hedgehog signaling, responses to alpha-interferon, hypoxia, and mTORC1, among others. Gene changes in both brain areas were analogous to those altered by corticosteroids and L-dopa, suggesting a role for endogenous glucocorticoids and catecholamines. AD completely prevented this ozone-induced transcriptional response. These findings show that short-term ozone inhalation promotes a shift in brainstem and hypothalamic gene expression that is dependent on the presence of circulating adrenal-derived stress hormones. This is likely to have profound downstream influence on systemic effects of ozone.
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Affiliation(s)
- Andres R Henriquez
- Oak Ridge Institute for Science and Education, Research Triangle Park, NC, United States
| | - John S House
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States.,Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, United States
| | - Samantha J Snow
- Environmental Public Health Division, National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States.,ICF, Durham, NC, United States
| | - Colette N Miller
- Environmental Public Health Division, National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States
| | - Mette C Schladweiler
- Environmental Public Health Division, National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States
| | - Anna Fisher
- Research Cores Unit, National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States
| | - Hongzu Ren
- Research Cores Unit, National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States
| | - Matthew Valdez
- Oak Ridge Institute for Science and Education, Research Triangle Park, NC, United States
| | - Prasada R Kodavanti
- Toxicity Assessment Division, National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States
| | - Urmila P Kodavanti
- Environmental Public Health Division, National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States
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38
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House JS, Hall J, Park SS, Planchart A, Money E, Maguire RL, Huang Z, Mattingly CJ, Skaar D, Tzeng JY, Darrah TH, Vengosh A, Murphy SK, Jirtle RL, Hoyo C. Cadmium exposure and MEG3 methylation differences between Whites and African Americans in the NEST Cohort. Environ Epigenet 2019; 5:dvz014. [PMID: 31528362 PMCID: PMC6736358 DOI: 10.1093/eep/dvz014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 06/21/2019] [Accepted: 07/19/2019] [Indexed: 05/06/2023]
Abstract
Cadmium (Cd) is a ubiquitous environmental pollutant associated with a wide range of health outcomes including cancer. However, obscure exposure sources often hinder prevention efforts. Further, although epigenetic mechanisms are suspected to link these associations, gene sequence regions targeted by Cd are unclear. Aberrant methylation of a differentially methylated region (DMR) on the MEG3 gene that regulates the expression of a cluster of genes including MEG3, DLK1, MEG8, MEG9 and DIO3 has been associated with multiple cancers. In 287 infant-mother pairs, we used a combination of linear regression and the Getis-Ord Gi* statistic to determine if maternal blood Cd concentrations were associated with offspring CpG methylation of the sequence region regulating a cluster of imprinted genes including MEG3. Correlations were used to examine potential sources and routes. We observed a significant geographic co-clustering of elevated prenatal Cd levels and MEG3 DMR hypermethylation in cord blood (P = 0.01), and these findings were substantiated in our statistical models (β = 1.70, se = 0.80, P = 0.03). These associations were strongest in those born to African American women (β = 3.52, se = 1.32, P = 0.01) compared with those born to White women (β = 1.24, se = 2.11, P = 0.56) or Hispanic women (β = 1.18, se = 1.24, P = 0.34). Consistent with Cd bioaccumulation during the life course, blood Cd levels increased with age (β = 0.015 µg/dl/year, P = 0.003), and Cd concentrations were significantly correlated between blood and urine (ρ > 0.47, P < 0.01), but not hand wipe, soil or house dust concentrations (P > 0.05). Together, these data support that prenatal Cd exposure is associated with aberrant methylation of the imprint regulatory element for the MEG3 gene cluster at birth. However, neither house-dust nor water are likely exposure sources, and ingestion via contaminated hands is also unlikely to be a significant exposure route in this population. Larger studies are required to identify routes and sources of exposure.
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Affiliation(s)
- John S House
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Jonathan Hall
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Sarah S Park
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Antonio Planchart
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Eric Money
- Center for Geospatial Analytics, North Carolina State University, Raleigh, NC, USA
- Department of Natural Resources, North Carolina State University, Raleigh, NC, USA
| | - Rachel L Maguire
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Zhiqing Huang
- Department of Obstetrics and Gynecology, Duke University School of Medicine, Durham, NC, USA
| | - Carolyn J Mattingly
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - David Skaar
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Jung Ying Tzeng
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - Thomas H Darrah
- Division of Climate, Water, and Environment, School of Earth Sciences, The Ohio State University, Columbus, OH, USA
| | - Avner Vengosh
- Nicholas School of the Environment, Duke University, Durham, NC, USA
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University School of Medicine, Durham, NC, USA
| | - Randy L Jirtle
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Cathrine Hoyo
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
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Sai K, Parsons C, House JS, Kathariou S, Ninomiya-Tsuji J. Necroptosis mediators RIPK3 and MLKL suppress intracellular Listeria replication independently of host cell killing. J Cell Biol 2019; 218:1994-2005. [PMID: 30975711 PMCID: PMC6548127 DOI: 10.1083/jcb.201810014] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 02/27/2019] [Accepted: 03/21/2019] [Indexed: 01/10/2023] Open
Abstract
RIPK3, a key mediator of necroptosis, has been implicated in the host defense against viral infection primary in immune cells. However, gene expression analysis revealed that RIPK3 is abundantly expressed not only in immune organs but also in the gastrointestinal tract, particularly in the small intestine. We found that orally inoculated Listeria monocytogenes, a bacterial foodborne pathogen, efficiently spread and caused systemic infection in Ripk3-deficient mice while almost no dissemination was observed in wild-type mice. Listeria infection activated the RIPK3-MLKL pathway in cultured cells, which resulted in suppression of intracellular replication of Listeria Surprisingly, Listeria infection-induced phosphorylation of MLKL did not result in host cell killing. We found that MLKL directly binds to Listeria and inhibits their replication in the cytosol. Our findings have revealed a novel functional role of the RIPK3-MLKL pathway in nonimmune cell-derived host defense against Listeria invasion, which is mediated through cell death-independent mechanisms.
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Affiliation(s)
- Kazuhito Sai
- Department of Biological Sciences, North Carolina State University, Raleigh, NC
| | - Cameron Parsons
- Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, NC
| | - John S House
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC
| | - Sophia Kathariou
- Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, NC
| | - Jun Ninomiya-Tsuji
- Department of Biological Sciences, North Carolina State University, Raleigh, NC
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40
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Snow SJ, Henriquez AR, House JS, Schladweiler MC, Miller CN, Kodavanti UP. Ozone‐Induced Systemic Metabolic Alterations are Regulated by Circulating Stress Hormones in Rats. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.802.75] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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41
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Messenger ZJ, Hall JR, Jima DD, House JS, Tam HW, Tokarz DA, Smart RC. C/EBPβ deletion in oncogenic Ras skin tumors is a synthetic lethal event. Cell Death Dis 2018; 9:1054. [PMID: 30323292 PMCID: PMC6189130 DOI: 10.1038/s41419-018-1103-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 08/22/2018] [Indexed: 12/30/2022]
Abstract
Therapeutic targeting of specific genetic changes in cancer has proven to be an effective therapy and the concept of synthetic lethality has emerged. CCAAT/enhancer-binding protein-β (C/EBPβ), a basic leucine zipper transcription factor, has important roles in cellular processes including differentiation, inflammation, survival, and energy metabolism. Using a genetically engineered mouse model, we report that the deletion C/EBPβ in pre-existing oncogenic Ha-Ras mouse skin tumors in vivo resulted in rapid tumor regression. Regressing tumors exhibited elevated levels of apoptosis and p53 protein/activity, while adjacent C/EBPβ-deleted skin did not. These results indicate that the deletion of C/EBPβ de-represses p53 in oncogenic Ras tumors but not in normal wild-type Ras keratinocytes, and that C/EBPβ is essential for survival of oncogenic Ras tumors. Co-deletion of C/EBPβ and p53 in oncogenic Ras tumors showed p53 is required for tumor regression and elevated apoptosis. In tumors, loss of a pathway that confers adaptability to a stress phenotype of cancer/tumorigenesis, such as DNA damage, could result in selective tumor cell killing. Our results show that oncogenic Ras tumors display a significant DNA damage/replicative stress phenotype and these tumors have acquired a dependence on C/EBPβ for their survival. RNAseq data analysis of regressing tumors deleted of C/EBPβ indicates a novel interface between p53, type-1 interferon response, and death receptor pathways, which function in concert to produce activation of extrinsic apoptosis pathways. In summary, the deletion of C/EBPβ in oncogenic Ras skin tumors is a synthetic lethal event, making it a promising target for future potential anticancer therapies.
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Affiliation(s)
| | - Jonathan R Hall
- Toxicology Program, Raleigh, NC, USA. .,Center of Human Health and the Environment, Raleigh, NC, USA. .,Department of Biological Sciences, Raleigh, NC, USA.
| | - Dereje D Jima
- Center of Human Health and the Environment, Raleigh, NC, USA.,Bioinformatics Research Center, Raleigh, NC, USA
| | - John S House
- Center of Human Health and the Environment, Raleigh, NC, USA.,Bioinformatics Research Center, Raleigh, NC, USA
| | | | - Debra A Tokarz
- Center of Human Health and the Environment, Raleigh, NC, USA.,Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC, USA
| | - Robert C Smart
- Toxicology Program, Raleigh, NC, USA. .,Center of Human Health and the Environment, Raleigh, NC, USA. .,Department of Biological Sciences, Raleigh, NC, USA.
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42
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Sakolish C, Weber EJ, Kelly EJ, Himmelfarb J, Mouneimne R, Grimm FA, House JS, Wade T, Han A, Chiu WA, Rusyn I. Technology Transfer of the Microphysiological Systems: A Case Study of the Human Proximal Tubule Tissue Chip. Sci Rep 2018; 8:14882. [PMID: 30291268 PMCID: PMC6173737 DOI: 10.1038/s41598-018-33099-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/21/2018] [Indexed: 01/08/2023] Open
Abstract
The adoption of a new technology into basic research, and industrial and clinical settings requires rigorous testing to build confidence in the reproducibility, reliability, robustness, and relevance of these models. Tissue chips are promising new technology, they have the potential to serve as a valuable tool in biomedical research, as well as pharmaceutical development with regards to testing for efficacy and safety. The principal goals of this study were to validate a previously established proximal tubule tissue chip model in an independent laboratory and to extend its utility to testing of nephrotoxic compounds. Here, we evaluated critical endpoints from the tissue chip developer laboratory, focusing on biological relevance (long-term viability, baseline protein and gene expression, ammoniagenesis, and vitamin D metabolism), and toxicity biomarkers. Tissue chip experiments were conducted in parallel with traditional 2D culture conditions using two different renal proximal tubule epithelial cell sources. The results of these studies were then compared to the findings reported by the tissue chip developers. While the overall transferability of this advanced tissue chip platform was a success, the reproducibility with the original report was greatly dependent on the cell source. This study demonstrates critical importance of developing microphysiological platforms using renewable cell sources.
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Affiliation(s)
- Courtney Sakolish
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Elijah J Weber
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA
| | - Edward J Kelly
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA
| | - Jonathan Himmelfarb
- Division of Nephrology, University of Washington Kidney Research Institute, Seattle, WA, USA
| | - Roula Mouneimne
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Fabian A Grimm
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - John S House
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Terry Wade
- Geochemical and Environmental Research Group, Texas A&M University, College Station, TX, USA
| | - Arum Han
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
| | - Weihsueh A Chiu
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.
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43
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House JS, Mendez M, Maguire RL, Gonzalez-Nahm S, Huang Z, Daniels J, Murphy SK, Fuemmeler BF, Wright FA, Hoyo C. Periconceptional Maternal Mediterranean Diet Is Associated With Favorable Offspring Behaviors and Altered CpG Methylation of Imprinted Genes. Front Cell Dev Biol 2018; 6:107. [PMID: 30246009 PMCID: PMC6137242 DOI: 10.3389/fcell.2018.00107] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 08/20/2018] [Indexed: 12/28/2022] Open
Abstract
Background: Maternal diet during pregnancy has been shown to influence the child neuro-developmental outcomes. Studies examining effects of dietary patterns on offspring behavior are sparse. Objective: Determine if maternal adherence to a Mediterranean diet is associated with child behavioral outcomes assessed early in life, and to evaluate the role of differentially methylated regions (DMRs) regulating genomically imprinted genes in these associations. Methods: Among 325 mother/infant pairs, we used regression models to evaluate the association between tertiles of maternal periconceptional Mediterranean diet adherence (MDA) scores derived from a Food Frequency Questionnaire, and social and emotional scores derived from the Infant Toddler Social and Emotional Assessment (ITSEA) questionnaire in the second year of life. Methylation of nine genomically imprinted genes was measured to determine if MDA was associated with CpG methylation. Results: Child depression was inversely associated with maternal MDA (Bonferroni-corrected p = 0.041). While controlling for false-discovery, compared to offspring of women with the lowest MDA tertile, those with MDA scores in middle and high MDA tertiles had decreased odds for atypical behaviors [OR (95% CI) = 0.40 (0.20, 0.78) for middle and 0.40 (0.17, 0.92) for highest tertile], for maladaptive behaviors [0.37 (0.18, 0.72) for middle tertile and 0.42 (0.18, 0.95) for highest tertile] and for an index of autism spectrum disorder behaviors [0.46 (0.23, 0.90) for middle and 0.35 (0.15, 0.80) for highest tertile]. Offspring of women with the highest MDA tertile were less likely to exhibit depressive [OR = 0.28 (0.12, 0.64)] and anxiety [0.42 (0.18, 0.97)] behaviors and increased odds of social relatedness [2.31 (1.04, 5.19)] behaviors when compared to low MDA mothers. Some associations varied by sex. Perinatal MDA score was associated with methylation differences for imprinted control regions of PEG10/SGCE [females: Beta (95% CI) = 1.66 (0.52, 2.80) - Bonferroni-corrected p = 0.048; males: -0.56 (-1.13, -0.00)], as well as both MEG3 and IGF2 in males [0.97 (0.00, 1.94)] and -0.92 (-1.65, -0.19) respectively. Conclusion: In this ethnically diverse cohort, maternal adherence to a Mediterranean diet in early pregnancy was associated with favorable neurobehavioral outcomes in early childhood and with sex-dependent methylation differences of MEG3, IGF2, and SGCE/PEG10 DMRs.
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Affiliation(s)
- John S House
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States.,Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, United States
| | - Michelle Mendez
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Rachel L Maguire
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, United States.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
| | - Sarah Gonzalez-Nahm
- Department of Health, Behavior and Society, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Zhiqing Huang
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, United States
| | - Julie Daniels
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, United States
| | - Bernard F Fuemmeler
- Department of Health Behavior and Policy, Virginia Commonwealth University, Richmond, VA, United States
| | - Fred A Wright
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States.,Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, United States.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States.,Department of Statistics, North Carolina State University, Raleigh, NC, United States
| | - Cathrine Hoyo
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, United States.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
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44
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Grimm FA, Blanchette A, House JS, Ferguson K, Hsieh NH, Dalaijamts C, Wright AA, Anson B, Wright FA, Chiu WA, Rusyn I. A human population-based organotypic in vitro model for cardiotoxicity screening. ALTEX 2018; 35:441-452. [PMID: 29999168 PMCID: PMC6231908 DOI: 10.14573/altex.1805301] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/05/2018] [Indexed: 12/11/2022]
Abstract
Assessing inter-individual variability in responses to xenobiotics remains a substantial challenge, both in drug development with respect to pharmaceuticals and in public health with respect to environmental chemicals. Although approaches exist to characterize pharmacokinetic variability, there are no methods to routinely address pharmacodynamic variability. In this study, we aimed to demonstrate the feasibility of characterizing inter-individual variability in a human in vitro model. Specifically, we hypothesized that genetic variability across a population of iPSC-derived cardiomyocytes translates into reproducible variability in both baseline phenotypes and drug responses. We measured baseline and drug-related effects in iPSC-derived cardiomyocytes from 27 healthy donors on kinetic Ca2+ flux and high-content live cell imaging. Cells were treated in concentration-response with cardiotoxic drugs: isoproterenol (β-adrenergic receptor agonist/positive inotrope), propranolol (β-adrenergic receptor antagonist/negative inotrope), and cisapride (hERG channel inhibitor/QT prolongation). Cells from four of the 27 donors were further evaluated in terms of baseline and treatment-related gene expression. Reproducibility of phenotypic responses was evaluated across batches and time. iPSC-derived cardiomyocytes exhibited reproducible donor-specific differences in baseline function and drug-induced effects. We demonstrate the feasibility of using a panel of population-based organotypic cells from healthy donors as an animal replacement experimental model. This model can be used to rapidly screen drugs and chemicals for inter-individual variability in cardiotoxicity. This approach demonstrates the feasibility of quantifying inter-individual variability in xenobiotic responses and can be expanded to other cell types for which in vitro populations can be derived from iPSCs.
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Affiliation(s)
- Fabian A Grimm
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Alexander Blanchette
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - John S House
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Kyle Ferguson
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Nan-Hung Hsieh
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Chimeddulam Dalaijamts
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Alec A Wright
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Blake Anson
- Cellular Dynamics International, Madison, WI, USA
| | - Fred A Wright
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - Weihsueh A Chiu
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
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Venkatratnam A, House JS, Konganti K, McKenney C, Threadgill DW, Chiu WA, Aylor DL, Wright FA, Rusyn I. Population-based dose-response analysis of liver transcriptional response to trichloroethylene in mouse. Mamm Genome 2018; 29:168-181. [PMID: 29353386 DOI: 10.1007/s00335-018-9734-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 01/17/2018] [Indexed: 12/23/2022]
Abstract
Studies of gene expression are common in toxicology and provide important clues to mechanistic understanding of adverse effects of chemicals. Most prior studies have been performed in a single strain or cell line; however, gene expression is heavily influenced by the genetic background, and these genotype-expression differences may be key drivers of inter-individual variation in response to chemical toxicity. In this study, we hypothesized that the genetically diverse Collaborative Cross mouse population can be used to gain insight and suggest mechanistic hypotheses for the dose- and genetic background-dependent effects of chemical exposure. This hypothesis was tested using a model liver toxicant trichloroethylene (TCE). Liver transcriptional responses to TCE exposure were evaluated 24 h after dosing. Transcriptomic dose-responses were examined for both TCE and its major oxidative metabolite trichloroacetic acid (TCA). As expected, peroxisome- and fatty acid metabolism-related pathways were among the most dose-responsive enriched pathways in all strains. However, nearly half of the TCE-induced liver transcriptional perturbation was strain-dependent, with abundant evidence of strain/dose interaction, including in the peroxisomal signaling-associated pathways. These effects were highly concordant between the administered TCE dose and liver levels of TCA. Dose-response analysis of gene expression at the pathway level yielded points of departure similar to those derived from the traditional toxicology studies for both non-cancer and cancer effects. Mapping of expression-genotype-dose relationships revealed some significant associations; however, the effects of TCE on gene expression in liver appear to be highly polygenic traits that are challenging to positionally map. This study highlights the usefulness of mouse population-based studies in assessing inter-individual variation in toxicological responses, but cautions that genetic mapping may be challenging because of the complexity in gene exposure-dose relationships.
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Affiliation(s)
- Abhishek Venkatratnam
- Department of Veterinary Integrative Biosciences, Texas A&M University, 4458 TAMU, College Station, Texas, 77843, USA.,Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina, 27599, USA
| | - John S House
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, 27695, USA.,Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, 27695, USA
| | - Kranti Konganti
- Department of Veterinary Integrative Biosciences, Texas A&M University, 4458 TAMU, College Station, Texas, 77843, USA
| | - Connor McKenney
- NCSU Undergraduate program in Genetics, North Carolina State University, Raleigh, North Carolina, 27695, USA
| | - David W Threadgill
- Department of Veterinary Integrative Biosciences, Texas A&M University, 4458 TAMU, College Station, Texas, 77843, USA
| | - Weihsueh A Chiu
- Department of Veterinary Integrative Biosciences, Texas A&M University, 4458 TAMU, College Station, Texas, 77843, USA
| | - David L Aylor
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, 27695, USA.,Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, 27695, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, 27695, USA
| | - Fred A Wright
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, 27695, USA.,Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, 27695, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, 27695, USA.,Department of Statistics, North Carolina State University, Raleigh, North Carolina, 27695, USA
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, 4458 TAMU, College Station, Texas, 77843, USA.
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46
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House JS, Grimm FA, Jima DD, Zhou YH, Rusyn I, Wright FA. A Pipeline for High-Throughput Concentration Response Modeling of Gene Expression for Toxicogenomics. Front Genet 2017; 8:168. [PMID: 29163636 PMCID: PMC5672545 DOI: 10.3389/fgene.2017.00168] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 10/18/2017] [Indexed: 12/21/2022] Open
Abstract
Cell-based assays are an attractive option to measure gene expression response to exposure, but the cost of whole-transcriptome RNA sequencing has been a barrier to the use of gene expression profiling for in vitro toxicity screening. In addition, standard RNA sequencing adds variability due to variable transcript length and amplification. Targeted probe-sequencing technologies such as TempO-Seq, with transcriptomic representation that can vary from hundreds of genes to the entire transcriptome, may reduce some components of variation. Analyses of high-throughput toxicogenomics data require renewed attention to read-calling algorithms and simplified dose–response modeling for datasets with relatively few samples. Using data from induced pluripotent stem cell-derived cardiomyocytes treated with chemicals at varying concentrations, we describe here and make available a pipeline for handling expression data generated by TempO-Seq to align reads, clean and normalize raw count data, identify differentially expressed genes, and calculate transcriptomic concentration–response points of departure. The methods are extensible to other forms of concentration–response gene-expression data, and we discuss the utility of the methods for assessing variation in susceptibility and the diseased cellular state.
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Affiliation(s)
- John S House
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States.,Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, United States
| | - Fabian A Grimm
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - Dereje D Jima
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States.,Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, United States
| | - Yi-Hui Zhou
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - Fred A Wright
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States.,Department of Statistics, North Carolina State University, Raleigh, NC, United States
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47
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Wyss AB, House JS, Hoppin JA, Richards M, Hankinson JL, Long S, Henneberger PK, Beane Freeman LE, Sandler DP, O'Connell EL, Cummings CB, Umbach DM, London SJ. Raw milk consumption and other early-life farm exposures and adult pulmonary function in the Agricultural Lung Health Study. Thorax 2017; 73:279-282. [PMID: 28689172 DOI: 10.1136/thoraxjnl-2017-210031] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/14/2017] [Accepted: 05/01/2017] [Indexed: 02/03/2023]
Abstract
Literature suggests that early exposure to the farming environment protects against atopy and asthma; few studies have examined pulmonary function. We evaluated associations between early-life farming exposures and pulmonary function in 3061 adults (mean age=63) from a US farming population using linear regression. Childhood raw milk consumption was associated with higher FEV1 (β=49.5 mL, 95% CI 2.8 to 96.1 mL, p=0.04) and FVC (β=66.2 mL, 95% CI 13.2 to 119.1 mL, p=0.01). We did not find appreciable associations with other early-life farming exposures. We report a novel association between raw milk consumption and higher pulmonary function that lasts into older adulthood.
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Affiliation(s)
- Annah B Wyss
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - John S House
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
| | - Jane A Hoppin
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, USA
| | | | | | | | - Paul K Henneberger
- Respiratory Health Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, West Virginia, USA
| | - Laura E Beane Freeman
- Occupational and Environmental Epidemiology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Elizabeth Long O'Connell
- Epidemiology Center, Public Health Sciences Group, Social & Scientific Systems, Durham, North Carolina, USA
| | - Christie Barker Cummings
- Epidemiology Center, Public Health Sciences Group, Social & Scientific Systems, Durham, North Carolina, USA
| | - David M Umbach
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA.,Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
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48
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House JS, Nichols CE, Li H, Brandenberger C, Virgincar RS, DeGraff LM, Driehuys B, Zeldin DC, London SJ. Vagal innervation is required for pulmonary function phenotype in Htr4-/- mice. Am J Physiol Lung Cell Mol Physiol 2017; 312:L520-L530. [PMID: 28130264 PMCID: PMC5407097 DOI: 10.1152/ajplung.00495.2016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/19/2017] [Accepted: 01/25/2017] [Indexed: 11/22/2022] Open
Abstract
Human genome-wide association studies have identified over 50 loci associated with pulmonary function and related phenotypes, yet follow-up studies to determine causal genes or variants are rare. Single nucleotide polymorphisms in serotonin receptor 4 (HTR4) are associated with human pulmonary function in genome-wide association studies and follow-up animal work has demonstrated that Htr4 is causally associated with pulmonary function in mice, although the precise mechanisms were not identified. We sought to elucidate the role of neural innervation and pulmonary architecture in the lung phenotype of Htr4-/- animals. We report here that the Htr4-/- phenotype in mouse is dependent on vagal innervation to the lung. Both ex vivo tracheal ring reactivity and in vivo flexiVent pulmonary functional analyses demonstrate that vagotomy abrogates the Htr4-/- airway hyperresponsiveness phenotype. Hyperpolarized 3He gas magnetic resonance imaging and stereological assessment of wild-type and Htr4-/- mice reveal no observable differences in lung volume, inflation characteristics, or pulmonary microarchitecture. Finally, control of breathing experiments reveal substantive differences in baseline breathing characteristics between mice with/without functional HTR4 in breathing frequency, relaxation time, flow rate, minute volume, time of inspiration and expiration and breathing pauses. These results suggest that HTR4's role in pulmonary function likely relates to neural innervation and control of breathing.
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Affiliation(s)
- John S House
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Cody E Nichols
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Huiling Li
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | | | - Rohan S Virgincar
- Center for In Vivo Microscopy, Duke University Medical Center, Durham, North Carolina.,Biomedical Engineering, Duke University, Durham, North Carolina
| | - Laura M DeGraff
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Bastiaan Driehuys
- Center for In Vivo Microscopy, Duke University Medical Center, Durham, North Carolina.,Biomedical Engineering, Duke University, Durham, North Carolina.,Radiology, Duke University Medical Center, Durham, North Carolina; and
| | - Darryl C Zeldin
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Stephanie J London
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina; .,Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
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49
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House JS, Wyss AB, Hoppin JA, Richards M, Long S, Umbach DM, Henneberger PK, Beane Freeman LE, Sandler DP, Long O'Connell E, Barker-Cummings C, London SJ. Early-life farm exposures and adult asthma and atopy in the Agricultural Lung Health Study. J Allergy Clin Immunol 2016; 140:249-256.e14. [PMID: 27845237 DOI: 10.1016/j.jaci.2016.09.036] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 09/01/2016] [Accepted: 09/08/2016] [Indexed: 01/28/2023]
Abstract
BACKGROUND Previous studies, mostly from Europe, suggest that early-life farming exposures protect against childhood asthma and allergy; few data exist on asthma and allergy in adults. OBJECTIVE We sought to examine associations between early-life farming exposures and current asthma and atopy in an older adult US farming population. METHODS We analyzed data from 1746 farmers and 1555 spouses (mean age, 63) from a case-control study nested within the Agricultural Health Study. Current asthma and early-life farming exposures were assessed via questionnaires. We defined atopy based on specific IgE > 0.70 IU/mL to at least 1 of 10 allergens measured in blood. We used logistic regression, adjusted for age, sex, race, state (Iowa or North Carolina), and smoking (pack years), to estimate associations between early-life exposures and asthma (1198 cases and 2031 noncases) or atopy (578 cases and 2526 noncases). RESULTS Exposure to the farming environment in utero and in early childhood had little or no association with asthma but was associated with reduced odds of atopy. The strongest association was seen for having a mother who performed farm activities while pregnant (odds ratio, 0.60; 95% CI, 0.48-0.74) and remained significant in models with correlated early-life exposures including early childhood farm animal contact and raw milk consumption. CONCLUSIONS In a large US farming population, early-life farm exposures, particularly maternal farming activities while pregnant, were strongly associated with reduced risk of atopy in adults. These results extend previous work done primarily on childhood outcomes and suggest that protective associations of early-life farming exposures on atopy endure across the life course.
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Affiliation(s)
- John S House
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC
| | - Annah B Wyss
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC
| | - Jane A Hoppin
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC; Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC
| | | | | | - David M Umbach
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC
| | - Paul K Henneberger
- Division of Respiratory Disease Studies, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV
| | - Laura E Beane Freeman
- Occupational and Environmental Epidemiology Branch, National Cancer Institute, Bethesda, Md
| | - Dale P Sandler
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC
| | | | | | - Stephanie J London
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC.
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50
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Graves JP, Gruzdev A, Bradbury JA, DeGraff LM, Li H, House JS, Hoopes SL, Edin ML, Zeldin DC. Quantitative Polymerase Chain Reaction Analysis of the Mouse Cyp2j Subfamily: Tissue Distribution and Regulation. Drug Metab Dispos 2015; 43:1169-80. [PMID: 25994032 DOI: 10.1124/dmd.115.064139] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/20/2015] [Indexed: 12/27/2022] Open
Abstract
Members of the cytochrome P450 CYP2J subfamily are expressed in multiple tissues in mice and humans. These enzymes are active in the metabolism of fatty acids to generate bioactive compounds. Herein we report new methods and results for quantitative polymerase chain reaction (qPCR) analysis for the seven genes (Cyp2j5, Cyp2j6, Cyp2j8, Cyp2j9, Cyp2j11, Cyp2j12, and Cyp2j13) of the mouse Cyp2j subfamily. SYBR Green primer sets were developed and compared with commercially available TaqMan primer/probe assays for specificity toward mouse Cyp2j cDNA, and analysis of tissue distribution and regulation of Cyp2j genes. Each TaqMan primer/probe set and SYBR Green primer set were shown to be specific for their intended mouse Cyp2j cDNA. Tissue distribution of the mouse Cyp2j isoforms confirmed similar patterns of expression between the two qPCR methods. Cyp2j5 and Cyp2j13 were highly expressed in male kidneys, and Cyp2j11 was highly expressed in both male and female kidneys. Cyp2j6 was expressed in multiple tissues, with the highest expression in the small intestine and duodenum. Cyp2j8 was detected in various tissues, with highest expression found in the skin. Cyp2j9 was highly expressed in the brain, liver, and lung. Cyp2j12 was predominately expressed in the brain. We also determined the Cyp2j isoform expression in Cyp2j5 knockout mice to determine whether there was compensatory regulation of other Cyp2j isoforms, and we assessed Cyp2j isoform regulation during various inflammatory models, including influenza A, bacterial lipopolysaccharide, house dust mite allergen, and corn pollen. Both qPCR methods detected similar suppression of Cyp2j6 and Cyp2j9 during inflammation in the lung.
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Affiliation(s)
- Joan P Graves
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - Artiom Gruzdev
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - J Alyce Bradbury
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - Laura M DeGraff
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - Huiling Li
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - John S House
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - Samantha L Hoopes
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - Matthew L Edin
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - Darryl C Zeldin
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
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