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Lewis SA, Cinco IR, Doratt BM, Blanton MB, Hoagland C, Newman N, Davies M, Grant KA, Messaoudi I. Chronic alcohol consumption dysregulates innate immune response to SARS-CoV-2 in the lung. EBioMedicine 2023; 97:104812. [PMID: 37793211 PMCID: PMC10562860 DOI: 10.1016/j.ebiom.2023.104812] [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: 05/17/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Alcohol consumption is widespread with over half of the individuals over 18 years of age in the U.S. reporting alcohol use in the last 30 days. Moreover, 9 million Americans engaged in binge or chronic heavy drinking (CHD) in 2019. CHD negatively impacts pathogen clearance and tissue repair, including in the respiratory tract, thereby increasing susceptibility to infection. Although, it has been hypothesized that chronic alcohol consumption negatively impacts COVID-19 outcomes; the interplay between chronic alcohol use and SARS-CoV-2 infection outcomes has yet to be elucidated. METHODS In this study we employed luminex, scRNA sequencing, and flow cytometry to investigate the impact of chronic alcohol consumption on SARS-CoV-2 anti-viral responses in bronchoalveolar lavage cell samples from humans with alcohol use disorder and rhesus macaques that engaged in chronic drinking. FINDINGS Our data show that in both humans (n = 6) and macaques (n = 11), the induction of key antiviral cytokines and growth factors was decreased with chronic ethanol consumption. Moreover, in macaques fewer differentially expressed genes mapped to Gene Ontology terms associated with antiviral immunity following 6 month of ethanol consumption while TLR signaling pathways were upregulated. INTERPRETATION These data are indicative of aberrant inflammation and reduced antiviral responses in the lung with chronic alcohol drinking. FUNDING This study was supported by NIH 1R01AA028735-04 (Messaoudi), U01AA013510-20 (Grant), R24AA019431-14 (Grant), R24AA019661 (Burnham), P-51OD011092 (ONPRC core grant support). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.
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Affiliation(s)
- Sloan A Lewis
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine, USA
| | - Isaac R Cinco
- Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, USA
| | - Brianna M Doratt
- Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, USA
| | - Madison B Blanton
- Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, USA; Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, USA
| | - Cherise Hoagland
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, USA
| | - Natali Newman
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, USA
| | - Michael Davies
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, USA
| | - Kathleen A Grant
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, USA
| | - Ilhem Messaoudi
- Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, USA.
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Shin SS, Bender M, Malherbe DC, Vasquez H, Doratt BM, Messaoudi I. SARS-Cov-2 Infection and Seroconversion Rates in Healthcare Providers Prior to COVID-19 Vaccine Rollout. Biol Res Nurs 2023; 25:505-515. [PMID: 36869766 PMCID: PMC9988593 DOI: 10.1177/10998004231161632] [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: 03/05/2023]
Abstract
OBJECTIVE A 6-month longitudinal surveillance study of asymptomatic healthcare providers (HCP) was carried out at a large urban academic medical center in the United States to assess whether their job occupation with higher exposure risks to SARS-CoV-2 would equate with higher risk of contracting COVID-19 at the beginning of the pandemic before COVID-19 vaccines were available. METHODS A longitudinal cohort study design was used to collect and analyze immunological and virological monitoring data and self-report survey assessments of personal protective equipment (PPE) availability, adherence to infection control guidelines, and time spent on COVID-19 wards. RESULTS Among 289 eligible participants, SARS-CoV-2 exposure risk was high with 48-69% participants working in COVID-19 units and more than 30% of them caring for COVID-19 patients. However, the seroconversion rate was low with only 2.1% of participants developing humoral or cellular immunity against SARS-CoV-2. CONCLUSION Our study findings suggest that, for this HCP cohort working at a large urban academic medical center, a low incidence of SARS-CoV-2 infection could be maintained under conditions of strict infection prevention protocols and reliable PPE availability.
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Affiliation(s)
- Sanghyuk S. Shin
- Sue & Bill Gross School of Nursing, University of California, Irvine, CA, USA
| | - Miriam Bender
- Sue & Bill Gross School of Nursing, University of California, Irvine, CA, USA
| | - Delphine C. Malherbe
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Hannah Vasquez
- Sue & Bill Gross School of Nursing, University of California, Irvine, CA, USA
| | - Brianna M. Doratt
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Ilhem Messaoudi
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
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Doratt BM, Sureshchandra S, True H, Rincon M, Marshall NE, Messaoudi I. Mild/asymptomatic COVID-19 in unvaccinated pregnant mothers impairs neonatal immune responses. JCI Insight 2023; 8:e172658. [PMID: 37698937 PMCID: PMC10629812 DOI: 10.1172/jci.insight.172658] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 05/30/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023] Open
Abstract
Maternal SARS-CoV-2 infection triggers placental inflammation and alters cord blood immune cell composition. However, most studies focus on outcomes of severe maternal infection. Therefore, we analyzed cord blood and chorionic villi from newborns of unvaccinated mothers who experienced mild/asymptomatic SARS-CoV-2 infection during pregnancy. We investigated immune cell rewiring using flow cytometry, single-cell RNA sequencing, and functional readouts using ex vivo stimulation with TLR agonists and pathogens. Maternal infection was associated with increased frequency of memory T and B cells and nonclassical monocytes in cord blood. Ex vivo T and B cell responses to stimulation were attenuated, suggesting a tolerogenic state. Maladaptive responses were also observed in cord blood monocytes, where antiviral responses were dampened but responses to bacterial TLRs were increased. Maternal infection was also associated with expansion and activation of placental Hofbauer cells, secreting elevated levels of myeloid cell-recruiting chemokines. Moreover, we reported increased activation of maternally derived monocytes/macrophages in the fetal placenta that were transcriptionally primed for antiviral responses. Our data indicate that even in the absence of vertical transmission or symptoms in the neonate, mild/asymptomatic maternal COVID-19 altered the transcriptional and functional state in fetal immune cells in circulation and in the placenta.
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Affiliation(s)
- Brianna M. Doratt
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, Kentucky, USA
| | - Suhas Sureshchandra
- Department of Physiology and Biophysics, School of Medicine, and
- Institute for Immunology, University of California, Irvine, California, USA
| | - Heather True
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, Kentucky, USA
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky, USA
| | - Monica Rincon
- Maternal-Fetal Medicine, Oregon Health and Science University, Portland, Oregon, USA
| | - Nicole E. Marshall
- Maternal-Fetal Medicine, Oregon Health and Science University, Portland, Oregon, USA
| | - Ilhem Messaoudi
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, Kentucky, USA
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Lewis SA, Doratt BM, Qiao Q, Blanton M, Grant KA, Messaoudi I. Integrated single cell analysis shows chronic alcohol drinking disrupts monocyte differentiation in the bone marrow. Stem Cell Reports 2023; 18:1884-1897. [PMID: 37657446 PMCID: PMC10545484 DOI: 10.1016/j.stemcr.2023.08.001] [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: 05/02/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 09/03/2023] Open
Abstract
Chronic heavy alcohol drinking (CHD) rewires monocytes and macrophages toward heightened inflammatory states with compromised antimicrobial defenses that persist after 1-month abstinence. To determine whether these changes are mediated through alterations in the bone marrow niche, we profiled monocytes and hematopoietic stem cell progenitors (HSCPs) from CHD rhesus macaques using a combination of functional assays and single cell genomics. CHD resulted in transcriptional profiles consistent with increased activation and inflammation within bone marrow resident monocytes and macrophages. Furthermore, CHD resulted in transcriptional signatures associated with increased oxidative and cellular stress in HSCP. Differentiation of HSCP in vitro revealed skewing toward monocytes expressing "neutrophil-like" markers with greater inflammatory responses to bacterial agonists. Further analyses of HSCPs showed broad epigenetic changes that were in line with exacerbated inflammatory responses within monocytes and their progenitors. In summary, CHD alters HSCPs in the bone marrow leading to the production of monocytes poised to generate dysregulated hyper-inflammatory responses.
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Affiliation(s)
- Sloan A Lewis
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Brianna M Doratt
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Qi Qiao
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Madison Blanton
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Kathleen A Grant
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY 40536, USA.
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Marshall NE, Blanton MB, Doratt BM, Malherbe DC, Rincon M, Messaoudi I. Monoclonal Antibody Therapy of Breastfeeding Patient Infected with SARS-CoV-2: A Case Report. Breastfeed Med 2023; 18:626-630. [PMID: 37615569 PMCID: PMC10460680 DOI: 10.1089/bfm.2023.0102] [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] [Indexed: 08/25/2023]
Abstract
Introduction: Although safety data demonstrated the efficacy and effectiveness of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination for all individuals over 6 months of age, including pregnant and breastfeeding individuals, optimal treatment courses for symptomatic pregnant and lactating individuals infected with SARS-CoV-2 remain to be defined. Case Description: A coronavirus disease 2019 (COVID-19)-vaccinated breastfeeding woman received anti-SARS-CoV-2 monoclonal antibody treatment casirivimab-imdevimab 5 days after diagnosis of a symptomatic breakthrough SARS-CoV-2 infection. Results and Conclusions: The patient did not present with obvious defects in innate or adaptive cellular subsets, but compared with controls had minimal maternal antibody response to recommended pregnancy vaccinations including SARS-CoV-2 and tetanus, diphtheria, pertussis (TDaP). The outcome of the monoclonal antibody infusion treatment was favorable as it transiently increased SARS-CoV-2 antibody titers in plasma and human milk compartments.
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Affiliation(s)
- Nicole E. Marshall
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, Oregon, USA
| | - Madison B. Blanton
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, Kentucky, USA
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky, USA
| | - Brianna M. Doratt
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Delphine C. Malherbe
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Monica Rincon
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, Oregon, USA
| | - Ilhem Messaoudi
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, Kentucky, USA
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Sureshchandra S, Doratt BM, True H, Mendoza N, Rincon M, Marshall NE, Messaoudi I. Multimodal profiling of term human decidua demonstrates immune adaptations with pregravid obesity. Cell Rep 2023; 42:112769. [PMID: 37432849 PMCID: PMC10528932 DOI: 10.1016/j.celrep.2023.112769] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 11/08/2022] [Revised: 03/24/2023] [Accepted: 06/23/2023] [Indexed: 07/13/2023] Open
Abstract
Leukocyte diversity of the first-trimester maternal-fetal interface has been extensively described; however, the immunological landscape of the term decidua remains poorly understood. We therefore profiled human leukocytes from term decidua collected via scheduled cesarean delivery. Relative to the first trimester, our analyses show a shift from NK cells and macrophages to T cells and enhanced immune activation. Although circulating and decidual T cells are phenotypically distinct, they demonstrate significant clonotype sharing. We also report significant diversity within decidual macrophages, the frequency of which positively correlates with pregravid maternal body mass index. Interestingly, the ability of decidual macrophages to respond to bacterial ligands is reduced with pregravid obesity, suggestive of skewing toward immunoregulation as a possible mechanism to safeguard the fetus against excessive maternal inflammation. These findings are a resource for future studies investigating pathological conditions that compromise fetal health and reproductive success.
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Affiliation(s)
- Suhas Sureshchandra
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA; Institute for Immunology, University of California, Irvine, Irvine, CA 92697, USA
| | - Brianna M Doratt
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, KY 40536, USA
| | - Heather True
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Norma Mendoza
- Institute for Immunology, University of California, Irvine, Irvine, CA 92697, USA
| | - Monica Rincon
- Maternal-Fetal Medicine, Oregon Health and Science University, Portland, OR 97239, USA
| | - Nicole E Marshall
- Maternal-Fetal Medicine, Oregon Health and Science University, Portland, OR 97239, USA
| | - Ilhem Messaoudi
- Institute for Immunology, University of California, Irvine, Irvine, CA 92697, USA; Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, KY 40536, USA.
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Fletcher P, O'Donnell KL, Doratt BM, Malherbe DC, Clancy CS, Rhoderick JF, Feldmann F, Hanley PW, Ksiazek TG, Geisbert TW, Messaoudi I, Marzi A. Single-dose VSV-based vaccine protects cynomolgus macaques from disease after Taï Forest virus infection. Emerg Microbes Infect 2023:2239950. [PMID: 37470396 PMCID: PMC10392270 DOI: 10.1080/22221751.2023.2239950] [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: 07/21/2023]
Abstract
Taï Forest virus (TAFV) is a lesser-known ebolavirus that causes lethal infections in chimpanzees and is responsible for a single human case. Limited research has been done on this human pathogen; however, with the recent emergence of filoviruses in West Africa, further investigation and countermeasure development against this virus is warranted.We developed a vesicular stomatitis virus (VSV)-based vaccine expressing the TAFV glycoprotein as the viral antigen and assessed it for protective efficacy in nonhuman primates (NHPs). Following a single high-dose vaccination, NHPs developed antigen-specific binding and neutralizing antibodies as well as modest T cell responses. Importantly, all vaccinated NHPs were uniformly protected from disease after lethal TAFV challenge while the naïve control group succumbed to the disease. Histopathologic lesions consistent with filovirus disease were present in control NHPs but were not observed in vaccinated NHPs. Transcriptional analysis of whole blood samples obtained after vaccination and challenge was performed to gain insight into molecular underpinnings conferring protection. Differentially expressed genes (DEG) detected 7 days post-vaccination were enriched to processes associated with innate immunity and antiviral responses. Only a small number of DEG was detected in vaccinated NHPs post-challenge while over 1,000 DEG were detected in control NHPs at end-stage disease which mapped to gene ontology terms indicative of defense responses and inflammation. Taken together, this data demonstrates the effective single-dose protection of the VSV-TAFV vaccine, and its potential for use in outbreaks.
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Affiliation(s)
- Paige Fletcher
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Kyle L O'Donnell
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Brianna M Doratt
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Delphine C Malherbe
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Chad S Clancy
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Joseph F Rhoderick
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Friederike Feldmann
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Patrick W Hanley
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Thomas G Ksiazek
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Thomas W Geisbert
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Ilhem Messaoudi
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Andrea Marzi
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
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Doratt BM, Sureshchandra S, True H, Rincon M, Marshall N, Messaoudi I. Mild/Asymptomatic Maternal SARS-CoV-2 Infection Leads to Immune Paralysis in Fetal Circulation and Immune Dysregulation in Fetal-Placental Tissues. bioRxiv 2023:2023.05.10.540233. [PMID: 37214938 PMCID: PMC10197637 DOI: 10.1101/2023.05.10.540233] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Few studies have addressed the impact of maternal mild/asymptomatic SARS-CoV-2 infection on the developing neonatal immune system. In this study, we analyzed umbilical cord blood and placental chorionic villi from newborns of unvaccinated mothers with mild/asymptomatic SARSCoV-2 infection during pregnancy using flow cytometry, single-cell transcriptomics, and functional assays. Despite the lack of vertical transmission, levels of inflammatory mediators were altered in cord blood. Maternal infection was also associated with increased memory T, B cells, and non-classical monocytes as well as increased activation. However, ex vivo responses to stimulation were attenuated. Finally, within the placental villi, we report an expansion of fetal Hofbauer cells and infiltrating maternal macrophages and rewiring towards a heightened inflammatory state. In contrast to cord blood monocytes, placental myeloid cells were primed for heightened antiviral responses. Taken together, this study highlights dysregulated fetal immune cell responses in response to mild maternal SARS-CoV-2 infection during pregnancy.
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Affiliation(s)
- Brianna M. Doratt
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington KY 40536
| | - Suhas Sureshchandra
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine CA 92697
- Institute for Immunology, University of California, Irvine CA 92697
| | - Heather True
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington KY 40536
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington KY 40536
| | - Monica Rincon
- Maternal-Fetal Medicine, Oregon Health and Science University, Portland OR 97239
| | - Nicole Marshall
- Maternal-Fetal Medicine, Oregon Health and Science University, Portland OR 97239
| | - Ilhem Messaoudi
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington KY 40536
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Lewis SA, Cinco IR, Doratt BM, Blanton MB, Hoagland C, Davies M, Grant KA, Messaoudi I. Chronic alcohol consumption dysregulates innate immune response to SARS-CoV-2 in the lung. bioRxiv 2023:2023.05.02.539139. [PMID: 37205543 PMCID: PMC10187161 DOI: 10.1101/2023.05.02.539139] [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] [Indexed: 05/21/2023]
Abstract
Alcohol consumption is widespread with over half of the individuals over 18 years of age in the U.S. reporting alcohol use in the last 30 days. Moreover, 9 million Americans engaged in binge or chronic heavy drinking (CHD) in 2019. CHD negatively impacts pathogen clearance and tissue repair, including in the respiratory tract, thereby increasing susceptibility to infection. Although, it has been hypothesized that chronic alcohol consumption negatively impacts COVID-19 outcomes; the interplay between chronic alcohol use and SARS-CoV-2 infection outcomes has yet to be elucidated. Therefore, in this study we investigated the impact of chronic alcohol consumption on SARS-CoV-2 anti-viral responses in bronchoalveolar lavage cell samples from humans with alcohol use disorder and rhesus macaques that engaged in chronic drinking. Our data show that in both humans and macaques, the induction of key antiviral cytokines and growth factors was decreased with chronic ethanol consumption. Moreover, in macaques fewer differentially expressed genes mapped to Gene Ontology terms associated with antiviral immunity following 6 month of ethanol consumption while TLR signaling pathways were upregulated. These data are indicative of aberrant inflammation and reduced antiviral responses in the lung with chronic alcohol drinking.
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Affiliation(s)
- Sloan A. Lewis
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine
| | - Isaac R. Cinco
- Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky
| | - Brianna M. Doratt
- Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky
| | - Madison B. Blanton
- Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky
- Pharmaceutical Sciences, College of Pharmacy, University of Kentucky
| | - Cherise Hoagland
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University
| | - Michael Davies
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University
| | - Kathleen A. Grant
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University
| | - Ilhem Messaoudi
- Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky
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Lewis SA, Doratt BM, Qiao Q, Blanton MB, Grant KA, Messaoudi I. Integrated single cell analysis shows chronic alcohol drinking disrupts monocyte differentiation in the bone marrow niche. bioRxiv 2023:2023.03.29.534727. [PMID: 37034734 PMCID: PMC10081177 DOI: 10.1101/2023.03.29.534727] [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] [Indexed: 05/04/2023]
Abstract
Chronic alcohol drinking rewires circulating monocytes and tissue-resident macrophages towards heightened inflammatory states with compromised anti-microbial defenses. As these effects remain consistent in short-lived monocytes after a 1-month abstinence period it is unclear whether these changes are restricted to the periphery or mediated through alterations in the progenitor niche. To test this hypothesis, we profiled monocytes/macrophages and hematopoietic stem cell progenitors (HSCP) of the bone marrow compartment from rhesus macaques after 12 months of ethanol consumption using a combination of functional assays and single cell genomics. Bone marrow-resident monocytes/macrophages from ethanol-consuming animals exhibited heightened inflammation. Differentiation of HSCP in vitro revealed skewing towards monocytes expressing neutrophil-like markers with heightened inflammatory responses to bacterial agonists. Single cell transcriptional analysis of HSCPs showed reduced proliferation but increased inflammatory markers in mature myeloid progenitors. We observed transcriptional signatures associated with increased oxidative and cellular stress as well as oxidative phosphorylation in immature and mature myeloid progenitors. Single cell analysis of the chromatin landscape showed altered drivers of differentiation in monocytes and progenitors. Collectively, these data indicate that chronic ethanol drinking results in remodeling of the transcriptional and epigenetic landscapes of the bone marrow compartment leading to altered functions in the periphery.
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Affiliation(s)
- Sloan A. Lewis
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
| | - Brianna M Doratt
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY 40536
| | - Qi Qiao
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY 40536
| | - Madison B. Blanton
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY 40536
| | - Kathleen A. Grant
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY 40536
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Marshall NE, Blanton MB, Doratt BM, Malherbe DC, Rincon M, True H, McDonald T, Beauregard C, Adatorwovor R, Messaoudi I. SARS-CoV-2 vaccine booster elicits robust prolonged maternal antibody responses and passive transfer to the offspring via the placenta and breastmilk. Am J Obstet Gynecol MFM 2023; 5:100830. [PMID: 36462615 PMCID: PMC9710099 DOI: 10.1016/j.ajogmf.2022.100830] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022]
Affiliation(s)
- Nicole E Marshall
- Department of Obstetrics and Gynecology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239
| | - Madison B Blanton
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY
| | - Brianna M Doratt
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY
| | - Delphine C Malherbe
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY
| | - Monica Rincon
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR
| | - Heather True
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY
| | - Taylor McDonald
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY
| | - Caroline Beauregard
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY
| | | | - Ilhem Messaoudi
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, 760 Press Ave., Lexington, KY 40536.
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12
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Sureshchandra S, Doratt BM, Mendza N, Varlamov O, Rincon M, Marshall NE, Messaoudi I. Maternal obesity blunts antimicrobial responses in fetal monocytes. eLife 2023; 12:81320. [PMID: 36645353 PMCID: PMC9894585 DOI: 10.7554/elife.81320] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 01/15/2023] [Indexed: 01/17/2023] Open
Abstract
Maternal pre-pregnancy (pregravid) obesity is associated with adverse outcomes for both mother and offspring. Amongst the complications for the offspring is increased susceptibility and severity of neonatal infections necessitating admission to the intensive care unit, notably bacterial sepsis and enterocolitis. Previous studies have reported aberrant responses to LPS and polyclonal stimulation by umbilical cord blood monocytes that were mediated by alterations in the epigenome. In this study, we show that pregravid obesity dysregulates umbilical cord blood monocyte responses to bacterial and viral pathogens. Specifically, interferon-stimulated gene expression and inflammatory responses to respiratory syncytial virus (RSV) and E. coli were significantly dampened, respectively . Although upstream signaling events were comparable, translocation of the key transcription factor NF-κB and chromatin accessibility at pro-inflammatory gene promoters following TLR stimulation was significantly attenuated. Using a rhesus macaque model of western style diet-induced obesity, we further demonstrate that this defect is detected in fetal peripheral monocytes and tissue-resident macrophages during gestation. Collectively, these data indicate that maternal obesity alters metabolic, signaling, and epigenetic profiles of fetal monocytes leading to a state of immune paralysis during late gestation and at birth.
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Affiliation(s)
- Suhas Sureshchandra
- Institute for Immunology, University of California, IrvineIrvineUnited States
- Department of Molecular Biology and Biochemistry, University of California, IrvineIrvineUnited States
| | - Brianna M Doratt
- Department of Molecular Biology and Biochemistry, University of California, IrvineIrvineUnited States
- Department of Microbiology, Immunology, and Molecular Genetics, University of KentuckyLexingtonUnited States
| | - Norma Mendza
- Department of Molecular Biology and Biochemistry, University of California, IrvineIrvineUnited States
| | - Oleg Varlamov
- Division of Cardiometabolic Health, Oregon National Primate Research Center, Oregon Health & Science UniversityBeavertonUnited States
| | - Monica Rincon
- Maternal-Fetal Medicine, Oregon Health & Science UniversityPortlandUnited States
| | - Nicole E Marshall
- Maternal-Fetal Medicine, Oregon Health & Science UniversityPortlandUnited States
| | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry, University of California, IrvineIrvineUnited States
- Maternal-Fetal Medicine, Oregon Health & Science UniversityPortlandUnited States
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13
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Nyamathi A, Shin SS, Doratt BM, Jones-Patten A, Salem B, Gelberg L, Lee D, Garfin D, Yadav K, Chang AH, White K, Arce N, Messaoudi I. Correlates of SARS-CoV-2 anti-RBD IgG antibody titers among persons experiencing homelessness in Los Angeles. Public Health Nurs 2023; 40:417-427. [PMID: 36633567 DOI: 10.1111/phn.13170] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 01/13/2023]
Abstract
OBJECTIVES People experiencing homelessness (PEH) have been especially impacted by the COVID-19 pandemic, likely due to increased vulnerabilities stemming from chronic diseases, substance use, and mental health conditions. DESIGN A case-control study to assess the presence of antibodies against SARS-CoV-2 among PEH and associations with key variables. SAMPLE A convenience sample of 97 PEH in Skid Row, Los Angeles. MEASUREMENTS A structured questionnaire assessing socio-demographic, mental health, drug and alcohol use, health care access, pandemic stress, and other COVID-19-specific questions. RESULTS We found high anti-receptor binding domain (RBD) IgG titers among five of 15 PEH who reported no prior COVID-19 diagnosis or being vaccinated, suggesting undiagnosed and/or asymptomatic COVID-19. While anti-RBD IgG titers across vaccination categories were not statistically significant (p = .069), participants vaccinated with Janssen had the lowest mean anti-RBD IgG titers. In multivariable analysis, we found negative associations between level of SARS-CoV-2 antibody titers with the Janssen vaccine and depression; thus, a need for integrated care for PEH with depression and COVID-19. CONCLUSIONS Further research is warranted to confirm the immune response, initial and over time, to SARS-CoV-2 infection and to COVID-19 vaccinations, particularly among PEH whose immune systems may be impacted by multiple health conditions.
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Affiliation(s)
- Adeline Nyamathi
- Sue & Bill Gross School of Nursing, University of California, Irvine, California
| | - Sanghyuk S Shin
- Sue & Bill Gross School of Nursing, University of California, Irvine, California
| | - Brianna M Doratt
- Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, Kentucky
| | | | - Benissa Salem
- School of Nursing, University of California, Los Angeles, California
| | - Lillian Gelberg
- David Geffen School of Medicine, University of California, Los Angeles, California
| | - Darlene Lee
- Susan Samueli Integrative Health Institute, University of California Irvine, Irvine, California
| | - Dana Garfin
- Sue & Bill Gross School of Nursing, University of California, Irvine, California
| | - Kartik Yadav
- Sue & Bill Gross School of Nursing, University of California, Irvine, California
| | - Alicia H Chang
- Los Angeles County Department of Public Health, Community & Field Services, Los Angeles, California
| | - Kathryn White
- Los Angeles Christian Health Center, Health Center, Los Angeles, California
| | - Nicholas Arce
- School of Social Ecology, University of California, Irvine, California
| | - Ilhem Messaoudi
- Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, Kentucky
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14
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Doratt BM, Vance E, Malherbe DC, Ebbert MT, Messaoudi I. Transcriptional response to VZV infection is modulated by RNA polymerase III in lung epithelial cell lines. Front Cell Infect Microbiol 2022; 12:943587. [PMID: 35959363 PMCID: PMC9359802 DOI: 10.3389/fcimb.2022.943587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 05/13/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
Ancestral RNA polymerase III (Pol III) is a multi-subunit polymerase responsible for transcription of short non-coding RNA, such as double-stranded short interspersed nuclear elements (SINEs). Although SINE ncRNAs are generally transcriptionally repressed, they can be induced in response to viral infections and can stimulate immune signaling pathways. Indeed, mutations in RNA Pol III have been associated with poor antiviral interferon response following infection with varicella zoster virus (VZV). In this study, we probed the role of Pol III transcripts in the detection and initial immune response to VZV by characterizing the transcriptional response following VZV infection of wild type A549 lung epithelial cells as well as A549 cells lacking specific RNA sensors MAVS and TLR3, or interferon-stimulated genes RNase L and PKR in presence or absence of functional RNA Pol III. Multiple components of the antiviral sensing and interferon signaling pathways were involved in restricting VZV replication in lung epithelial cells thus suggesting an innate defense system with built-in redundancy. In addition, RNA Pol III silencing altered the antiviral transcriptional program indicating that it plays an essential role in the sensing of VZV infection.
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Affiliation(s)
- Brianna M. Doratt
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, United States
| | - Elizabeth Vance
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, United States
- Department of Internal Medicine, Division of Biomedical Informatics, University of Kentucky, Lexington, KY, United States
- Department of Neuroscience, University of Kentucky, Lexington, KY, United States
| | - Delphine C. Malherbe
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, United States
| | - Mark T.W. Ebbert
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, United States
- Department of Internal Medicine, Division of Biomedical Informatics, University of Kentucky, Lexington, KY, United States
- Department of Neuroscience, University of Kentucky, Lexington, KY, United States
| | - Ilhem Messaoudi
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, United States
- *Correspondence: Ilhem Messaoudi,
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15
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Lewis SA, Doratt BM, Sureshchandra S, Jankeel A, Newman N, Shen W, Grant KA, Messaoudi I. Ethanol Consumption Induces Nonspecific Inflammation and Functional Defects in Alveolar Macrophages. Am J Respir Cell Mol Biol 2022; 67:112-124. [PMID: 35380939 PMCID: PMC9273227 DOI: 10.1165/rcmb.2021-0346oc] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 04/05/2022] [Indexed: 11/24/2022] Open
Abstract
Chronic alcohol drinking is associated with increased susceptibility to viral and bacterial respiratory pathogens. In this study, we use a rhesus macaque model of voluntary ethanol self-administration to study the effects of long-term alcohol drinking on the immunological landscape of the lung. We report a heightened inflammatory state in alveolar macrophages (AMs) obtained from ethanol (EtOH)-drinking animals that is accompanied by increased chromatin accessibility in intergenic regions that regulate inflammatory genes and contain binding motifs for transcription factors AP-1, IRF8, and NFKB p-65. In line with these transcriptional and epigenetic changes at the basal state, AMs from EtOH-drinking animals generate elevated inflammatory mediator responses to lipopolysaccharides and respiratory syncytial virus. However, the transcriptional analysis revealed an inefficient induction of interferon-stimulated genes with EtOH in response to the respiratory syncytial virus, suggesting disruption of antimicrobial defenses. Correspondingly, AMs from EtOH-drinking animals exhibited transcriptional shifts indicative of increased oxidative stress and oxidative phosphorylation, which was coupled with higher cytosolic reactive oxygen species and mitochondrial potential. This heightened oxidative stress state was accompanied by decreased ability to phagocytose bacteria. Bulk RNA and assay for transposase-accessible chromatin sequencing data further revealed reduced expression and chromatin accessibility of loci associated with tissue repair and maintenance with chronic EtOH drinking. Similarly, analysis of single-cell RNA sequencing data revealed shifts in cell states from tissue maintenance to inflammatory responses with EtOH. Collectively, these data provide novel insight into mechanisms by which chronic EtOH drinking increases susceptibility to infection in patients with alcohol use disorders.
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Affiliation(s)
- Sloan A. Lewis
- Department of Molecular Biology and Biochemistry
- Institute for Immunology, and
| | - Brianna M. Doratt
- Department of Molecular Biology and Biochemistry
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, Kentucky; and
| | - Suhas Sureshchandra
- Department of Molecular Biology and Biochemistry
- Institute for Immunology, and
| | | | - Natali Newman
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon
| | - Weining Shen
- Department of Statistics, University of California, Irvine, Irvine, California
| | - Kathleen A. Grant
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon
| | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry
- Institute for Immunology, and
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, Kentucky; and
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16
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Sureshchandra S, Zulu MZ, Doratt BM, Jankeel A, Tifrea D, Edwards R, Rincon M, Marshall NE, Messaoudi I. Single cell RNA sequencing reveals immunological rewiring at the maternal-fetal interface following asymptomatic/mild SARS-CoV-2 infection. Cell Rep 2022; 39:110938. [PMID: 35662411 PMCID: PMC9130636 DOI: 10.1016/j.celrep.2022.110938] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 03/21/2022] [Accepted: 05/18/2022] [Indexed: 11/06/2022] Open
Abstract
While severe coronavirus 2019 (COVID-19) is associated with immune activation at the maternal-fetal interface, responses to asymptomatic/mild severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection during pregnancy remain unknown. Here, we assess immunological adaptations in blood and term decidua in response to asymptomatic/mild disease in pregnant women. We report attenuated antigen presentation and type I interferon (IFN) signaling pathways, loss of tissue-resident decidual macrophages, and upregulated cytokine/chemokine signaling in monocyte-derived decidual macrophages. Furthermore, we describe increased frequencies of activated tissue-resident T cells and decreased abundance of regulatory T cells with infection while frequencies of cytotoxic CD4/CD8 T cells are increased in the blood. In contrast to decidual macrophages, type I IFN signaling is higher in decidual T cells. Finally, infection leads to a narrowing of T cell receptor diversity in both blood and decidua. Collectively, these observations indicate that asymptomatic/mild COVID-19 during pregnancy results in remodeling of the immunological landscape of the maternal-fetal interface, with a potential for long-term adverse outcomes for the offspring.
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17
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Sureshchandra S, Lewis SA, Doratt BM, Jankeel A, Coimbra Ibraim I, Messaoudi I. Single-cell profiling of T and B cell repertoires following SARS-CoV-2 mRNA vaccine. JCI Insight 2021; 6:e153201. [PMID: 34935643 PMCID: PMC8783687 DOI: 10.1172/jci.insight.153201] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [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: 07/14/2021] [Accepted: 10/29/2021] [Indexed: 12/13/2022] Open
Abstract
mRNA vaccines for SARS-CoV-2 have shown exceptional clinical efficacy, providing robust protection against severe disease. However, our understanding of transcriptional and repertoire changes following full vaccination remains incomplete. We used scRNA-Seq and functional assays to compare humoral and cellular responses to 2 doses of mRNA vaccine with responses observed in convalescent individuals with asymptomatic disease. Our analyses revealed enrichment of spike-specific B cells, activated CD4+ T cells, and robust antigen-specific polyfunctional CD4+ T cell responses following vaccination. On the other hand, although clonally expanded CD8+ T cells were observed following both vaccination and natural infection, CD8+ T cell responses were relatively weak and variable. In addition, TCR gene usage was variable, reflecting the diversity of repertoires and MHC polymorphism in the human population. Natural infection induced expansion of CD8+ T cell clones that occupy distinct clusters compared to those induced by vaccination and likely recognize a broader set of viral antigens of viral epitopes presented by the virus not seen in the mRNA vaccine. Our study highlights a coordinated adaptive immune response in which early CD4+ T cell responses facilitate the development of the B cell response and substantial expansion of effector CD8+ T cells, together capable of contributing to future recall responses.
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Affiliation(s)
- Suhas Sureshchandra
- Department of Molecular Biology and Biochemistry
- Institute for Immunology, and
| | - Sloan A. Lewis
- Department of Molecular Biology and Biochemistry
- Institute for Immunology, and
| | - Brianna M. Doratt
- Department of Molecular Biology and Biochemistry
- Institute for Immunology, and
| | | | | | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry
- Institute for Immunology, and
- Center for Virus Research, University of California, Irvine, Irvine, California, USA
- Department fo Microbiology, Immunology and Molecular Genetics, University of Kentucky, Levington, Kentucky, USA
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18
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Rhoades NS, Pinski AN, Monsibais AN, Jankeel A, Doratt BM, Cinco IR, Ibraim I, Messaoudi I. Acute SARS-CoV-2 infection is associated with an increased abundance of bacterial pathogens, including Pseudomonas aeruginosa in the nose. Cell Rep 2021; 36:109637. [PMID: 34433082 PMCID: PMC8361213 DOI: 10.1016/j.celrep.2021.109637] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [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: 05/26/2021] [Revised: 07/12/2021] [Accepted: 08/06/2021] [Indexed: 01/08/2023] Open
Abstract
Research conducted on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogenesis and coronavirus disease 2019 (COVID-19) generally focuses on the systemic host response, especially that generated by severely ill patients, with few studies investigating the impact of acute SARS-CoV-2 at the site of infection. We show that the nasal microbiome of SARS-CoV-2-positive patients (CoV+, n = 68) at the time of diagnosis is unique when compared to CoV− healthcare workers (n = 45) and CoV− outpatients (n = 21). This shift is marked by an increased abundance of bacterial pathogens, including Pseudomonas aeruginosa, which is also positively associated with viral RNA load. Additionally, we observe a robust host transcriptional response in the nasal epithelia of CoV+ patients, indicative of an antiviral innate immune response and neuronal damage. These data suggest that the inflammatory response caused by SARS-CoV-2 infection is associated with an increased abundance of bacterial pathogens in the nasal cavity that could contribute to increased incidence of secondary bacterial infections.
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Affiliation(s)
- Nicholas S Rhoades
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Amanda N Pinski
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Alisha N Monsibais
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Allen Jankeel
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Brianna M Doratt
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Isaac R Cinco
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Izabela Ibraim
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA.
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19
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Rhoades NS, Pinski A, Monsibais AN, Jankeel A, Doratt BM, Cinco IR, Ibraim I, Messaoudi I. Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including Pseudomonas Aeruginosa. bioRxiv 2021. [PMID: 34031657 DOI: 10.1101/2021.05.20.445008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Much of the research conducted on SARS-CoV-2 and COVID-19 has focused on the systemic host response, especially that generated by severely ill patients. Very few studies have investigated the impact of acute SARS-CoV-2 within the nasopharynx, the site of initial infection and viral replication. In this study we profiled changes in the nasal microbial communities as well as in host transcriptional profile during acute SARS-CoV-2 infection using 16S amplicon sequencing and RNA sequencing. These analyses were coupled to viral genome sequencing. Our microbiome analysis revealed that the nasal microbiome of COVID patients was unique and was marked by an expansion of bacterial pathogens. Some of these microbes (i.e. Acinetobacter ) were shared with COVID negative health care providers from the same medical center but absent in COVID negative outpatients seeking care at the same institutions suggesting acquisition of nosocomial respiratory pathogens. Specifically, we report a distinct increase in the prevalence and abundance of the pathogen Pseudomonas aeruginosa in COVID patients that correlated with viral RNA load. These data suggest that the inflammatory environment caused by SARS-CoV-2 infection and potentially exposure to the hospital environment leads to an expansion of bacterial pathogens in the nasal cavity that could contribute to increased incidence of secondary bacterial infections. Additionally, we observed a robust host transcriptional response in the nasal epithelia of COVID patients, indicative of an antiviral innate immune repones and neuronal damage. Finally, analysis of viral genomes did not reveal an association between viral loads and viral sequences.
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