AJRCCM Articles in Press. Published on 06-May-2015 as 10.1164/rccm.201502-0223OC
Page 1 of 51
The Host Response to the Lung Microbiome in Chronic Obstructive Pulmonary Disease Marc A. Sze1,8, Pedro A. Dimitriu2,8, Masaru Suzuki3, John E. McDonough1, Josh D. Campbell4, John F. Brothers4, John R. Erb-Downward5, Gary B. Huffnagle5, Shizu Hayashi3, W. Mark Elliott1, Joel Cooper7, Don D. Sin1, Marc E. Lenburg4, Avrum Spira4, William W. Mohn2, James C. Hogg3. 1
The Heart Lung Innovation Centre, Providence Heart-Lung Institute at St. Paul's Hospital, Department of Medicine, University of British Columbia, Vancouver, BC, Canada V6Z 1Y6 2
Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3 3
The Heart Lung Innovation Centre, Providence Heart-Lung Institute at St. Paul's Hospital, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada V6Z 1Y6 4
Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA 5
University of Michigan, Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine 7
Department of Cardiovascular and Thoracic Surgery, University of Pennsylvania
8
Both authors contributed equally
Corresponding author: James C. Hogg Current Address: Room 166 – 1081 Burrard Street Vancouver, BC Canada V6Z 1Y6 Email: [email protected] Phone: (604)-806-8346 ext. 62949 Fax: (604)-806-8351 Contributions: MAS (performed & designed experiments, data analysis, wrote first draft), PAD (data analysis, intellectual contributions, helped design microbiome experiments), MS (tissue procurement, quantitative histology measurements), JEM (tissue procurement, MicroCT measurements), JDC (Bioinformatic support, gene expression analysis), JFB (Bioinformatic support), JRE-D (Touchdown Sequencing, Bioinformatic support), GBH (Touchdown Sequencing, intellectual contributions), SH (intellectual contributions), WME (tissue procurement, histology), JC (tissue procurement), DDS (intellectual contributions), MEL (gene expression analysis, bioinformatic support), AS (gene expression analysis, intellectual contributions, WWM (helped design microbiome experiments, intellectual contributions), JCH (conceived & designed experiments, intellectual contributions) 1
Copyright © 2015 by the American Thoracic Society
AJRCCM Articles in Press. Published on 06-May-2015 as 10.1164/rccm.201502-0223OC
Running Title: COPD and the lung microbiome Total Word Count: 3,698 Methods: 852 Funding Agencies: Supported by Merck external studies agreement IIS 38978 (UBC #F1003533), CIHR # CIF-9768, the Tula Foundation, and partial funding provided by NIH grant R01HL114447
2
Copyright © 2015 by the American Thoracic Society
Page 2 of 51
AJRCCM Articles in Press. Published on 06-May-2015 as 10.1164/rccm.201502-0223OC
Page 3 of 51
Abstract: Rationale: The relatively sparse but diverse microbiome in human lungs may become less diverse in chronic obstructive pulmonary disease (COPD). This report examines the relationship of this microbiome to emphysematous tissue destruction, number of terminal bronchioles, infiltrating inflammatory cells, and host gene expression. Methods: A culture-independent pyrosequencing microbiome analysis was used to examine the V3-V5 regions of the bacterial 16S rDNA in 40 samples of lung from 5 patients with (GOLD 4) COPD and 28 samples from 4 donors (controls). A second protocol based on the V1-V3 regions was used to verify the bacterial microbiome results. Within lung tissue samples the microbiome was compared to results of microCT, infiltrating inflammatory cells measured using quantitative histology, and host gene expression. Results: A total of 10 Operational Taxonomic Units (OTUs) were found to be able to discriminate between control and GOLD 4 lung tissue, which included known pathogens such as Haemophilus influenzae. We also observed a decline in microbial diversity that was associated with emphysematous destruction, remodeling of the bronchiolar and alveolar tissue, and the infiltration of the tissue by CD4+ T cells. Specific OTUs were also associated with neutrophils, eosinophils and B cell infiltration (P
Page 1 of 51
The Host Response to the Lung Microbiome in Chronic Obstructive Pulmonary Disease Marc A. Sze1,8, Pedro A. Dimitriu2,8, Masaru Suzuki3, John E. McDonough1, Josh D. Campbell4, John F. Brothers4, John R. Erb-Downward5, Gary B. Huffnagle5, Shizu Hayashi3, W. Mark Elliott1, Joel Cooper7, Don D. Sin1, Marc E. Lenburg4, Avrum Spira4, William W. Mohn2, James C. Hogg3. 1
The Heart Lung Innovation Centre, Providence Heart-Lung Institute at St. Paul's Hospital, Department of Medicine, University of British Columbia, Vancouver, BC, Canada V6Z 1Y6 2
Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3 3
The Heart Lung Innovation Centre, Providence Heart-Lung Institute at St. Paul's Hospital, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada V6Z 1Y6 4
Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA 5
University of Michigan, Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine 7
Department of Cardiovascular and Thoracic Surgery, University of Pennsylvania
8
Both authors contributed equally
Corresponding author: James C. Hogg Current Address: Room 166 – 1081 Burrard Street Vancouver, BC Canada V6Z 1Y6 Email: [email protected] Phone: (604)-806-8346 ext. 62949 Fax: (604)-806-8351 Contributions: MAS (performed & designed experiments, data analysis, wrote first draft), PAD (data analysis, intellectual contributions, helped design microbiome experiments), MS (tissue procurement, quantitative histology measurements), JEM (tissue procurement, MicroCT measurements), JDC (Bioinformatic support, gene expression analysis), JFB (Bioinformatic support), JRE-D (Touchdown Sequencing, Bioinformatic support), GBH (Touchdown Sequencing, intellectual contributions), SH (intellectual contributions), WME (tissue procurement, histology), JC (tissue procurement), DDS (intellectual contributions), MEL (gene expression analysis, bioinformatic support), AS (gene expression analysis, intellectual contributions, WWM (helped design microbiome experiments, intellectual contributions), JCH (conceived & designed experiments, intellectual contributions) 1
Copyright © 2015 by the American Thoracic Society
AJRCCM Articles in Press. Published on 06-May-2015 as 10.1164/rccm.201502-0223OC
Running Title: COPD and the lung microbiome Total Word Count: 3,698 Methods: 852 Funding Agencies: Supported by Merck external studies agreement IIS 38978 (UBC #F1003533), CIHR # CIF-9768, the Tula Foundation, and partial funding provided by NIH grant R01HL114447
2
Copyright © 2015 by the American Thoracic Society
Page 2 of 51
AJRCCM Articles in Press. Published on 06-May-2015 as 10.1164/rccm.201502-0223OC
Page 3 of 51
Abstract: Rationale: The relatively sparse but diverse microbiome in human lungs may become less diverse in chronic obstructive pulmonary disease (COPD). This report examines the relationship of this microbiome to emphysematous tissue destruction, number of terminal bronchioles, infiltrating inflammatory cells, and host gene expression. Methods: A culture-independent pyrosequencing microbiome analysis was used to examine the V3-V5 regions of the bacterial 16S rDNA in 40 samples of lung from 5 patients with (GOLD 4) COPD and 28 samples from 4 donors (controls). A second protocol based on the V1-V3 regions was used to verify the bacterial microbiome results. Within lung tissue samples the microbiome was compared to results of microCT, infiltrating inflammatory cells measured using quantitative histology, and host gene expression. Results: A total of 10 Operational Taxonomic Units (OTUs) were found to be able to discriminate between control and GOLD 4 lung tissue, which included known pathogens such as Haemophilus influenzae. We also observed a decline in microbial diversity that was associated with emphysematous destruction, remodeling of the bronchiolar and alveolar tissue, and the infiltration of the tissue by CD4+ T cells. Specific OTUs were also associated with neutrophils, eosinophils and B cell infiltration (P
