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Boix-Amorós A, Badri MH, Manasson J, Blank RB, Haberman RH, Neimann AL, Girija PV, Jimenez Hernandez A, Heguy A, Koralov SB, Bonneau R, Clemente JC, Scher JU. Alterations in the cutaneous microbiome of patients with psoriasis and psoriatic arthritis reveal similarities between non-lesional and lesional skin. Ann Rheum Dis 2023; 82:507-514. [PMID: 36600182 DOI: 10.1136/ard-2022-223389] [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: 09/20/2022] [Accepted: 12/01/2022] [Indexed: 12/14/2022]
Abstract
OBJECTIVES To investigate the cutaneous microbiome spanning the entire psoriatic disease spectrum, and to evaluate distinguishing features of psoriasis (PsO) and psoriatic arthritis (PsA). METHODS Skin swabs were collected from upper and lower extremities of healthy individuals and patients with PsO and PsA. Psoriatic patients contributed both lesional (L) and contralateral non-lesional (NL) samples. Microbiota were analysed using 16S rRNA sequencing. RESULTS Compared with healthy skin, alpha diversity in psoriatic NL and L skin was significantly reduced (p<0.05) and samples clustered separately in plots of beta diversity (p<0.05). Kocuria and Cutibacterium were enriched in healthy subjects, while Staphylococcus was enriched in psoriatic disease. Microbe-microbe association networks revealed a higher degree of similarity between psoriatic NL and L skin compared with healthy skin despite the absence of clinically evident inflammation. Moreover, the relative abundance of Corynebacterium was higher in NL PsA samples compared with NL PsO samples (p<0.05), potentially serving as a biomarker for disease progression. CONCLUSIONS These findings show differences in diversity, bacterial composition and microbe-microbe interactions between healthy and psoriatic skin, both L and NL. We further identified bacterial biomarkers that differentiate disease phenotypes, which could potentially aid in predicting the transition from PsO to PsA.
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Affiliation(s)
- Alba Boix-Amorós
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Michelle H Badri
- Department of Biology, New York University, New York, New York, USA
| | - Julia Manasson
- Division of Rheumatology, Department of Medicine and Psoriatic Arthritis Center, New York University Grossman School of Medicine, New York, New York, USA
| | - Rebecca B Blank
- Division of Rheumatology, Department of Medicine and Psoriatic Arthritis Center, New York University Grossman School of Medicine, New York, New York, USA
| | - Rebecca H Haberman
- Division of Rheumatology, Department of Medicine and Psoriatic Arthritis Center, New York University Grossman School of Medicine, New York, New York, USA
| | - Andrea L Neimann
- Ronald O. Perelman Department of Dermatology, New York University Grossman School of Medicine, New York, New York, USA
| | - Parvathy V Girija
- Division of Rheumatology, Department of Medicine and Psoriatic Arthritis Center, New York University Grossman School of Medicine, New York, New York, USA
| | - Anthony Jimenez Hernandez
- Division of Rheumatology, Department of Medicine and Psoriatic Arthritis Center, New York University Grossman School of Medicine, New York, New York, USA
| | - Adriana Heguy
- NYU Langone Health Genome Technology Center, Department of Pathology, New York University Grossman School of Medicine, New York, New York, USA
- Department of Pathology, New York University Grossman School of Medicine, New York, New York, USA
| | - Sergei B Koralov
- Department of Pathology, New York University Grossman School of Medicine, New York, New York, USA
| | - Richard Bonneau
- Department of Biology, New York University, New York, New York, USA
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York, USA
| | - Jose C Clemente
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jose U Scher
- Division of Rheumatology, Department of Medicine and Psoriatic Arthritis Center, New York University Grossman School of Medicine, New York, New York, USA
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Zhang XS, Yin YS, Wang J, Battaglia T, Krautkramer K, Li WV, Li J, Brown M, Zhang M, Badri MH, Armstrong AJS, Strauch CM, Wang Z, Nemet I, Altomare N, Devlin JC, He L, Morton JT, Chalk JA, Needles K, Liao V, Mount J, Li H, Ruggles KV, Bonneau RA, Dominguez-Bello MG, Bäckhed F, Hazen SL, Blaser MJ. Maternal cecal microbiota transfer rescues early-life antibiotic-induced enhancement of type 1 diabetes in mice. Cell Host Microbe 2021; 29:1249-1265.e9. [PMID: 34289377 PMCID: PMC8370265 DOI: 10.1016/j.chom.2021.06.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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: 12/24/2020] [Revised: 04/27/2021] [Accepted: 06/18/2021] [Indexed: 01/04/2023]
Abstract
Early-life antibiotic exposure perturbs the intestinal microbiota and accelerates type 1 diabetes (T1D) development in the NOD mouse model. Here, we found that maternal cecal microbiota transfer (CMT) to NOD mice after early-life antibiotic perturbation largely rescued the induced T1D enhancement. Restoration of the intestinal microbiome was significant and persistent, remediating the antibiotic-depleted diversity, relative abundance of particular taxa, and metabolic pathways. CMT also protected against perturbed metabolites and normalized innate and adaptive immune effectors. CMT restored major patterns of ileal microRNA and histone regulation of gene expression. Further experiments suggest a gut-microbiota-regulated T1D protection mechanism centered on Reg3γ, in an innate intestinal immune network involving CD44, TLR2, and Reg3γ. This regulation affects downstream immunological tone, which may lead to protection against tissue-specific T1D injury.
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Affiliation(s)
- Xue-Song Zhang
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA; Human Microbiome Program, New York University Langone Medical Center, New York, NY, USA.
| | - Yue Sandra Yin
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA; Human Microbiome Program, New York University Langone Medical Center, New York, NY, USA
| | - Jincheng Wang
- Department of Biochemistry and Microbiology, Rutgers University - New Brunswick, New Brunswick, NJ, USA
| | - Thomas Battaglia
- Human Microbiome Program, New York University Langone Medical Center, New York, NY, USA
| | - Kimberly Krautkramer
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Göteborg 41345, Sweden
| | - Wei Vivian Li
- Department of Biostatistics and Epidemiology, Rutgers University School of Public Health, Piscataway, NJ, USA
| | - Jackie Li
- Human Microbiome Program, New York University Langone Medical Center, New York, NY, USA
| | - Mark Brown
- Cardiovascular & Metabolic Sciences, Lerner Research Institute Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Meifan Zhang
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA; Human Microbiome Program, New York University Langone Medical Center, New York, NY, USA
| | - Michelle H Badri
- Human Microbiome Program, New York University Langone Medical Center, New York, NY, USA; New York University, Center for Data Science, New York, NY, USA
| | - Abigail J S Armstrong
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Christopher M Strauch
- Cardiovascular & Metabolic Sciences, Lerner Research Institute Cleveland Clinic, Cleveland, OH, USA
| | - Zeneng Wang
- Cardiovascular & Metabolic Sciences, Lerner Research Institute Cleveland Clinic, Cleveland, OH, USA
| | - Ina Nemet
- Cardiovascular & Metabolic Sciences, Lerner Research Institute Cleveland Clinic, Cleveland, OH, USA
| | - Nicole Altomare
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Joseph C Devlin
- Human Microbiome Program, New York University Langone Medical Center, New York, NY, USA
| | - Linchen He
- Department of Population Health, New York University Langone Medical Center, New York, NY, USA
| | - Jamie T Morton
- Human Microbiome Program, New York University Langone Medical Center, New York, NY, USA; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - John Alex Chalk
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Kelly Needles
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Viviane Liao
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Julia Mount
- Human Microbiome Program, New York University Langone Medical Center, New York, NY, USA
| | - Huilin Li
- Department of Population Health, New York University Langone Medical Center, New York, NY, USA
| | - Kelly V Ruggles
- Human Microbiome Program, New York University Langone Medical Center, New York, NY, USA
| | - Richard A Bonneau
- Human Microbiome Program, New York University Langone Medical Center, New York, NY, USA; New York University, Center for Data Science, New York, NY, USA; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology, Rutgers University - New Brunswick, New Brunswick, NJ, USA; Institute for Food, Nutrition and Health, Rutgers University - New Brunswick, New Brunswick, NJ, USA
| | - Fredrik Bäckhed
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Göteborg 41345, Sweden; Region västra Götaland, Sahlgrenska University Hospital, Department of Clinical Physiology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stanley L Hazen
- Cardiovascular & Metabolic Sciences, Lerner Research Institute Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, OH 44195, USA; Heart, Vascular & Thoracic Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Martin J Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA; Human Microbiome Program, New York University Langone Medical Center, New York, NY, USA.
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3
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Manasson J, Wallach DS, Guggino G, Stapylton M, Badri MH, Solomon G, Reddy SM, Coras R, Aksenov AA, Jones DR, Girija PV, Neimann AL, Heguy A, Segal LN, Dorrestein PC, Bonneau R, Guma M, Ciccia F, Ubeda C, Clemente JC, Scher JU. Interleukin-17 Inhibition in Spondyloarthritis Is Associated With Subclinical Gut Microbiome Perturbations and a Distinctive Interleukin-25-Driven Intestinal Inflammation. Arthritis Rheumatol 2020; 72:645-657. [PMID: 31729183 DOI: 10.1002/art.41169] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 11/12/2019] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To characterize the ecological effects of biologic therapies on the gut bacterial and fungal microbiome in psoriatic arthritis (PsA)/spondyloarthritis (SpA) patients. METHODS Fecal samples from PsA/SpA patients pre- and posttreatment with tumor necrosis factor inhibitors (TNFi; n = 15) or an anti-interleukin-17A monoclonal antibody inhibitor (IL-17i; n = 14) underwent sequencing (16S ribosomal RNA, internal transcribed spacer and shotgun metagenomics) and computational microbiome analysis. Fecal levels of fatty acid metabolites and cytokines/proteins implicated in PsA/SpA pathogenesis or intestinal inflammation were correlated with sequence data. Additionally, ileal biopsies obtained from SpA patients who developed clinically overt Crohn's disease (CD) after treatment with IL-17i (n = 5) were analyzed for expression of IL-23/Th17-related cytokines, IL-25/IL-17E-producing cells, and type 2 innate lymphoid cells (ILC2s). RESULTS There were significant shifts in abundance of specific taxa after treatment with IL-17i compared to TNFi, particularly Clostridiales (P = 0.016) and Candida albicans (P = 0.041). These subclinical alterations correlated with changes in bacterial community co-occurrence, metabolic pathways, IL-23/Th17-related cytokines, and various fatty acids. Ileal biopsies showed that clinically overt CD was associated with expansion of IL-25/IL-17E-producing tuft cells and ILC2s (P < 0.05), compared to pre-IL-17i treatment levels. CONCLUSION In a subgroup of SpA patients, the initiation of IL-17A blockade correlated with features of subclinical gut inflammation and intestinal dysbiosis of certain bacterial and fungal taxa, most notably C albicans. Further, IL-17i-related CD was associated with overexpression of IL-25/IL-17E-producing tuft cells and ILC2s. These results may help to explain the potential link between inhibition of a specific IL-17 pathway and the (sub)clinical gut inflammation observed in SpA.
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Affiliation(s)
- Julia Manasson
- New York University School of Medicine, New York, New York
| | | | | | | | | | - Gary Solomon
- New York University School of Medicine, New York, New York
| | - Soumya M Reddy
- New York University School of Medicine, New York, New York
| | | | - Alexander A Aksenov
- Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego
| | - Drew R Jones
- New York University School of Medicine, New York, New York
| | | | | | - Adriana Heguy
- New York University School of Medicine, New York, New York
| | | | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego
| | - Richard Bonneau
- Simons Foundation, New York University, and Courant Institute of Mathematical Sciences, New York, New York
| | | | | | - Carles Ubeda
- La Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, Valencia, Spain, and CIBERESP, Madrid, Spain
| | | | - Jose U Scher
- New York University School of Medicine, New York, New York
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4
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Morton JT, Aksenov AA, Nothias LF, Foulds JR, Quinn RA, Badri MH, Swenson TL, Van Goethem MW, Northen TR, Vazquez-Baeza Y, Wang M, Bokulich NA, Watters A, Song SJ, Bonneau R, Dorrestein PC, Knight R. Learning representations of microbe-metabolite interactions. Nat Methods 2019; 16:1306-1314. [PMID: 31686038 PMCID: PMC6884698 DOI: 10.1038/s41592-019-0616-3] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 09/19/2019] [Indexed: 12/26/2022]
Abstract
Integrating multiomics datasets is critical for microbiome research; however, inferring interactions across omics datasets has multiple statistical challenges. We solve this problem by using neural networks (https://github.com/biocore/mmvec) to estimate the conditional probability that each molecule is present given the presence of a specific microorganism. We show with known environmental (desert soil biocrust wetting) and clinical (cystic fibrosis lung) examples, our ability to recover microbe-metabolite relationships, and demonstrate how the method can discover relationships between microbially produced metabolites and inflammatory bowel disease.
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Affiliation(s)
- James T Morton
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Alexander A Aksenov
- Collaborative Mass Spectrometry Innovaftion Center, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Louis Felix Nothias
- Collaborative Mass Spectrometry Innovaftion Center, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - James R Foulds
- Department of Information Systems, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Robert A Quinn
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | | | - Tami L Swenson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Marc W Van Goethem
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - Yoshiki Vazquez-Baeza
- Jacobs School of Engineering, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovaftion Center, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Nicholas A Bokulich
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Aaron Watters
- Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Se Jin Song
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Richard Bonneau
- Department of Biology, New York University, New York, NY, USA
- Flatiron Institute, Simons Foundation, New York, NY, USA
- Computer Science Department, Courant Institute, New York, NY, USA
- Center For Data Science, New York University, New York, NY, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovaftion Center, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
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5
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Tsay JCJ, Wu BG, Badri MH, Clemente JC, Shen N, Meyn P, Li Y, Yie TA, Lhakhang T, Olsen E, Murthy V, Michaud G, Sulaiman I, Tsirigos A, Heguy A, Pass H, Weiden MD, Rom WN, Sterman DH, Bonneau R, Blaser MJ, Segal LN. Airway Microbiota Is Associated with Upregulation of the PI3K Pathway in Lung Cancer. Am J Respir Crit Care Med 2018; 198:1188-1198. [PMID: 29864375 PMCID: PMC6221574 DOI: 10.1164/rccm.201710-2118oc] [Citation(s) in RCA: 203] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 06/04/2018] [Indexed: 12/17/2022] Open
Abstract
RATIONALE In lung cancer, upregulation of the PI3K (phosphoinositide 3-kinase) pathway is an early event that contributes to cell proliferation, survival, and tissue invasion. Upregulation of this pathway was recently described as associated with enrichment of the lower airways with bacteria identified as oral commensals. OBJECTIVES We hypothesize that host-microbe interactions in the lower airways of subjects with lung cancer affect known cancer pathways. METHODS Airway brushings were collected prospectively from subjects with lung nodules at time of diagnostic bronchoscopy, including 39 subjects with final lung cancer diagnoses and 36 subjects with noncancer diagnoses. In addition, samples from 10 healthy control subjects were included. 16S ribosomal RNA gene amplicon sequencing and paired transcriptome sequencing were performed on all airway samples. In addition, an in vitro model with airway epithelial cells exposed to bacteria/bacterial products was performed. MEASUREMENTS AND MAIN RESULTS The composition of the lower airway transcriptome in the patients with cancer was significantly different from the control subjects, which included up-regulation of ERK (extracellular signal-regulated kinase) and PI3K signaling pathways. The lower airways of patients with lung cancer were enriched for oral taxa (Streptococcus and Veillonella), which was associated with up-regulation of the ERK and PI3K signaling pathways. In vitro exposure of airway epithelial cells to Veillonella, Prevotella, and Streptococcus led to upregulation of these same signaling pathways. CONCLUSIONS The data presented here show that several transcriptomic signatures previously identified as relevant to lung cancer pathogenesis are associated with enrichment of the lower airway microbiota with oral commensals.
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Affiliation(s)
| | | | - Michelle H. Badri
- Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, New York
| | - Jose C. Clemente
- Department of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Nan Shen
- Department of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Peter Meyn
- New York University Genomic Technology Center, New York, New York; and
| | - Yonghua Li
- Division of Pulmonary and Critical Care Medicine
| | - Ting-An Yie
- Division of Pulmonary and Critical Care Medicine
| | - Tenzin Lhakhang
- New York University Genomic Technology Center, New York, New York; and
| | - Evan Olsen
- Division of Pulmonary and Critical Care Medicine
| | - Vivek Murthy
- Division of Pulmonary and Critical Care Medicine
| | | | | | | | - Adriana Heguy
- New York University Genomic Technology Center, New York, New York; and
| | | | | | | | | | - Richard Bonneau
- Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, New York
- New York University Center for Data Science, New York, New York
| | - Martin J. Blaser
- Department of Medicine, New York University School of Medicine, New York, New York
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6
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Wang J, Lesko M, Badri MH, Kapoor BC, Wu BG, Li Y, Smaldone GC, Bonneau R, Kurtz ZD, Condos R, Segal LN. Lung microbiome and host immune tone in subjects with idiopathic pulmonary fibrosis treated with inhaled interferon-γ. ERJ Open Res 2017; 3:00008-2017. [PMID: 28717640 PMCID: PMC5507144 DOI: 10.1183/23120541.00008-2017] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 04/14/2017] [Indexed: 01/27/2023] Open
Abstract
Therapies targeting inflammation reveal inconsistent results in idiopathic pulmonary fibrosis (IPF). Aerosolised interferon (IFN)-γ has been proposed as a novel therapy. Changes in the host airway microbiome are associated with the inflammatory milieu and may be associated with disease progression. Here, we evaluate whether treatment with aerosolised IFN-γ in IPF impacts either the lower airway microbiome or the host immune phenotype. Patients with IPF who enrolled in an aerosolised IFN-γ trial underwent bronchoscopy at baseline and after 6 months. 16S rRNA sequencing of bronchoalveolar lavage fluid (BALF) was used to evaluate the lung microbiome. Biomarkers were measured by Luminex assay in plasma, BALF and BAL cell supernatant. The compPLS framework was used to evaluate associations between taxa and biomarkers. IFN-γ treatment did not change α or β diversity of the lung microbiome and few taxonomic changes occurred. While none of the biomarkers changed in plasma, there was an increase in IFN-γ and a decrease in Fit-3 ligand, IFN-α2 and interleukin-5 in BAL cell supernatant, and a decrease in tumour necrosis factor-β in BALF. Multiple correlations between microbial taxa common to the oral mucosa and host inflammatory biomarkers were found. These data suggest that the lung microbiome is independently associated with the host immune tone and may have a potential mechanistic role in IPF. Lower airway microbiome and immunological tone are associated in IPF, an effect independent of IFN-γ treatmenthttp://ow.ly/cTDo30bsJiN
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Affiliation(s)
- Jing Wang
- Division of Pulmonary and Critical Care Medicine, Beijing Chaoyang Hospital, The Capital University of Medicine, Beijing, China.,Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Melissa Lesko
- Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Michelle H Badri
- Dept of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Bianca C Kapoor
- Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Benjamin G Wu
- Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Yonghua Li
- Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Gerald C Smaldone
- Division of Pulmonary, Critical Care and Sleep Medicine, State University of New York at Stony Brook, Stony Brook, NY, USA
| | - Richard Bonneau
- Dept of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA.,Courant Institute of Mathematical Sciences, New York University, New York, NY, USA.,Simons Center for Data Analysis, Simons Foundation, New York, NY, USA
| | - Zachary D Kurtz
- Dept of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Rany Condos
- Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, NY, USA
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