1
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Perier C, Nasinghe E, Charles I, Ssetaba LJ, Ahyong V, Bangs D, Beatty PR, Czudnochowski N, Diallo A, Dugan E, Fabius JM, Fong Baker H, Gardner J, Isaacs S, Joanah B, Kalantar K, Kateete D, Knight M, Krasilnikov M, Krogan NJ, Langelier C, Lee E, Li LM, Licht D, Lien K, Lyons Z, Mboowa G, Mwebaza I, Mwesigwa S, Nalwadda G, Nichols R, Penaranda ME, Petnic S, Phelps M, Popper SJ, Rape M, Reingold A, Robbins R, Rosenberg OS, Savage DF, Schildhauer S, Settles ML, Sserwadda I, Stanley S, Tato CM, Tsitsiklis A, Van Dis E, Vanaerschot M, Vinden J, Cox JS, Joloba ML, Schaletzky J. Workshop-based learning and networking: a scalable model for research capacity strengthening in low- and middle-income countries. Glob Health Action 2022; 15:2062175. [PMID: 35730550 PMCID: PMC9225690 DOI: 10.1080/16549716.2022.2062175] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Science education and research have the potential to drive profound change in low- and middle-income countries (LMICs) through encouraging innovation, attracting industry, and creating job opportunities. However, in LMICs, research capacity is often limited, and acquisition of funding and access to state-of-the-art technologies is challenging. The Alliance for Global Health and Science (the Alliance) was founded as a partnership between the University of California, Berkeley (USA) and Makerere University (Uganda), with the goal of strengthening Makerere University’s capacity for bioscience research. The flagship program of the Alliance partnership is the MU/UCB Biosciences Training Program, an in-country, hands-on workshop model that trains a large number of students from Makerere University in infectious disease and molecular biology research. This approach nucleates training of larger and more diverse groups of students, development of mentoring and bi-directional research partnerships, and support of the local economy. Here, we describe the project, its conception, implementation, challenges, and outcomes of bioscience research workshops. We aim to provide a blueprint for workshop implementation, and create a valuable resource for bioscience research capacity strengthening in LMICs.
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Affiliation(s)
- Celine Perier
- H. Wheeler Center for Emerging & Neglected Diseases (CEND), University of California, Berkeley, CA, USA
| | | | - Isabelle Charles
- H. Wheeler Center for Emerging & Neglected Diseases (CEND), University of California, Berkeley, CA, USA
| | | | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Derek Bangs
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - P Robert Beatty
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Amy Diallo
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Eli Dugan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Jacqueline M Fabius
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA
| | - Hildy Fong Baker
- School of Public Health, Center for Global Public Health (CGPH), University of California, Berkeley, CA, USA
| | - Jackson Gardner
- Department of Medicine, University of California, San Francisco, CA, USA
| | | | - Birungi Joanah
- School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | | | - David Kateete
- School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | - Matt Knight
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Maria Krasilnikov
- Department of Molecular Biology and Microbiology, Tufts Graduate School of Biomedical Sciences, Boston, MA, USA
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA.,Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | | | - Eric Lee
- Graduate Group in Infectious Diseases and Immunity, School of Public Health, University of California, Berkeley, CA, USA
| | - Lucy M Li
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Daniel Licht
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Katie Lien
- Pritzker School of Medicine, University of Chicago, Chicago, IL, USA
| | - Zilose Lyons
- California China Climate Institute, University of California, Berkeley, CA, USA
| | - Gerald Mboowa
- School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | - Ivan Mwebaza
- School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | | | | | - Robert Nichols
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Sarah Petnic
- Quality and Clinical Excellence Department, Providence Queen of the Valley Medical Center, Napa, CA, USA
| | | | - Stephen J Popper
- Sustainable Sciences Institute, San Francisco, CA, USA.,School of Public Health, Department of Infectious Disease and Vaccinology, University of California, Berkeley, CA, USA
| | - Michael Rape
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Arthur Reingold
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, USA
| | | | - Oren S Rosenberg
- Department of Medicine, University of California, San Francisco, CA, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | | | - Ivan Sserwadda
- School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | - Sarah Stanley
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.,Division of Infectious Disease and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA
| | | | | | - Erik Van Dis
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Joanna Vinden
- Division of Infectious Diseases and Immunity, School of Public Health, University of California, Berkeley, CA, USA
| | - Jeffery S Cox
- H. Wheeler Center for Emerging & Neglected Diseases (CEND), University of California, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Moses L Joloba
- School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | - Julia Schaletzky
- H. Wheeler Center for Emerging & Neglected Diseases (CEND), University of California, Berkeley, CA, USA
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2
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Wick KD, Fang X, Maishan M, Matsumoto S, Spottiswoode N, Sarma A, Simoneau C, Khakoo M, Langelier C, Calfee CS, Gotts JE, Matthay MA. Impact of e-cigarette aerosol on primary human alveolar epithelial type 2 cells. Am J Physiol Lung Cell Mol Physiol 2022; 323:L152-L164. [PMID: 35670478 PMCID: PMC9559034 DOI: 10.1152/ajplung.00503.2021] [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: 12/14/2021] [Revised: 05/03/2022] [Accepted: 06/01/2022] [Indexed: 11/22/2022] Open
Abstract
Electronic cigarettes (e-cigarettes) are designed to simulate combustible cigarette smoking and to aid in smoking cessation. Although the number of e-cigarette users has been increasing, the potential health impacts and biological effects of e-cigarettes are still not fully understood. Previous research has focused on the biological effects of e-cigarettes on lung cancer cell lines and distal airway epithelial cells; however, there have been few published studies on the effect of e-cigarettes on primary lung alveolar epithelial cells. The primary purpose of this study was to investigate the direct effect of e-cigarette aerosol on primary human lung alveolar epithelial type 2 (AT2) cells, both alone and in the presence of viral infection. The Melo-3 atomizer caused direct AT2 cell toxicity, whereas the more popular Juul pod's aerosol did not have a detectable cytotoxic effect on AT2 cells. Juul nicotine aerosol also did not increase short-term susceptibility to viral infection. However, 3 days of exposure upregulated genes central to the generation of reactive oxygen species, lipid peroxidation, and carcinogen metabolism and downregulated key innate immune system genes related to cytokine and chemokine signaling. These findings have implications for the potentially injurious impact of long-term use of popular low-power e-cigarette pods on the human alveolar epithelium. Gene expression data might be an important endpoint for evaluating the potential harmful effects of vaping devices that do not cause overt toxicity.
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Affiliation(s)
- Katherine D Wick
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - Xiaohui Fang
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - Mazharul Maishan
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - Shotaro Matsumoto
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - Natasha Spottiswoode
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, California
| | - Aartik Sarma
- Division of Pulmonary and Critical Care, Department of Medicine, University of California, San Francisco, California
| | - Camille Simoneau
- Gladstone Institutes, University of California, San Francisco, California
| | - Manisha Khakoo
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - Chaz Langelier
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, California
- Chan Zuckerberg Biohub, San Francisco, California
| | - Carolyn S Calfee
- Cardiovascular Research Institute, University of California, San Francisco, California
- Division of Pulmonary and Critical Care, Department of Medicine, University of California, San Francisco, California
| | - Jeffrey E Gotts
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - Michael A Matthay
- Cardiovascular Research Institute, University of California, San Francisco, California
- Department of Medicine, University of California, San Francisco, California
- Department of Anesthesia, University of California, San Francisco, California
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3
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Ditz B, Sarma A, Kerstjens HAM, Liesker JJW, Bathoorn E, Vonk JM, Bernal V, Horvatovich P, Guryev V, Caldera S, Langelier C, Faiz A, Christenson SA, van den Berge M. The sputum transcriptome better predicts COPD exacerbations after the withdrawal of inhaled corticosteroids than sputum eosinophils. ERJ Open Res 2021; 7:00097-2021. [PMID: 34235210 PMCID: PMC8255541 DOI: 10.1183/23120541.00097-2021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/26/2021] [Indexed: 12/13/2022] Open
Abstract
Introduction Continuing inhaled corticosteroid (ICS) use does not benefit all patients with COPD, yet it is difficult to determine which patients may safely sustain ICS withdrawal. Although eosinophil levels can facilitate this decision, better biomarkers could improve personalised treatment decisions. Methods We performed transcriptional profiling of sputum to explore the molecular biology and compared the predictive value of an unbiased gene signature versus sputum eosinophils for exacerbations after ICS withdrawal in COPD patients. RNA-sequencing data of induced sputum samples from 43 COPD patients were associated with the time to exacerbation after ICS withdrawal. Expression profiles of differentially expressed genes were summarised to create gene signatures. In addition, we built a Bayesian network model to determine coregulatory networks related to the onset of COPD exacerbations after ICS withdrawal. Results In multivariate analyses, we identified a gene signature (LGALS12, ALOX15, CLC, IL1RL1, CD24, EMR4P) associated with the time to first exacerbation after ICS withdrawal. The addition of this gene signature to a multiple Cox regression model explained more variance of time to exacerbations compared to a model using sputum eosinophils. The gene signature correlated with sputum eosinophil as well as macrophage cell counts. The Bayesian network model identified three coregulatory gene networks as well as sex to be related to an early versus late/nonexacerbation phenotype. Conclusion We identified a sputum gene expression signature that exhibited a higher predictive value for predicting COPD exacerbations after ICS withdrawal than sputum eosinophilia. Future studies should investigate the utility of this signature, which might enhance personalised ICS treatment in COPD patients. Sputum gene expression may have utility in biomarker development for identifying subjects who are at higher risk of exacerbation after ICS withdrawalhttps://bit.ly/3gYl2OL
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Affiliation(s)
- Benedikt Ditz
- Dept of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
| | - Aartik Sarma
- University of California, San Francisco, CA, USA
| | - Huib A M Kerstjens
- Dept of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
| | - Jeroen J W Liesker
- Dept of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
| | - Erik Bathoorn
- Dept of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Judith M Vonk
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,Dept of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Victor Bernal
- Dept of Analytical Biochemistry, Groningen Research Institute of Pharmacy, Groningen, The Netherlands
| | - Peter Horvatovich
- Dept of Analytical Biochemistry, Groningen Research Institute of Pharmacy, Groningen, The Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Saharai Caldera
- Division of Infectious Diseases, Dept of Medicine, University of California, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Chaz Langelier
- Division of Infectious Diseases, Dept of Medicine, University of California, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Alen Faiz
- Dept of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,University of Technology Sydney, Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life Sciences, Sydney, Australia.,These authors contributed equally
| | | | - Maarten van den Berge
- Dept of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,These authors contributed equally
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4
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Dugger DT, Fung M, Zlock L, Caldera S, Sharp L, Hays SR, Singer JP, Leard LE, Golden JA, Shah RJ, Kukreja J, Gordon E, Finkbeiner W, Kleinhenz ME, Langelier C, Greenland JR. Cystic Fibrosis Lung Transplant Recipients Have Suppressed Airway Interferon Responses during Pseudomonas Infection. Cell Rep Med 2020; 1. [PMID: 32754722 PMCID: PMC7402593 DOI: 10.1016/j.xcrm.2020.100055] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Lung transplantation can be lifesaving in end-stage cystic fibrosis (CF), but long-term survival is limited by chronic lung allograft dysfunction (CLAD). Persistent upper airway Pseudomonas aeruginosa (PsA) colonization can seed the allograft. While de novo PsA infection is associated with CLAD in non-CF recipients, this association is less clear for CF recipients experiencing PsA recolonization. Here, we evaluate host and pathogen contributions to this phenomenon. In the context of PsA infection, brushings from the airways of CF recipients demonstrate type 1 interferon gene suppression. Airway epithelial cell (AEC) cultures demonstrate similar findings in the absence of pathogens or immune cells, contrasting with the pre-transplant CF AEC phenotype. Type 1 interferon promoters are relatively hypermethylated in CF AECs. CF subjects in this cohort have more mucoid PsA, while non-CF PsA subjects have decreased microbiome α diversity. Peri-transplant protocols may benefit from consideration of this host and microbiome equilibrium. Lung allograft Pseudomonas infection outcomes are better for recipients with CF In CF, infected allograft airway cells demonstrate suppression of interferon genes Differential DNA methylation may contribute to this distinct epithelial phenotype Increased α diversity and mucoid forms characterize CF Pseudomonas infection
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Affiliation(s)
- Daniel T Dugger
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Monica Fung
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lorna Zlock
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Saharai Caldera
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Louis Sharp
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Steven R Hays
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jonathan P Singer
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lorriana E Leard
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jefferey A Golden
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Rupal J Shah
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jasleen Kukreja
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Erin Gordon
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Walter Finkbeiner
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mary Ellen Kleinhenz
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chaz Langelier
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94143, USA
| | - John R Greenland
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Medical Service, Veterans Affairs Health Care System, San Francisco, CA 94121, USA.,Lead Contact
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5
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Ross JT, Nesseler N, Leligdowicz A, Zemans RL, Mahida RY, Minus E, Langelier C, Gotts JE, Matthay MA. The ex vivo perfused human lung is resistant to injury by high-dose S. pneumoniae bacteremia. Am J Physiol Lung Cell Mol Physiol 2020; 319:L218-L227. [PMID: 32519893 DOI: 10.1152/ajplung.00053.2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Few patients with bacteremia from a nonpulmonary source develop acute respiratory distress syndrome (ARDS). However, the mechanisms that protect the lung from injury in bacteremia have not been identified. We simulated bacteremia by adding Streptococcus pneumoniae to the perfusate of the ex vivo perfused human lung model. In contrast to a pneumonia model in which bacteria were instilled into the distal air spaces of one lobe, injection of high doses of S. pneumoniae into the perfusate was not associated with alveolar epithelial injury as demonstrated by low protein permeability of the alveolar epithelium, intact alveolar fluid clearance, and the absence of alveolar edema. Unexpectedly, the ex vivo human lung rapidly cleared large quantities of S. pneumoniae even though the perfusate had very few intravascular phagocytes and lacked immunoglobulins or complement. The bacteria were cleared in part by the small number of neutrophils in the perfusate, alveolar macrophages in the airspaces, and probably by interstitial pathways. Together, these findings identify one mechanism by which the lung and the alveolar epithelium are protected from injury in bacteremia.
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Affiliation(s)
- James T Ross
- Department of Surgery, University of California San Francisco, San Francisco, California
| | - Nicolas Nesseler
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California.,Department of Anesthesia and Critical Care, Pontchaillou, University Hospital of Rennes, Rennes, France.,University Rennes, CHU de Rennes, Inra, Inserm, Institut NUMECAN-UMR_A 1341, UMR_S 1241, Rennes, France.,University Rennes, CHU Rennes, Inserm, CIC 1414 (Centre d'Investigation Clinique de Rennes), Rennes, France
| | - Aleksandra Leligdowicz
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California.,Interdepartmental Division of Critical Care Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Rachel L Zemans
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Rahul Y Mahida
- Birmingham Acute Care Research Group, Institute of Inflammation and Aging, University of Birmingham, Birmingham, United Kingdom
| | | | - Chaz Langelier
- Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Jeffrey E Gotts
- Department of Medicine, Cardiovascular Research Institute, University of California San Francisco, San Francisco, California
| | - Michael A Matthay
- Departments of Medicine and Anesthesia, Cardiovascular Research Institute, University of California San Francisco, San Francisco, California
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6
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Panzer AR, Lynch SV, Langelier C, Christie JD, McCauley K, Nelson M, Cheung CK, Benowitz NL, Cohen MJ, Calfee CS. Lung Microbiota Is Related to Smoking Status and to Development of Acute Respiratory Distress Syndrome in Critically Ill Trauma Patients. Am J Respir Crit Care Med 2019; 197:621-631. [PMID: 29035085 DOI: 10.1164/rccm.201702-0441oc] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
RATIONALE Cigarette smoking is associated with increased risk of acute respiratory distress syndrome (ARDS) in patients after severe trauma; however, the mechanisms underlying this association are unknown. OBJECTIVES To determine whether cigarette smoking contributes to ARDS development after trauma by altering community composition of the lung microbiota. METHODS We studied the lung microbiota of mechanically ventilated patients admitted to the ICU after severe blunt trauma. To do so, we used 16S ribosomal RNA gene amplicon sequencing of endotracheal aspirate samples obtained on ICU admission (n = 74) and at 48 hours after admission (n = 30). Cigarette smoke exposure (quantified using plasma cotinine), ARDS development, and other clinical parameters were correlated with lung microbiota composition. MEASUREMENTS AND MAIN RESULTS Smoking status was significantly associated with lung bacterial community composition at ICU admission (P = 0.007 by permutational multivariate ANOVA [PERMANOVA]) and at 48 hours (P = 0.03 by PERMANOVA), as well as with significant enrichment of potential pathogens, including Streptococcus, Fusobacterium, Prevotella, Haemophilus, and Treponema. ARDS development was associated with lung community composition at 48 hours (P = 0.04 by PERMANOVA) and was characterized by relative enrichment of Enterobacteriaceae and of specific taxa enriched at baseline in smokers, including Prevotella and Fusobacterium. CONCLUSIONS After severe blunt trauma, a history of smoking is related to lung microbiota composition, both at the time of ICU admission and at 48 hours. ARDS development is also correlated with respiratory microbial community structure at 48 hours and with taxa that are relatively enriched in smokers at ICU admission. The data derived from this pilot study suggest that smoking-related changes in the lung microbiota could be related to ARDS development after severe trauma.
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Affiliation(s)
| | - Susan V Lynch
- 1 Division of Gastroenterology, Department of Medicine
| | - Chaz Langelier
- 2 Division of Infectious Diseases, Department of Medicine
| | - Jason D Christie
- 3 Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Mary Nelson
- 4 Department of Surgery.,5 Zuckerberg San Francisco General Hospital, San Francisco, California
| | - Christopher K Cheung
- 4 Department of Surgery.,5 Zuckerberg San Francisco General Hospital, San Francisco, California
| | - Neal L Benowitz
- 6 Division of Clinical Pharmacology, Department of Medicine.,5 Zuckerberg San Francisco General Hospital, San Francisco, California
| | - Mitchell J Cohen
- 7 Department of Surgery, Denver Health Medical Center, Denver, Colorado; and.,8 Department of Surgery, University of Colorado, Aurora, Colorado
| | - Carolyn S Calfee
- 9 Division of Pulmonary and Critical Care Medicine, Department of Medicine.,10 Department of Anesthesia.,11 Cardiovascular Research Institute, and.,12 Center for Tobacco Control Research and Education, University of California, San Francisco, San Francisco, California
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7
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Langelier C. Raff-ining our understanding of pneumococcal invasion. Sci Transl Med 2019. [DOI: 10.1126/scitranslmed.aaw5322] [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: 11/02/2022]
Abstract
Differential raffinose metabolism influences
Streptococcus pneumoniae
tissue tropism and disease phenotype.
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Affiliation(s)
- Chaz Langelier
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA 94049. USA
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8
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Abstract
Whole-blood transcriptional profiling identifies a five-gene signature for tuberculosis screening among people living with HIV.
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Affiliation(s)
- Chaz Langelier
- Division of Infectious Diseases, University of California San Francisco, San Francisco, CA 94049, USA
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9
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Langelier C. Ironing out the mechanisms of chronic bacterial infection. Sci Transl Med 2018. [DOI: 10.1126/scitranslmed.aav3885] [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: 11/02/2022]
Abstract
Molecular evaluation reveals an important role for nutrient-dependent intracellular trafficking in chronic bacterial otitis media.
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Affiliation(s)
- Chaz Langelier
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA 94049, USA
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10
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Langelier C. The resistance potential of a quintessential commensal. Sci Transl Med 2018. [DOI: 10.1126/scitranslmed.aau7387] [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: 11/02/2022]
Abstract
Whole-genome sequencing and microbiome analysis illuminate the emergence of invasive, linezolid-resistant
Staphylococcus epidermidis.
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Affiliation(s)
- Chaz Langelier
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA 94049, USA
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11
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Langelier C. A molecular warning system for invasive pneumococcus. Sci Transl Med 2018. [DOI: 10.1126/scitranslmed.aau0470] [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: 11/02/2022]
Abstract
A genome-wide association study of
Streptococcus pneumoniae
identifies and validates bacterial loci associated with invasive infection.
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Affiliation(s)
- Chaz Langelier
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA 94049, USA
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12
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Langelier C. A firsthand view of how secondhand smoke disrupts airway immunity. Sci Transl Med 2018. [DOI: 10.1126/scitranslmed.aat4478] [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: 11/02/2022]
Abstract
Chronic tobacco smoke exposure exacerbates
Haemophilus influenzae
infection by disrupting innate and adaptive immune responses in mice.
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Affiliation(s)
- Chaz Langelier
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA 94049, USA
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13
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Langelier C. A proactive charcoal approach shields the gut microbiome from systemic antibiotics. Sci Transl Med 2018. [DOI: 10.1126/scitranslmed.aas8966] [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: 11/02/2022]
Abstract
A new activated charcoal agent protects beneficial gut microbiota from the adverse effects of systemic antibiotic therapy.
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Affiliation(s)
- Chaz Langelier
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA 94049, USA
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14
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Li R, Faden DL, Fakhry C, Langelier C, Jiao Y, Wang Y, Wilkerson MD, Pedamallu CS, Old M, Lang J, Loyo M, Ahn SM, Tan M, Gooi Z, Chan J, Richmon J, Wood LD, Hruban RH, Bishop J, Westra WH, Chung CH, Califano J, Gourin CG, Bettegowda C, Meyerson M, Papadopoulos N, Kinzler KW, Vogelstein B, DeRisi JL, Koch WM, Agrawal N. Clinical, genomic, and metagenomic characterization of oral tongue squamous cell carcinoma in patients who do not smoke. Head Neck 2014; 37:1642-9. [PMID: 24954188 DOI: 10.1002/hed.23807] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [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: 12/16/2013] [Revised: 04/19/2014] [Accepted: 06/18/2014] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Evidence suggests the incidence of oral tongue squamous cell carcinoma is increasing in young patients, many who have no history of tobacco use. METHODS We clinically reviewed 89 patients with oral tongue cancer. Exomic sequencing of tumor DNA from 6 nonsmokers was performed and compared to previously sequenced cases. RNA from 20 tumors was evaluated by massively parallel sequencing to search for potentially oncogenic viruses. RESULTS Non-smokers (53 of 89) were younger than smokers (36 of 89; mean, 50.4 vs 61.9 years; p < .001), and seemed more likely to be women (58.5% vs 38.9%; p = .069). Nonsmokers had fewer TP53 mutations (p = .02) than smokers. No tumor-associated viruses were detected. CONCLUSION The young age of nonsmoking patients with oral tongue cancer and fewer TP53 mutations suggest a viral role in this disease. Our efforts to identify such a virus were unsuccessful. Further studies are warranted to elucidate the drivers of carcinogenesis in these patients.
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Affiliation(s)
- Ryan Li
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Daniel L Faden
- Department of Otolaryngology-Head and Neck Surgery, University of California San Francisco, San Francisco, California
| | - Carole Fakhry
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Milton J. Dance Head and Neck Center, Greater Baltimore Medical Center, Baltimore, Maryland
| | - Chaz Langelier
- Department of Medicine, University of California San Francisco, San Francisco, California
| | - Yuchen Jiao
- The Ludwig Center and the Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
| | - Yuxuan Wang
- The Ludwig Center and the Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
| | - Matthew D Wilkerson
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Chandra Sekhar Pedamallu
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Matthew Old
- Department of Otolaryngology-Head and Neck Surgery, Ohio State University, Columbus, Ohio
| | - James Lang
- Department of Otolaryngology-Head and Neck Surgery, Ohio State University, Columbus, Ohio
| | - Myriam Loyo
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sun Mi Ahn
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Marietta Tan
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Zhen Gooi
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jason Chan
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jeremy Richmon
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Laura D Wood
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland
| | - Ralph H Hruban
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland
| | - Justin Bishop
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland
| | - William H Westra
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland
| | - Christine H Chung
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Joseph Califano
- Milton J. Dance Head and Neck Center, Greater Baltimore Medical Center, Baltimore, Maryland
| | - Christine G Gourin
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Chetan Bettegowda
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Matthew Meyerson
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Nickolas Papadopoulos
- The Ludwig Center and the Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
| | - Kenneth W Kinzler
- The Ludwig Center and the Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
| | - Bert Vogelstein
- The Ludwig Center and the Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
| | - Joseph L DeRisi
- Howard Hughes Medical Institute, Chevy Chase, Maryland.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California
| | - Wayne M Koch
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Nishant Agrawal
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland.,The Ludwig Center and the Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
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15
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Rutishauser RL, Langelier C, Baxi SM, Hanks D, Chin-Hong P. Think global, act local: chronic dysuria and sterile pyuria in an Eritrean-American woman. Case Reports 2014; 2014:bcr-2013-201546. [DOI: 10.1136/bcr-2013-201546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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