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Shields PG, Ying KL, Brasky TM, Freudenheim JL, Li Z, McElroy JP, Reisinger SA, Song MA, Weng DY, Wewers MD, Whiteman NB, Yang Y, Mathé EA. A Pilot Cross-Sectional Study of Immunological and Microbiome Profiling Reveals Distinct Inflammatory Profiles for Smokers, Electronic Cigarette Users, and Never-Smokers. Microorganisms 2023; 11:1405. [PMID: 37374908 PMCID: PMC10303504 DOI: 10.3390/microorganisms11061405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/11/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Smokers (SM) have increased lung immune cell counts and inflammatory gene expression compared to electronic cigarette (EC) users and never-smokers (NS). The objective of this study is to further assess associations for SM and EC lung microbiomes with immune cell subtypes and inflammatory gene expression in samples obtained by bronchoscopy and bronchoalveolar lavage (n = 28). RNASeq with the CIBERSORT computational algorithm were used to determine immune cell subtypes, along with inflammatory gene expression and microbiome metatranscriptomics. Macrophage subtypes revealed a two-fold increase in M0 (undifferentiated) macrophages for SM and EC users relative to NS, with a concordant decrease in M2 (anti-inflammatory) macrophages. There were 68, 19, and 1 significantly differentially expressed inflammatory genes (DEG) between SM/NS, SM/EC users, and EC users/NS, respectively. CSF-1 and GATA3 expression correlated positively and inversely with M0 and M2 macrophages, respectively. Correlation profiling for DEG showed distinct lung profiles for each participant group. There were three bacteria genera-DEG correlations and three bacteria genera-macrophage subtype correlations. In this pilot study, SM and EC use were associated with an increase in undifferentiated M0 macrophages, but SM differed from EC users and NS for inflammatory gene expression. The data support the hypothesis that SM and EC have toxic lung effects influencing inflammatory responses, but this may not be via changes in the microbiome.
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Affiliation(s)
- Peter G. Shields
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH 43210, USA; (K.L.Y.)
- Department Internal Medicine, The Ohio State University College of Medicine, Columbus, OH 43205, USA
| | - Kevin L. Ying
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH 43210, USA; (K.L.Y.)
- Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Theodore M. Brasky
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH 43210, USA; (K.L.Y.)
- Department Internal Medicine, The Ohio State University College of Medicine, Columbus, OH 43205, USA
| | - Jo L. Freudenheim
- Department of Epidemiology and Environmental Health, University at Buffalo, Buffalo, NY 14261, USA
| | - Zihai Li
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH 43210, USA; (K.L.Y.)
| | - Joseph P. McElroy
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH 43210, USA; (K.L.Y.)
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Sarah A. Reisinger
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH 43210, USA; (K.L.Y.)
| | - Min-Ae Song
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH 43210, USA
| | - Daniel Y. Weng
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH 43210, USA; (K.L.Y.)
| | - Mark D. Wewers
- Pulmonary and Critical Care Medicine, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Noah B. Whiteman
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH 43210, USA; (K.L.Y.)
| | - Yiping Yang
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH 43210, USA; (K.L.Y.)
| | - Ewy A. Mathé
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH 43210, USA; (K.L.Y.)
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institute of Health, Rockville, MD 20892, USA
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Ying KL, Brasky TM, Freudenheim JL, McElroy JP, Nickerson QA, Song MA, Weng DY, Wewers MD, Whiteman NB, Mathé EA, Shields PG. Saliva and Lung Microbiome Associations with Electronic Cigarette Use and Smoking. Cancer Prev Res (Phila) 2022; 15:435-446. [PMID: 35667088 PMCID: PMC9256774 DOI: 10.1158/1940-6207.capr-21-0601] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/17/2022] [Accepted: 04/06/2022] [Indexed: 01/07/2023]
Abstract
The microbiome has increasingly been linked to cancer. Little is known about the lung and oral cavity microbiomes in smokers, and even less for electronic cigarette (EC) users, compared with never-smokers. In a cross-sectional study (n = 28) of smokers, EC users, and never-smokers, bronchoalveolar lavage and saliva samples underwent metatranscriptome profiling to examine associations with lung and oral microbiomes. Pairwise comparisons assessed differentially abundant bacteria species. Total bacterial load was similar between groups, with no differences in bacterial diversity across lung microbiomes. In lungs, 44 bacteria species differed significantly (FDR < 0.1) between smokers/never-smokers, with most decreased in smokers. Twelve species differed between smokers/EC users, all decreased in smokers of which Neisseria sp. KEM232 and Curvibacter sp. AEP1-3 were observed. Among the top five decreased species in both comparisons, Neisseria elongata, Neisseria sicca, and Haemophilus parainfluenzae were observed. In the oral microbiome, 152 species were differentially abundant for smokers/never-smokers, and 17 between smokers/electronic cigarette users, but only 21 species were differentially abundant in both the lung and oral cavity. EC use is not associated with changes in the lung microbiome compared with never-smokers, indicating EC toxicity does not affect microbiota. Statistically different bacteria in smokers compared with EC users and never-smokers were almost all decreased, potentially due to toxic effects of cigarette smoke. The low numbers of overlapping oral and lung microbes suggest that the oral microbiome is not a surrogate for analyzing smoking-related effects in the lung. PREVENTION RELEVANCE The microbiome affects cancer and other disease risk. The effects of e-cig usage on the lung microbiome are essentially unknown. Given the importance of lung microbiome dysbiosis populated by oral species which have been observed to drive lung cancer progression, it is important to study effects of e-cig use on microbiome.
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Affiliation(s)
- Kevin L. Ying
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH,Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH
| | - Theodore M. Brasky
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH,Department Internal Medicine, The Ohio State University College of Medicine, Columbus, OH
| | - Jo L. Freudenheim
- Department of Epidemiology and Environmental Health, University at Buffalo, Buffalo, NY
| | - Joseph P. McElroy
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH,Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH
| | - Quentin A. Nickerson
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH
| | - Min-Ae Song
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH
| | - Daniel Y. Weng
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH
| | - Mark D. Wewers
- Pulmonary and Critical Care Medicine, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio
| | - Noah B. Whiteman
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH
| | - Ewy A. Mathé
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH,Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH,Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institute of Health, Rockville, MD
| | - Peter G. Shields
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH,Department Internal Medicine, The Ohio State University College of Medicine, Columbus, OH
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Tong P, Gautam A, Windsor IW, Travers M, Chen Y, Garcia N, Whiteman NB, McKay LGA, Storm N, Malsick LE, Honko AN, Lelis FJN, Habibi S, Jenni S, Cai Y, Rennick LJ, Duprex WP, McCarthy KR, Lavine CL, Zuo T, Lin J, Zuiani A, Feldman J, MacDonald EA, Hauser BM, Griffths A, Seaman MS, Schmidt AG, Chen B, Neuberg D, Bajic G, Harrison SC, Wesemann DR. Memory B cell repertoire for recognition of evolving SARS-CoV-2 spike. Cell 2021; 184:4969-4980.e15. [PMID: 34332650 PMCID: PMC8299219 DOI: 10.1016/j.cell.2021.07.025] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/14/2021] [Accepted: 07/15/2021] [Indexed: 12/18/2022]
Abstract
Memory B cell reserves can generate protective antibodies against repeated SARS-CoV-2 infections, but with unknown reach from original infection to antigenically drifted variants. We charted memory B cell receptor-encoded antibodies from 19 COVID-19 convalescent subjects against SARS-CoV-2 spike (S) and found seven major antibody competition groups against epitopes recurrently targeted across individuals. Inclusion of published and newly determined structures of antibody-S complexes identified corresponding epitopic regions. Group assignment correlated with cross-CoV-reactivity breadth, neutralization potency, and convergent antibody signatures. Although emerging SARS-CoV-2 variants of concern escaped binding by many members of the groups associated with the most potent neutralizing activity, some antibodies in each of those groups retained affinity-suggesting that otherwise redundant components of a primary immune response are important for durable protection from evolving pathogens. Our results furnish a global atlas of S-specific memory B cell repertoires and illustrate properties driving viral escape and conferring robustness against emerging variants.
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Affiliation(s)
- Pei Tong
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Avneesh Gautam
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ian W Windsor
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Laboratory of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Meghan Travers
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yuezhou Chen
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nicholas Garcia
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Noah B Whiteman
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Lindsay G A McKay
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02115, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115, USA
| | - Nadia Storm
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02115, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115, USA
| | - Lauren E Malsick
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02115, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115, USA
| | - Anna N Honko
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02115, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115, USA
| | - Felipe J N Lelis
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Shaghayegh Habibi
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Simon Jenni
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Yongfei Cai
- Laboratory of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Linda J Rennick
- The Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; The Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - W Paul Duprex
- The Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; The Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Kevin R McCarthy
- The Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; The Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Christy L Lavine
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Teng Zuo
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Junrui Lin
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Adam Zuiani
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Elizabeth A MacDonald
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Blake M Hauser
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Anthony Griffths
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02115, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
| | - Bing Chen
- Laboratory of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
| | - Donna Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Goran Bajic
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Laboratory of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Stephen C Harrison
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Laboratory of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Duane R Wesemann
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA.
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4
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Tong P, Gautam A, Windsor I, Travers M, Chen Y, Garcia N, Whiteman NB, McKay LG, Lelis FJ, Habibi S, Cai Y, Rennick LJ, Duprex WP, McCarthy KR, Lavine CL, Zuo T, Lin J, Zuiani A, Feldman J, MacDonald EA, Hauser BM, Griffths A, Seaman MS, Schmidt AG, Chen B, Neuberg D, Bajic G, Harrison SC, Wesemann DR. Memory B cell repertoire for recognition of evolving SARS-CoV-2 spike. bioRxiv 2021:2021.03.10.434840. [PMID: 33758863 PMCID: PMC7987022 DOI: 10.1101/2021.03.10.434840] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Memory B cell reserves can generate protective antibodies against repeated SARS-CoV-2 infections, but with an unknown reach from original infection to antigenically drifted variants. We charted memory B cell receptor-encoded monoclonal antibodies (mAbs) from 19 COVID-19 convalescent subjects against SARS-CoV-2 spike (S) and found 7 major mAb competition groups against epitopes recurrently targeted across individuals. Inclusion of published and newly determined structures of mAb-S complexes identified corresponding epitopic regions. Group assignment correlated with cross-CoV-reactivity breadth, neutralization potency, and convergent antibody signatures. mAbs that competed for binding the original S isolate bound differentially to S variants, suggesting the protective importance of otherwise-redundant recognition. The results furnish a global atlas of the S-specific memory B cell repertoire and illustrate properties conferring robustness against emerging SARS-CoV-2 variants.
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Affiliation(s)
- Pei Tong
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Avneesh Gautam
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ian Windsor
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Meghan Travers
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yuezhou Chen
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nicholas Garcia
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Noah B. Whiteman
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Lindsay G.A. McKay
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02115, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115, USA
| | - Felipe J.N. Lelis
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Shaghayegh Habibi
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yongfei Cai
- Laboratory of Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Linda J. Rennick
- The Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
- The Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA
| | - W. Paul Duprex
- The Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
- The Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA
| | - Kevin R. McCarthy
- The Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
- The Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA
| | - Christy L. Lavine
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Teng Zuo
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Junrui Lin
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Adam Zuiani
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Elizabeth A. MacDonald
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Blake M. Hauser
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Anthony Griffths
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02115, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115, USA
| | - Michael S. Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Aaron G. Schmidt
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Microbiology, Harvard Medical School, Boston MA 02115
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
| | - Bing Chen
- Laboratory of Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
| | - Donna Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Goran Bajic
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Laboratory of Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Stephen C Harrison
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Laboratory of Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Duane R. Wesemann
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
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Ying KL, Song MA, Weng DY, Nickerson QA, McElory JP, Brasky TM, Whiteman NB, Wewers MD, Freudenheim JL, Mathé EA, Shields PG. Abstract 1163: Lung and salivary microbiome in electronic cigarette users, never-smokers, and smokers: A pilot cross-sectional study. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-1163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Little is known about the microbiomes of the lung and oral cavity with electronic cigarette (e-cig) use and how they compare to those of smokers and never-smokers. E-cigs have been promoted as a safe alternative to smoking cigarettes. Given the recent outbreak of E-cigarette or Vaping product use Associated Lung Injury (EVALI) there is an urgent need for understanding the biological effects of e-cig use on the lung and oral cavity, including effects on the microbiome. Previous studies have been limited to 16S-rRNA sequencing which were used to detect bacteria genera. In this study, we used metatranscriptome profiling to study differentially abundant bacteria species in the oral and lung microbiome of never-smokers, smokers, and e-cig users.
Methods: A cross-sectional study of 10 never-smokers, 8 cigarette smokers, and 10 e-cig users was conducted, with saliva and bronchoalveolar lavage (BAL) collected for each study participant. RNA was extracted from saliva and BAL samples for total transcriptome RNA-seq analysis. Sequences were aligned with bowtie2 v.2.2.8 to the human genome (hg19) and non-aligned reads were aligned and annotated using NCBI metagenomes database and Kraken v.1. Differences in the microbiome by smoking status were determined by pairwise comparisons using limma-voom with FDR q-value cutoffs <0.2.
Results: The distribution of richness and evenness of bacterial communities measured by Shannon diversity in our metatranscriptome data did not significantly differ between the three smoking status groups. When comparing levels of bacteria species between groups in the saliva, 234 were differentially abundant between smokers and never-smokers, and 39 were differentially abundant between smokers and e-cig users. In the lung, 87 bacterial species were differentially abundant between smokers and never-smokers and 36 were differentially abundant between smokers and e-cig users. Notably, no bacteria species were differentially abundant when comparing e-cig users and never-smokers in both the saliva and lung samples. There are 50 bacterial species found to be differentially abundant in both the lung and saliva samples, 47 of which are decreased in smokers. These 47 bacteria species included common commensal oral microbiome species such as Haemophilus parainfluenzae, Capnocytophaga gingivalis and Neisseria species. The 3 species that were increased in smokers were Lactobacillus species.
Conclusion: Our findings suggests that smoking cigarettes may alter populations of common commensal species in both the oral and lung microbiome. The lack of differentially abundant bacterial species between electronic cigarette users and never-smokers indicates that e-cigs may alter bacterial species to a lesser extent than smoking.
Citation Format: Kevin L. Ying, Min-Ae Song, Daniel Y. Weng, Quentin A. Nickerson, Joseph P. McElory, Theodore M. Brasky, Noah B. Whiteman, Mark D. Wewers, Jo L. Freudenheim, Ewy A. Mathé, Peter G. Shields. Lung and salivary microbiome in electronic cigarette users, never-smokers, and smokers: A pilot cross-sectional study [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1163.
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Ying KL, Song MA, Weng DY, Nickerson QA, McElroy JP, Brasky TM, Whiteman NB, Wewers MD, Freudenheim JL, Mathe EA, Shields PG. Abstract A34: Lung and salivary microbiome in electronic cigarette users, never-smokers, and smokers: A pilot cross-sectional study. Cancer Res 2020. [DOI: 10.1158/1538-7445.mvc2020-a34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Little is known about the microbiomes of the lung and oral cavity with electronic cigarette (e-cig) use and how they compare to those of smokers and never-smokers. E-cigs have been promoted as a safe alternative to smoking cigarettes. Given the recent outbreak of E-cigarette or Vaping product use Associated Lung Injury (EVALI), there is an urgent need for understanding the biologic effects of e-cig use on the lung and oral cavity, including effects on the microbiome. Previous studies have been limited to 16S-rRNA sequencing, which was used to detect bacteria genera. In this study, we used metatranscriptome profiling to study differentially abundant bacteria species in the oral and lung microbiome of never-smokers, smokers, and e-cig users.
Methods: A cross-sectional study of 10 never-smokers, 8 cigarette smokers, and 10 e-cig users was conducted, with saliva and bronchoalveolar lavage (BAL) collected for each study participant. RNA was extracted from saliva and BAL samples for total transcriptome RNA-seq analysis. Sequences were aligned with bowtie2 v.2.2.8 to the human genome (hg19) and nonaligned reads were aligned and annotated using NCBI metagenomes database and Kraken v.1. Differences in the microbiome by smoking status were determined by pairwise comparisons using limma-voom with FDR q-value cutoffs <0.2.
Results: The distribution of richness and evenness of bacterial communities measured by Shannon diversity in our metatranscriptome data did not significantly differ between the three smoking status groups. When comparing levels of bacteria species between groups in the saliva, 234 were differentially abundant between smokers and never-smokers, and 39 were differentially abundant between smokers and e-cig users. In the lung, 87 bacterial species were differentially abundant between smokers and never-smokers and 36 were differentially abundant between smokers and e-cig users. Notably, no bacteria species were differentially abundant when comparing e-cig users and never-smokers in both the saliva and lung samples. There are 50 bacterial species found to be differentially abundant in both the lung and saliva samples, 47 of which are decreased in smokers. These 47 bacteria species included common commensal oral microbiome species such as Haemophilus parainfluenzae, Capnocytophaga gingivalis, and Neisseria species. The 3 species that were increased in smokers were Lactobacillus species.
Conclusion: Our findings suggests that smoking cigarettes may alter populations of common commensal species in both the oral and lung microbiome. The lack of differentially abundant bacterial species between electronic cigarette users and never-smokers indicates that e-cigs may alter bacterial species to a lesser extent than smoking.
Citation Format: Kevin L. Ying, Min-Ae Song, Daniel Y. Weng, Quentin A. Nickerson, Joseph P. McElroy, Theodore M. Brasky, Noah B. Whiteman, Mark D. Wewers, Jo L. Freudenheim, Ewy A. Mathe, Peter G. Shields. Lung and salivary microbiome in electronic cigarette users, never-smokers, and smokers: A pilot cross-sectional study [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr A34.
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