1
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Resztak JA, Wei J, Zilioli S, Sendler E, Alazizi A, Mair-Meijers HE, Wu P, Wen X, Slatcher RB, Zhou X, Luca F, Pique-Regi R. Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single-cell resolution. Genome Res 2023; 33:839-856. [PMID: 37442575 PMCID: PMC10519413 DOI: 10.1101/gr.276765.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/08/2023] [Indexed: 07/15/2023]
Abstract
Synthetic glucocorticoids, such as dexamethasone, have been used as a treatment for many immune conditions, such as asthma and, more recently, severe COVID-19. Single-cell data can capture more fine-grained details on transcriptional variability and dynamics to gain a better understanding of the molecular underpinnings of inter-individual variation in drug response. Here, we used single-cell RNA-seq to study the dynamics of the transcriptional response to glucocorticoids in activated peripheral blood mononuclear cells from 96 African American children. We used novel statistical approaches to calculate a mean-independent measure of gene expression variability and a measure of transcriptional response pseudotime. Using these approaches, we showed that glucocorticoids reverse the effects of immune stimulation on both gene expression mean and variability. Our novel measure of gene expression response dynamics, based on the diagonal linear discriminant analysis, separated individual cells by response status on the basis of their transcriptional profiles and allowed us to identify different dynamic patterns of gene expression along the response pseudotime. We identified genetic variants regulating gene expression mean and variability, including treatment-specific effects, and showed widespread genetic regulation of the transcriptional dynamics of the gene expression response.
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Affiliation(s)
- Justyna A Resztak
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Julong Wei
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Samuele Zilioli
- Department of Psychology, Wayne State University, Detroit, Michigan 48201, USA
- Department of Family Medicine and Public Health Sciences, Wayne State University, Detroit, Michigan 48201, USA
| | - Edward Sendler
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Adnan Alazizi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Henriette E Mair-Meijers
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Peijun Wu
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Richard B Slatcher
- Department of Psychology, University of Georgia, Athens, Georgia 30602, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA;
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
- Department of Biology, University of Rome "Tor Vergata," 00133 Rome, Italy
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA;
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
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2
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Occean JR, Wani AH, Donglasan J, Aiello AE, Galea S, Koenen KC, Qu A, Wildman DE, Uddin M. DNA methylation of Nuclear Factor of Activated T Cells 1 mediates the prospective relation between exposure to different traumatic event types and post-traumatic stress disorder. Psychiatry Res 2022; 311:114510. [PMID: 35349860 PMCID: PMC9018623 DOI: 10.1016/j.psychres.2022.114510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 02/26/2022] [Accepted: 03/12/2022] [Indexed: 11/25/2022]
Abstract
The mechanisms through which exposure to differing trauma types become biologically embedded to shape the risk for post-traumatic stress disorder (PTSD) is unclear. DNA methylation (5-mC), particularly in stress-relevant genes, may play a role in this relationship. Here, we conducted path analysis using generalized structural equation modeling to investigate whether blood-derived 5-mC in Nuclear Factor of Activated T Cells 1 (NFATC1) mediates the prospective association between each of five different trauma types ("assaultive violence", "other injury or shocking experience", "learning of trauma to loved one", "sudden, unexpected death of a close friend or relative", and "other") and lifetime PTSD. All five trauma types were significantly associated with reduced methylation at NFATC1 CpG site, cg17057218. Two of the five trauma types were significantly associated with increased methylation at NFATC1 CpG site, cg22324981. Moreover, methylation at cg17057218 significantly mediated 21-32% of the total effect for four of the five trauma types, while methylation at cg22324981 mediated 27-40% of the total effect for two of the five trauma types. These CpG sites were differentially associated with transcription factor binding sites and chromatin state signatures. NFATC1 5-mC may be a potential mechanism in the relationship between some trauma types and prospective risk for PTSD.
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Affiliation(s)
- James R. Occean
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA,Present address: Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Agaz H. Wani
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Janelle Donglasan
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Allison E. Aiello
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sandro Galea
- Boston University School of Public Health, Boston University, Boston, MA, USA
| | - Karestan C. Koenen
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Psychiatric and Neurodevelopmental Genetics Unit & Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Annie Qu
- Department of Statistics, University of California Irvine, Irvine, CA, USA
| | - Derek E. Wildman
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Monica Uddin
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
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3
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Xue F, Tang X, Kim G, Koenen KC, Martin CL, Galea S, Wildman D, Uddin M, Qu A. Heterogeneous Mediation Analysis on Epigenomic PTSD and Traumatic Stress in a Predominantly African American Cohort. J Am Stat Assoc 2022; 117:1669-1683. [PMID: 36875798 PMCID: PMC9980467 DOI: 10.1080/01621459.2022.2089572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
DNA methylation (DNAm) has been suggested to play a critical role in post-traumatic stress disorder (PTSD), through mediating the relationship between trauma and PTSD. However, this underlying mechanism of PTSD for African Americans still remains unknown. To fill this gap, in this article, we investigate how DNAm mediates the effects of traumatic experiences on PTSD symptoms in the Detroit Neighborhood Health Study (DNHS) (2008-2013) which involves primarily African Americans adults. To achieve this, we develop a new mediation analysis approach for high-dimensional potential DNAm mediators. A key novelty of our method is that we consider heterogeneity in mediation effects across subpopulations. Specifically, mediators in different subpopulations could have opposite effects on the outcome, and thus could be difficult to identify under a traditional homogeneous model framework. In contrast, the proposed method can estimate heterogeneous mediation effects and identifies subpopulations in which individuals share similar effects. Simulation studies demonstrate that the proposed method outperforms existing methods for both homogeneous and heterogeneous data. We also present our mediation analysis results of a dataset with 125 participants and more than 450,000 CpG sites from the DNHS study. The proposed method finds three subgroups of subjects and identifies DNAm mediators corresponding to genes such as HSP90AA1 and NFATC1 which have been linked to PTSD symptoms in literature. Our finding could be useful in future finer-grained investigation of PTSD mechanism and in the development of new treatments for PTSD.
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Affiliation(s)
- Fei Xue
- Purdue University, West Lafayette, IN
| | - Xiwei Tang
- University of Virginia, Charlottesville, VA
| | - Grace Kim
- University of Illinois College of Medicine, Chicago, IL
| | | | - Chantel L Martin
- The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | | | - Annie Qu
- University of California Irvine, Irvine, CA
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4
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Miller EM, Law EA, Ajeen R, Karasik J, Mendoza C, Abernathy H, Garrett H, King E, Wallace J, Zelek M, Edwards JK, Xiong K, Beatty C, Fleischauer AT, Ciccone EJ, Shook-Sa BE, Aiello AE, Boyce RM. SARS-CoV-2 infection in central North Carolina: Protocol for a population-based longitudinal cohort study and preliminary participant results. PLoS One 2021; 16:e0259070. [PMID: 34695156 PMCID: PMC8544868 DOI: 10.1371/journal.pone.0259070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 10/11/2021] [Indexed: 11/19/2022] Open
Abstract
Public health surveillance systems likely underestimate the true prevalence and incidence of SARS-CoV-2 infection due to limited access to testing and the high proportion of subclinical infections in community-based settings. This ongoing prospective, observational study aimed to generate accurate estimates of the prevalence and incidence of, and risk factors for, SARS-CoV-2 infection among residents of a central North Carolina county. From this cohort, we collected survey data and nasal swabs every two weeks and venous blood specimens every month. Nasal swabs were tested for the presence of SARS-CoV-2 virus (evidence of active infection), and serum specimens for SARS-CoV-2-specific antibodies (evidence of prior infection). As of June 23, 2021, we have enrolled a total of 153 participants from a county with an estimated 76,285 total residents. The anticipated study duration is at least 24 months, pending the evolution of the pandemic. Study data are being shared on a monthly basis with North Carolina state health authorities and future analyses aim to compare study data to state-wide metrics over time. Overall, the use of a probability-based sampling design and a well-characterized cohort will enable collection of critical data that can be used in planning and policy decisions for North Carolina and may be informative for other states with similar demographic characteristics.
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Affiliation(s)
- Elyse M. Miller
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Elle A. Law
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Rawan Ajeen
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Jaclyn Karasik
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Carmen Mendoza
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Haley Abernathy
- Institute of Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Haley Garrett
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Elise King
- Institute of Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - John Wallace
- North Carolina Institute of Public Health, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Michael Zelek
- Chatham County Public Health Department, Pittsboro, NC, United States of America
| | - Jessie K. Edwards
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Khou Xiong
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Cherese Beatty
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Aaron T. Fleischauer
- Division of State and Local Readiness, United States Centers for Disease Control and Prevention, Atlanta, GA, United States of America
- Epidemiology Branch, North Carolina Department of Health and Human Services, Raleigh, NC, United States of America
| | - Emily J. Ciccone
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Bonnie E. Shook-Sa
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Allison E. Aiello
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Ross M. Boyce
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
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5
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Resztak JA, Wei J, Zilioli S, Sendler E, Alazizi A, Mair-meijers HE, Wu P, Slatcher RB, Zhou X, Luca F, Pique-regi R. Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single cell resolution.. [PMID: 35313584 PMCID: PMC8936121 DOI: 10.1101/2021.09.30.462672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Synthetic glucocorticoids, such as dexamethasone, have been used as treatment for many immune conditions, such as asthma and more recently severe COVID-19. Single cell data can capture more fine-grained details on transcriptional variability and dynamics to gain a better understanding of the molecular underpinnings of inter-individual variation in drug response. Here, we used single cell RNA-seq to study the dynamics of the transcriptional response to glucocorticoids in activated Peripheral Blood Mononuclear Cells from 96 African American children. We employed novel statistical approaches to calculate a mean-independent measure of gene expression variability and a measure of transcriptional response pseudotime. Using these approaches, we demonstrated that glucocorticoids reverse the effects of immune stimulation on both gene expression mean and variability. Our novel measure of gene expression response dynamics, based on the diagonal linear discriminant analysis, separated individual cells by response status on the basis of their transcriptional profiles and allowed us to identify different dynamic patterns of gene expression along the response pseudotime. We identified genetic variants regulating gene expression mean and variability, including treatment-specific effects, and demonstrated widespread genetic regulation of the transcriptional dynamics of the gene expression response.
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6
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Jiang Y, Farrell AK, Tobin ET, Mair-Meijers H, Wildman DE, Luca F, Slatcher RB, Zilioli S. Socioeconomic status, financial stress, and glucocorticoid resistance among youth with asthma: Testing the moderation effects of maternal involvement and warmth. Brain Behav Immun 2021; 96:92-99. [PMID: 34015429 PMCID: PMC8319072 DOI: 10.1016/j.bbi.2021.05.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/11/2021] [Accepted: 05/15/2021] [Indexed: 10/21/2022] Open
Abstract
OBJECTIVES Children who grow up in more socioeconomically disadvantaged homes experience greater levels of inflammation and worse asthma symptoms than children from more advantaged families. However, recent evidence suggests that certain family-level factors can mitigate health disparities associated with socioeconomic status (SES). In a sample of youth with asthma, we investigated the potential buffering effects of maternal involvement and warmth on SES disparities in asthma-related immune responses, assessed via glucocorticoid resistance (GR) of immune cells. METHODS One hundred and forty-three youth (10-16 years of age) with asthma completed measures of maternal involvement and warmth, and their primary caregivers reported their levels of education, income, and financial stress. Peripheral blood mononuclear cells from youth's blood were isolated, cultured, and assayed to determine mitogen-stimulated (PMA/INO + Etho) and mitogen/hydrocortisone-stimulated (PMA/INO + Cort) levels of two Th-2 cytokines (i.e., interleukin-5, interleukin-13) and one Th-1 cytokine (i.e., interferon-γ). GR was calculated by subtracting log-transformed cytokine concentration in the PMA/INO + Etho samples from log-transformed cytokine concentration in the PMA/INO + Cort samples. RESULTS Both maternal involvement and warmth moderated the indirect pathway from family SES to GR of Th-2 cytokines via financial stress. Specifically, we found that low family SES was associated with elevated GR of Th-2 cytokines via increased financial stress among youth reporting low levels of maternal involvement and warmth, but not among those reporting high levels of maternal involvement or warmth. CONCLUSIONS These results highlight the protective role of maternal involvement and warmth in health-related biological processes modulated by family SES among youth with asthma.
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Affiliation(s)
- Yanping Jiang
- Department of Psychology, Wayne State University, United States.
| | | | - Erin T. Tobin
- Behavioral Health and General Internal Medicine, Henry Ford Health System
| | | | - Derek E. Wildman
- Genomics Program, College of Public Health, University of South Florida
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University,Department of Obstetrics and Gynecology, Wayne State University
| | | | - Samuele Zilioli
- Department of Psychology, Wayne State University, United States; Department of Family Medicine and Public Health Sciences, Wayne State University, United States.
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7
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Resztak JA, Farrell AK, Mair-Meijers H, Alazizi A, Wen X, Wildman DE, Zilioli S, Slatcher RB, Pique-Regi R, Luca F. Psychosocial experiences modulate asthma-associated genes through gene-environment interactions. eLife 2021; 10:e63852. [PMID: 34142656 PMCID: PMC8282343 DOI: 10.7554/elife.63852] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 06/16/2021] [Indexed: 01/04/2023] Open
Abstract
Social interactions and the overall psychosocial environment have a demonstrated impact on health, particularly for people living in disadvantaged urban areas. Here, we investigated the effect of psychosocial experiences on gene expression in peripheral blood immune cells of children with asthma in Metro Detroit. Using RNA-sequencing and a new machine learning approach, we identified transcriptional signatures of 19 variables including psychosocial factors, blood cell composition, and asthma symptoms. Importantly, we found 169 genes associated with asthma or allergic disease that are regulated by psychosocial factors and 344 significant gene-environment interactions for gene expression levels. These results demonstrate that immune gene expression mediates the link between negative psychosocial experiences and asthma risk.
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Affiliation(s)
- Justyna A Resztak
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | | | | | - Adnan Alazizi
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Xiaoquan Wen
- Department of Biostatistics, University of MichiganAnn ArborUnited States
| | - Derek E Wildman
- College of Public Health, University of South FloridaTampaUnited States
| | - Samuele Zilioli
- Department of Psychology, Wayne State UniversityDetroitUnited States
- Department of Family Medicine and Public Health Sciences, Wayne State UniversityDetroitUnited States
| | | | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
- Department of Obstetrics and Gynecology, Wayne State UniversityDetroitUnited States
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
- Department of Obstetrics and Gynecology, Wayne State UniversityDetroitUnited States
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8
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Ciccone EJ, Zivich PN, Lodge EK, Zhu D, Law E, Miller E, Taylor JL, Chung S, Xu J, Volfovsky A, Beatty C, Abernathy H, King E, Garrett HE, Markmann AJ, Rebuli ME, Sellers S, Weber DJ, Reyes R, Alavian N, Juliano JJ, Boyce RM, Aiello AE. SARS-CoV-2 Infection in Health Care Personnel and Their Household Contacts at a Tertiary Academic Medical Center: Protocol for a Longitudinal Cohort Study. JMIR Res Protoc 2021; 10:e25410. [PMID: 33769944 PMCID: PMC8092024 DOI: 10.2196/25410] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/06/2021] [Accepted: 03/17/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Health care personnel (HCP) are at high risk for exposure to the SARS-CoV-2 virus. While personal protective equipment (PPE) may mitigate this risk, prospective data collection on its use and other risk factors for seroconversion in this population is needed. OBJECTIVE The primary objectives of this study are to (1) determine the incidence of, and risk factors for, SARS-CoV-2 infection among HCP at a tertiary care medical center and (2) actively monitor PPE use, interactions between study participants via electronic sensors, secondary cases in households, and participant mental health and well-being. METHODS To achieve these objectives, we designed a prospective, observational study of SARS-CoV-2 infection among HCP and their household contacts at an academic tertiary care medical center in North Carolina, USA. Enrolled HCP completed frequent surveys on symptoms and work activities and provided serum and nasal samples for SARS-CoV-2 testing every 2 weeks. Additionally, interactions between participants and their movement within the clinical environment were captured with a smartphone app and Bluetooth sensors. Finally, a subset of participants' households was randomly selected every 2 weeks for further investigation, and enrolled households provided serum and nasal samples via at-home collection kits. RESULTS As of December 31, 2020, 211 HCP and 53 household participants have been enrolled. Recruitment and follow-up are ongoing and expected to continue through September 2021. CONCLUSIONS Much remains to be learned regarding the risk of SARS-CoV-2 infection among HCP and their household contacts. Through the use of a multifaceted prospective study design and a well-characterized cohort, we will collect critical information regarding SARS-CoV-2 transmission risks in the health care setting and its linkage to the community. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) DERR1-10.2196/25410.
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Affiliation(s)
- Emily J Ciccone
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Paul N Zivich
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, United States
- Carolina Population Center, University of North Carolina, Chapel Hill, NC, United States
| | - Evans K Lodge
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, United States
- Carolina Population Center, University of North Carolina, Chapel Hill, NC, United States
- School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Deanna Zhu
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, United States
- School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Elle Law
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, United States
| | - Elyse Miller
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, United States
| | - Jasmine L Taylor
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
| | - Suemin Chung
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
| | - Jason Xu
- Department of Statistical Science, Duke University, Durham, NC, United States
| | - Alexander Volfovsky
- Department of Statistical Science, Duke University, Durham, NC, United States
| | - Cherese Beatty
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, United States
| | - Haley Abernathy
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
| | - Elise King
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
| | - Haley E Garrett
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, United States
| | - Alena J Markmann
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Meghan E Rebuli
- Department of Pediatrics, Center for Environmental Medicine, Asthma and Lung Biology, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Subhashini Sellers
- Division of Pulmonary Diseases and Critical Care Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - David J Weber
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, United States
| | - Raquel Reyes
- Division of Hospital Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Naseem Alavian
- Division of Hospital Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Jonathan J Juliano
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, United States
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Ross M Boyce
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Allison E Aiello
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, United States
- Carolina Population Center, University of North Carolina, Chapel Hill, NC, United States
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9
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Wiarda JE, Boggiatto PM, Bayles DO, Waters WR, Thacker TC, Palmer MV. Severity of bovine tuberculosis is associated with innate immune-biased transcriptional signatures of whole blood in early weeks after experimental Mycobacterium bovis infection. PLoS One 2020; 15:e0239938. [PMID: 33166313 PMCID: PMC7652326 DOI: 10.1371/journal.pone.0239938] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 09/15/2020] [Indexed: 11/19/2022] Open
Abstract
Mycobacterium bovis, the causative agent of bovine tuberculosis, is a pathogen that impacts both animal and human health. Consequently, there is a need to improve understanding of disease dynamics, identification of infected animals, and characterization of the basis of immune protection. This study assessed the transcriptional changes occurring in cattle during the early weeks following a M. bovis infection. RNA-seq analysis of whole blood-cell transcriptomes revealed two distinct transcriptional clusters of infected cattle at both 4- and 10-weeks post-infection that correlated with disease severity. Cattle exhibiting more severe disease were transcriptionally divergent from uninfected animals. At 4-weeks post-infection, 25 genes had commonly increased expression in infected cattle compared to uninfected cattle regardless of disease severity. Ten weeks post-infection, differential gene expression was only observed when severely-affected cattle were compared to uninfected cattle. This indicates a transcriptional divergence based on clinical status following infection. In cattle with more severe disease, biological processes and cell type enrichment analyses revealed overrepresentation of innate immune-related processes and cell types in infected animals. Collectively, our findings demonstrate two distinct transcriptional profiles occur in cattle following M. bovis infection, which correlate to clinical status.
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Affiliation(s)
- Jayne E. Wiarda
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States of America
- Immunobiology Graduate Program, Iowa State University, Ames, IA, United States of America
- Oak Ridge Institute for Science and Education, Agricultural Research Service Participation Program, Oak Ridge, TN, United States of America
| | - Paola M. Boggiatto
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States of America
| | - Darrell O. Bayles
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States of America
| | - W. Ray Waters
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States of America
| | - Tyler C. Thacker
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States of America
| | - Mitchell V. Palmer
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States of America
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Gautam A, Donohue D, Hoke A, Miller SA, Srinivasan S, Sowe B, Detwiler L, Lynch J, Levangie M, Hammamieh R, Jett M. Investigating gene expression profiles of whole blood and peripheral blood mononuclear cells using multiple collection and processing methods. PLoS One 2019; 14:e0225137. [PMID: 31809517 PMCID: PMC6897427 DOI: 10.1371/journal.pone.0225137] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 10/29/2019] [Indexed: 01/07/2023] Open
Abstract
Gene expression profiling using blood samples is a valuable tool for biomarker discovery in clinical studies. Different whole blood RNA collection and processing methods are highly variable and might confound comparisons of results across studies. The main aim of the current study is to compare how blood storage, extraction methodologies, and the blood components themselves may influence gene expression profiling. Whole blood and peripheral blood mononuclear cell (PBMC) samples were collected in triplicate from five healthy donors. Whole blood was collected in RNAgard® and PAXgene® Blood RNA Tubes, as well as in collection tubes with anticoagulants such as dipotassium ethylenediaminetetraacetic acid (K2EDTA) and Acid Citrate Dextrose Solution A (ACD-A). PBMCs were separated using sodium citrate Cell Preparation Tubes (CPT™), FICOLL™, magnetic separation, and the LeukoLOCK™ methods. After blood collection, the LeukoLOCK™, K2EDTA and ACD-A blood tubes were shipped overnight using cold conditions and samples from the rest of the collection were immediately frozen with or without pre-processing. The RNA was isolated from whole blood and PBMCs using a total of 10 different experimental conditions employing several widely utilized RNA isolation methods. The RNA quality was assessed by RNA Integrity Number (RIN), which showed that all PBMC procedures had the highest RIN values when blood was stabilized in TRIzol® Reagent before RNA extraction. Initial data analysis showed that human blood stored and shipped at 4°C overnight performed equally well when checked for quality using RNA integrity number when compared to frozen stabilized blood. Comparisons within and across donor/method replicates showed signal-to-noise patterns which were not captured by RIN value alone. Pathway analysis using the top 1000 false discovery rate (FDR) corrected differentially expressed genes (DEGs) showed frozen vs. cold shipping conditions greatly impacted gene expression patterns in whole blood. However, the top 1000 FDR corrected DEGs from PBMCs preserved after frozen vs. cold shipping conditions (LeukoLOCK™ preserved in RNAlater®) revealed no significantly affected pathways. Our results provide novel insight into how RNA isolation, various storage, handling, and processing methodologies can influence RNA quality and apparent gene expression using blood samples. Careful consideration is necessary to avoid bias resulting from downstream processing. Better characterization of the effects of collection method idiosyncrasies will facilitate further research in understanding the effect of gene expression variability in human sample types.
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Affiliation(s)
- Aarti Gautam
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
| | - Duncan Donohue
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
- The Geneva Foundation, US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
| | - Allison Hoke
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
- Oak Ridge Institute for Science and Education, Fort Detrick, US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
| | - Stacy Ann Miller
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
- Oak Ridge Institute for Science and Education, Fort Detrick, US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
| | - Seshamalini Srinivasan
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
- The Geneva Foundation, US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
| | - Bintu Sowe
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
- Oak Ridge Institute for Science and Education, Fort Detrick, US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
| | - Leanne Detwiler
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
- The Geneva Foundation, US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
| | - Jesse Lynch
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
- Oak Ridge Institute for Science and Education, Fort Detrick, US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
| | - Michael Levangie
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
- The Geneva Foundation, US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
| | - Rasha Hammamieh
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
| | - Marti Jett
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
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Kim GS, Smith AK, Xue F, Michopoulos V, Lori A, Armstrong DL, Aiello AE, Koenen KC, Galea S, Wildman DE, Uddin M. Methylomic profiles reveal sex-specific differences in leukocyte composition associated with post-traumatic stress disorder. Brain Behav Immun 2019; 81:280-291. [PMID: 31228611 PMCID: PMC6754791 DOI: 10.1016/j.bbi.2019.06.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/18/2019] [Accepted: 06/18/2019] [Indexed: 02/07/2023] Open
Abstract
Post-traumatic stress disorder (PTSD) is a debilitating mental disorder precipitated by trauma exposure. However, only some persons exposed to trauma develop PTSD. There are sex differences in risk; twice as many women as men develop a lifetime diagnosis of PTSD. Methylomic profiles derived from peripheral blood are well-suited for investigating PTSD because DNA methylation (DNAm) encodes individual response to trauma and may play a key role in the immune dysregulation characteristic of PTSD pathophysiology. In the current study, we leveraged recent methodological advances to investigate sex-specific differences in DNAm-based leukocyte composition that are associated with lifetime PTSD. We estimated leukocyte composition on a combined methylation array dataset (483 participants, ∼450 k CpG sites) consisting of two civilian cohorts, the Detroit Neighborhood Health Study and Grady Trauma Project. Sex-stratified Mann-Whitney U test and two-way ANCOVA revealed that lifetime PTSD was associated with significantly higher monocyte proportions in males, but not in females (Holm-adjusted p-val < 0.05). No difference in monocyte proportions was observed between current and remitted PTSD cases in males, suggesting that this sex-specific difference may reflect a long-standing trait of lifetime history of PTSD, rather than current state of PTSD. Associations with lifetime PTSD or PTSD status were not observed in any other leukocyte subtype and our finding in monocytes was confirmed using cell estimates based on a different deconvolution algorithm, suggesting that our sex-specific findings are robust across cell estimation approaches. Overall, our main finding of elevated monocyte proportions in males, but not in females with lifetime history of PTSD provides evidence for a sex-specific difference in peripheral blood leukocyte composition that is detectable in methylomic profiles and that may reflect long-standing changes associated with PTSD diagnosis.
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Affiliation(s)
- Grace S Kim
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Medical Scholars Program, University of Illinois College of Medicine, Urbana, IL, USA
| | - Alicia K Smith
- Department of Psychiatry & Behavioral Sciences, Emory University, Atlanta, GA, USA; Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, USA
| | - Fei Xue
- Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Vasiliki Michopoulos
- Department of Psychiatry & Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Adriana Lori
- Department of Psychiatry & Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Don L Armstrong
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Allison E Aiello
- Gillings School of Global Public Health, University of North Carolina - Chapel Hill, Chapel Hill, NC, USA
| | - Karestan C Koenen
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Sandro Galea
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Derek E Wildman
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Monica Uddin
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
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12
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Unequivocal Biomarker for Parkinson’s Disease: A Hunt that Remains a Pester. Neurotox Res 2019; 36:627-644. [DOI: 10.1007/s12640-019-00080-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/17/2019] [Accepted: 06/19/2019] [Indexed: 12/14/2022]
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PTSD is associated with an increase in aged T cell phenotypes in adults living in Detroit. Psychoneuroendocrinology 2016; 67:133-41. [PMID: 26894484 PMCID: PMC4826331 DOI: 10.1016/j.psyneuen.2016.01.024] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 01/27/2016] [Accepted: 01/27/2016] [Indexed: 01/25/2023]
Abstract
BACKGROUND Psychosocial stress is thought to play a key role in the acceleration of immunological aging. This study investigated the relationship between lifetime and past-year history of post-traumatic stress disorder (PTSD) and the distribution of T cell phenotypes thought to be characteristic of immunological aging. METHODS Data were from 85 individuals who participated in the community-based Detroit Neighborhood Health Study. Immune markers assessed included the CD4:CD8 ratio, the ratio of late-differentiated effector (CCR7-CD45RA+CD27-CD28-) to naïve (CCR7+CD45RA+CD27+CD28+) T cells, the percentage of KLRG1-expressing cells, and the percentage of CD57-expressing cells. RESULTS In models adjusted for age, gender, race/ethnicity, education, smoking status, and medication use, we found that past-year PTSD was associated with statistically significant differences in the CD8+ T cell population, including a higher ratio of late-differentiated effector to naïve T cells, a higher percentage of KLRG1+ cells, and a higher percentage of CD57+ cells. The percentage of CD57+ cells in the CD4 subset was also significantly higher and the CD4:CD8 ratio significantly lower among individuals who had experienced past-year PTSD. Lifetime PTSD was also associated with differences in several parameters of immune aging. CONCLUSIONS PTSD is associated with an aged immune phenotype and should be evaluated as a potential catalyzer of accelerated immunological aging in future studies.
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