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Buschur KL, Pottinger TD, Vogel-Claussen J, Powell CA, Aguet F, Allen NB, Ardlie K, Bluemke DA, Durda P, Hermann EA, Hoffman EA, Lima JA, Liu Y, Malinsky D, Manichaikul A, Motahari A, Post WS, Prince MR, Rich SS, Rotter JI, Smith BM, Tracy RP, Watson K, Winther HB, Lappalainen T, Barr RG. Peripheral Blood Mononuclear Cell Gene Expression Associated with Pulmonary Microvascular Perfusion: The Multi-Ethnic Study of Atherosclerosis Chronic Obstructive Pulmonary Disease. Ann Am Thorac Soc 2024; 21:884-894. [PMID: 38335160 PMCID: PMC11160125 DOI: 10.1513/annalsats.202305-417oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 02/09/2024] [Indexed: 02/12/2024] Open
Abstract
Rationale: Chronic obstructive pulmonary disease (COPD) and emphysema are associated with endothelial damage and altered pulmonary microvascular perfusion. The molecular mechanisms underlying these changes are poorly understood in patients, in part because of the inaccessibility of the pulmonary vasculature. Peripheral blood mononuclear cells (PBMCs) interact with the pulmonary endothelium. Objectives: To test the association between gene expression in PBMCs and pulmonary microvascular perfusion in COPD. Methods: The Multi-Ethnic Study of Atherosclerosis (MESA) COPD Study recruited two independent samples of COPD cases and controls with ⩾10 pack-years of smoking history. In both samples, pulmonary microvascular blood flow, pulmonary microvascular blood volume, and mean transit time were assessed on contrast-enhanced magnetic resonance imaging, and PBMC gene expression was assessed by microarray. Additional replication was performed in a third sample with pulmonary microvascular blood volume measures on contrast-enhanced dual-energy computed tomography. Differential expression analyses were adjusted for age, gender, race/ethnicity, educational attainment, height, weight, smoking status, and pack-years of smoking. Results: The 79 participants in the discovery sample had a mean age of 69 ± 6 years, 44% were female, 25% were non-White, 34% were current smokers, and 66% had COPD. There were large PBMC gene expression signatures associated with pulmonary microvascular perfusion traits, with several replicated in the replication sets with magnetic resonance imaging (n = 47) or dual-energy contrast-enhanced computed tomography (n = 157) measures. Many of the identified genes are involved in inflammatory processes, including nuclear factor-κB and chemokine signaling pathways. Conclusions: PBMC gene expression in nuclear factor-κB, inflammatory, and chemokine signaling pathways was associated with pulmonary microvascular perfusion in COPD, potentially offering new targetable candidates for novel therapies.
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Affiliation(s)
| | | | - Jens Vogel-Claussen
- Department of Diagnostic and Interventional Radiology, Hannover Medical School, Hannover, Germany
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Francois Aguet
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Norrina B. Allen
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Kristin Ardlie
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - David A. Bluemke
- Department of Radiology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Peter Durda
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | | | - Eric A. Hoffman
- Department of Radiology, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - João A.C. Lima
- Division of Cardiology, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland
| | - Yongmei Liu
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | | | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Amin Motahari
- Department of Radiology, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Wendy S. Post
- Division of Cardiology, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland
| | | | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, California
| | - Benjamin M. Smith
- Department of Medicine
- Research Institute, McGill University Health Center, Montreal, Québec, Canada
| | - Russell P. Tracy
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Karol Watson
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California; and
| | - Hinrich B. Winther
- Department of Diagnostic and Interventional Radiology, Hannover Medical School, Hannover, Germany
| | - Tuuli Lappalainen
- Department of Biostatistics
- Department of Systems Biology, Columbia University Medical Center, New York, New York
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
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Trivedi A, Bade G, Madan K, Ahmed Bhat M, Guleria R, Talwar A. Effect of Smoking and Its Cessation on the Transcript Profile of Peripheral Monocytes in COPD Patients. Int J Chron Obstruct Pulmon Dis 2022; 17:65-77. [PMID: 35027824 PMCID: PMC8749770 DOI: 10.2147/copd.s337635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/13/2021] [Indexed: 11/23/2022] Open
Abstract
Rationale Smoking is the primary cause of chronic obstructive pulmonary disease (COPD); however, only 10–20% of smokers develop the disease suggesting possible genomic association in the causation of the disease. In the present study, we aimed to explore the whole genome transcriptomics of blood monocytes from COPD smokers (COPD-S), COPD Ex-smokers (COPD-ExS), Control smokers (CS), and Control Never-smokers (CNS) to understand the differential effects of smoking, COPD and that of smoking cessation. Methods Exploratory analyses in form of principal component analysis (PCA) and hierarchical component analysis (uHCA) were performed to evaluate the similarity in gene expression patterns, while differential expression analyses of different supervised groups of smokers and never smokers were performed to study the differential effect of smoking, COPD and smoking cessation. Differentially expressed genes among groups were subjected to post-hoc enrichment analysis. Candidate genes were subjected to external validation by quantitative RT-PCR experiments. Results CNS made a cluster completely segregated from the other three subgroups (CS, COPDS and COPD-ExS). About 550, 8 and 5 genes showed differential expression, respectively, between CNS and CS, between CS and COPD-S, and between COPD-S and COPD-ExS. Apoptosis, immune response, cell adhesion, and inflammation were the top process networks identified in enrichment analysis. Two candidate genes (CASP9 and TNFRSF1A) found to be integral to several pathways in enrichment analysis were validated in an external validation experiment. Conclusion Control never smokers had formed a cluster distinctively separated from all smokers (COPDS, COPD-ExS, and CS), while amongst all smokers, control smokers had aggregated in a separate cluster. Smoking cessation appeared beneficial if started at an early stage as many genes altered due to smoking started reverting towards the baseline, whereas only a few COPD-related genes showed reversal after smoking cessation.
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Affiliation(s)
- Anjali Trivedi
- Department of Physiology, All India Institute of Medical Sciences, New Delhi, India
| | - Geetanjali Bade
- Department of Physiology, All India Institute of Medical Sciences, New Delhi, India
| | - Karan Madan
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Muzaffer Ahmed Bhat
- Department of Physiology, All India Institute of Medical Sciences, New Delhi, India
| | - Randeep Guleria
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Anjana Talwar
- Department of Physiology, All India Institute of Medical Sciences, New Delhi, India
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3
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Casanova NG, Zhou T, Gonzalez-Garay ML, Lussier YA, Sweiss N, Ma SF, Noth I, Knox KS, Garcia JGN. MicroRNA and protein-coding gene expression analysis in idiopathic pulmonary fibrosis yields novel biomarker signatures associated to survival. Transl Res 2021; 228:1-12. [PMID: 32711186 PMCID: PMC7779721 DOI: 10.1016/j.trsl.2020.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 07/09/2020] [Accepted: 07/16/2020] [Indexed: 02/04/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive interstitial lung disease of unknown etiology that poses significant challenges in early diagnosis and prediction of progression. Analyses of microRNA and gene expression in IPF have yielded potentially predictive information. However, the relationship between microRNA/gene expression and quantitative phenotypic value in IPF remains controversial, as is the added value of this approach to current molecular signatures in IPF. To identify biomarkers predictive of survival in IPF via a microRNA-driven strategy. We profiled microRNA and protein-coding gene expression in peripheral blood mononuclear cells from 70 IPF subjects in a discovery cohort. We linked the microRNA/gene expression level with the quantitative phenotypic variation in IPF, including diffusing capacity of the lung for carbon monoxide and the forced vital capacity percent predicted. In silico analyses of expression profiles and quantitative phenotypic data allowed the generation of 2 sets of IPF molecular signatures (unique for microRNAs and protein-coding genes) that predict IPF survival. Each signature performed well in a validation cohort comprised of IPF patients aggregated from distinct patient populations recruited from different sites. Resampling test suggests that the protein-coding gene based signature is comparable and potentially superior to published IPF prognostic gene signatures. In conclusion, these results highlight the utility of microRNA-driven peripheral blood molecular signatures as valuable and novel biomarkers associated to individuals at high survival risk and for potentially facilitating individualized therapies in this enigmatic disorder.
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Affiliation(s)
- Nancy G Casanova
- Department of Medicine, University of Arizona Health Sciences, Tucson, Arizona
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada
| | | | - Yves A Lussier
- Center for Biomedical Informatics and Biostatistics, University of Arizona, Tucson, Arizona
| | - Nadera Sweiss
- Section of Rheumatology Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Shwu-Fan Ma
- Section of Pulmonary/Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Imre Noth
- Division of Pulmonary and Critical Care Department of Medicine, University of Virginia, Charlottesville, Virginia
| | - Kenneth S Knox
- Department of Medicine, College of Medicine-Phoenix, University of Arizona Health Sciences, Phoenix, Arizona
| | - Joe G N Garcia
- Department of Medicine, University of Arizona Health Sciences, Tucson, Arizona.
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Bhattacharya S, Mereness JA, Baran AM, Misra RS, Peterson DR, Ryan RM, Reynolds AM, Pryhuber GS, Mariani TJ. Lymphocyte-Specific Biomarkers Associated With Preterm Birth and Bronchopulmonary Dysplasia. Front Immunol 2021; 11:563473. [PMID: 33552042 PMCID: PMC7859626 DOI: 10.3389/fimmu.2020.563473] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 12/07/2020] [Indexed: 01/11/2023] Open
Abstract
Many premature babies who are born with neonatal respiratory distress syndrome (RDS) go on to develop Bronchopulmonary Dysplasia (BPD) and later Post-Prematurity Respiratory Disease (PRD) at one year corrected age, characterized by persistent or recurrent lower respiratory tract symptoms frequently related to inflammation and viral infection. Transcriptomic profiles were generated from sorted peripheral blood CD8+ T cells of preterm and full-term infants enrolled with consent in the NHLBI Prematurity and Respiratory Outcomes Program (PROP) at the University of Rochester and the University at Buffalo. We identified outcome-related gene expression patterns following standard methods to identify markers for oxygen utilization and BPD as outcomes in extremely premature infants. We further identified predictor gene sets for BPD based on transcriptomic data adjusted for gestational age at birth (GAB). RNA-Seq analysis was completed for CD8+ T cells from 145 subjects. Among the subjects with highest risk for BPD (born at <29 weeks gestational age (GA); n=72), 501 genes were associated with oxygen utilization. In the same set of subjects, 571 genes were differentially expressed in subjects with a diagnosis of BPD and 105 genes were different in BPD subjects as defined by physiologic challenge. A set of 92 genes could predict BPD with a moderately high degree of accuracy. We consistently observed dysregulation of TGFB, NRF2, HIPPO, and CD40-associated pathways in BPD. Using gene expression data from both premature and full-term subjects (n=116), we identified a 28 gene set that predicted the PRD status with a moderately high level of accuracy, which also were involved in TGFB signaling. Transcriptomic data from sort-purified peripheral blood CD8+ T cells from 145 preterm and full-term infants identified sets of molecular markers of inflammation associated with independent development of BPD in extremely premature infants at high risk for the disease and of PRD among the preterm and full-term subjects.
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Affiliation(s)
- Soumyaroop Bhattacharya
- Division of Neonatology, Department of Pediatrics, University of Rochester, Rochester, NY, United States
| | - Jared A Mereness
- Division of Neonatology, Department of Pediatrics, University of Rochester, Rochester, NY, United States
| | - Andrea M Baran
- Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY, United States
| | - Ravi S Misra
- Division of Neonatology, Department of Pediatrics, University of Rochester, Rochester, NY, United States
| | - Derick R Peterson
- Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY, United States
| | - Rita M Ryan
- Department of Pediatrics, University at Buffalo, Buffalo, NY, United States.,Department of Pediatrics, Case Western Reserve University, Cleveland, OH, United States
| | | | - Gloria S Pryhuber
- Division of Neonatology, Department of Pediatrics, University of Rochester, Rochester, NY, United States
| | - Thomas J Mariani
- Division of Neonatology, Department of Pediatrics, University of Rochester, Rochester, NY, United States
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Oxidative stress and Nrf2 expression in peripheral blood mononuclear cells derived from COPD patients: an observational longitudinal study. Respir Res 2020; 21:37. [PMID: 32000766 PMCID: PMC6993453 DOI: 10.1186/s12931-020-1292-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 01/14/2020] [Indexed: 12/29/2022] Open
Abstract
Background A persistent low inflammatory-oxidative status and the inadequacy of the antioxidant nuclear factor-E2-related factor 2 (Nrf2) have been implicated in chronic obstructive pulmonary disease (COPD) progression. Therefore this study was aimed to assess the association between lung function decline and oxidative-inflammatory markers and Nrf2 signaling pathway expression in peripheral blood mononuclear cells (PBMCs) over time. Methods 33 mild-moderate COPD outpatients (mean age 66.9 ± 6.9 years) were age-sex matched with 37 no-COPD subjects. A clinical evaluation, blood sampling tests and a spirometry were performed at baseline and after a mean follow-up of 49.7 ± 6.9 months. Results In COPD, compared to no-COPD, we found a faster lung function decline at follow-up. Although similar prevalence of smoking, hypertension, diabetes and dyslipidemia, systemic markers of inflammation (hs-CRP and white blood cells, WBCs) and oxidative stress (8-isoprostane) were significantly increased in COPD at follow-up, while the antioxidant glutathione (GSH) was significantly reduced. Moreover the expression of Nrf2 and of Nrf2-related genes heme oxygenase (HO)-1 and glutamate-cysteine ligase catalytic (GCLC) subunit in PBMCS were significantly down-regulated in COPD at follow-up, whereas no changes were observed in no-COPD. The percent variation (Δ) of FEV1 detected after the follow-up in COPD patients was directly correlated with ΔNrf2 (r = 0.826 p < 0.001), ΔHO-1 (r = 0.820, p < 0.001) and ΔGCLC (r = 0.840, p < 0.001). Moreover ΔFEV1 was also directly correlated with ΔGSH (r = 0.595, p < 0.01) and inversely correlated with Δ8-iso (r = − 0.587, p < 0.01) and with baseline smoking history (r = − 0.39, p < 0.03). No correlation was found between ΔFEV1, ΔCRP and ΔWBCs. By means of hierarchical stepwise multiple linear regression, taking into account other baseline key factors related to FEV1, ΔNrf2, ΔHO-1and ΔGCLC were found to be significant predictors of ΔFEV1, explaining 89.5% of its variance. Conclusions Although our results must be confirmed in larger trial they suggest that the down-regulation of Nrf2/ARE gene expression in PBMCs may be one of the determinants of FEV1 decline and of COPD progression. Therefore the future possibility to counteract Nrf2 decline in COPD patients may help in reducing the negative effects of the oxidative stress-induced progression of the disease.
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6
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Morrow JD, Chase RP, Parker MM, Glass K, Seo M, Divo M, Owen CA, Castaldi P, DeMeo DL, Silverman EK, Hersh CP. RNA-sequencing across three matched tissues reveals shared and tissue-specific gene expression and pathway signatures of COPD. Respir Res 2019; 20:65. [PMID: 30940135 PMCID: PMC6446359 DOI: 10.1186/s12931-019-1032-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 03/25/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Multiple gene expression studies have been performed separately in peripheral blood, lung, and airway tissues to study COPD. We performed RNA-sequencing gene expression profiling of large-airway epithelium, alveolar macrophage and peripheral blood samples from the same subset of COPD cases and controls from the COPDGene study who underwent bronchoscopy at a single center. Using statistical and gene set enrichment approaches, we sought to improve the understanding of COPD by studying gene sets and pathways across these tissues, beyond the individual genomic determinants. METHODS We performed differential expression analysis using RNA-seq data obtained from 63 samples from 21 COPD cases and controls (includes four non-smokers) via the R package DESeq2. We tested associations between gene expression and variables related to lung function, smoking history, and CT scan measures of emphysema and airway disease. We examined the correlation of differential gene expression across the tissues and phenotypes, hypothesizing that this would reveal preserved and private gene expression signatures. We performed gene set enrichment analyses using curated databases and findings from prior COPD studies to provide biological and disease relevance. RESULTS The known smoking-related genes CYP1B1 and AHRR were among the top differential expression results for smoking status in the large-airway epithelium data. We observed a significant overlap of genes primarily across large-airway and macrophage results for smoking and airway disease phenotypes. We did not observe specific genes differentially expressed in all three tissues for any of the phenotypes. However, we did observe hemostasis and immune signaling pathways in the overlaps across all three tissues for emphysema, and amyloid and telomere-related pathways for smoking. In peripheral blood, the emphysema results were enriched for B cell related genes previously identified in lung tissue studies. CONCLUSIONS Our integrative analyses across COPD-relevant tissues and prior studies revealed shared and tissue-specific disease biology. These replicated and novel findings in the airway and peripheral blood have highlighted candidate genes and pathways for COPD pathogenesis.
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Affiliation(s)
- Jarrett D Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA.
| | - Robert P Chase
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Margaret M Parker
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Minseok Seo
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Miguel Divo
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Caroline A Owen
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Peter Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
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Kang J, Kim KT, Lee JH, Kim EK, Kim TH, Yoo KH, Lee JS, Kim WJ, Kim JH, Oh YM. Predicting treatable traits for long-acting bronchodilators in patients with stable COPD. Int J Chron Obstruct Pulmon Dis 2017; 12:3557-3565. [PMID: 29263660 PMCID: PMC5732547 DOI: 10.2147/copd.s151909] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Purpose There is currently no measure to predict a treatability of long-acting β-2 agonist (LABA) or long-acting muscarinic antagonist (LAMA) in patients with chronic obstructive pulmonary disease (COPD). We aimed to build prediction models for the treatment response to these bronchodilators, in order to determine the most responsive medication for patients with COPD. Methods We performed a prospective open-label crossover study, in which each long-acting bronchodilator was given in a random order to 65 patients with stable COPD for 4 weeks, with a 4-week washout period in between. We analyzed 14 baseline clinical traits, expression profiles of 31,426 gene transcripts, and damaged-gene scores of 6,464 genes acquired from leukocytes. The gene expression profiles were measured by RNA microarray and the damaged-gene scores were obtained after DNA exome sequencing. Linear regression analyses were performed to build prediction models after using factor and correlation analyses. Results Using a prediction model for a LABA, traits found associated with the treatment response were post-bronchodilator forced expiratory volume in 1 second, bronchodilator reversibility (BDR) to salbutamol, expression of three genes (CLN8, PCSK5, and SKP2), and damage scores of four genes (EPG5, FNBP4, SCN10A, and SPTBN5) (R2=0.512, p<0.001). Traits associated with the treatment response to a LAMA were COPD assessment test score, BDR, expression of four genes (C1orf115, KIAA1618, PRKX, and RHOQ) and damage scores of three genes (FBN3, FDFT1, and ZBED6) (R2=0.575, p<0.001). The prediction models consisting only of clinical traits appeared too weak to predict the treatment response, with R2=0.231 for the LABA model and R2=0.121 for the LAMA model. Conclusion Adding the expressions of genes and damaged-gene scores to the clinical traits may improve the predictability of treatment response to long-acting bronchodilators.
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Affiliation(s)
- Jieun Kang
- Department of Pulmonology and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul
| | - Ki Tae Kim
- Seoul National University Biomedical Informatics and Systems Biomedical Informatics Research Center, Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul
| | - Ji-Hyun Lee
- Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam
| | - Eun Kyung Kim
- Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam
| | - Tae-Hyung Kim
- Division of Pulmonology, Department of Internal Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri
| | - Kwang Ha Yoo
- Department of Internal Medicine, Konkuk University Hospital, Konkuk University School of Medicine, Seoul
| | - Jae Seung Lee
- Department of Pulmonology and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul
| | - Woo Jin Kim
- Department of Internal Medicine and Environmental Health Center, Kangwon National University Hospital, School of Medicine, Kangwon National University, Chuncheon, South Korea
| | - Ju Han Kim
- Seoul National University Biomedical Informatics and Systems Biomedical Informatics Research Center, Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul
| | - Yeon-Mok Oh
- Department of Pulmonology and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul
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8
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Reinhold D, Morrow JD, Jacobson S, Hu J, Ringel B, Seibold MA, Hersh CP, Kechris KJ, Bowler RP. Meta-analysis of peripheral blood gene expression modules for COPD phenotypes. PLoS One 2017; 12:e0185682. [PMID: 29016655 PMCID: PMC5633174 DOI: 10.1371/journal.pone.0185682] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 09/18/2017] [Indexed: 12/22/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) occurs typically in current or former smokers, but only a minority of people with smoking history develops the disease. Besides environmental factors, genetics is an important risk factor for COPD. However, the relationship between genetics, environment and phenotypes is not well understood. Sample sizes for genome-wide expression studies based on lung tissue have been small due to the invasive nature of sample collection. Increasing evidence for the systemic nature of the disease makes blood a good alternative source to study the disease, but there have also been few large-scale blood genomic studies in COPD. Due to the complexity and heterogeneity of COPD, examining groups of interacting genes may have more relevance than identifying individual genes. Therefore, we used Weighted Gene Co-expression Network Analysis to find groups of genes (modules) that are highly connected. However, module definitions may vary between individual data sets. To alleviate this problem, we used a consensus module definition based on two cohorts, COPDGene and ECLIPSE. We studied the relationship between the consensus modules and COPD phenotypes airflow obstruction and emphysema. We also used these consensus module definitions on an independent cohort (TESRA) and performed a meta analysis involving all data sets. We found several modules that are associated with COPD phenotypes, are enriched in functional categories and are overrepresented for cell-type specific genes. Of the 14 consensus modules, three were strongly associated with airflow obstruction (meta p ≤ 0.0002), and two had some association with emphysema (meta p ≤ 0.06); some associations were stronger in the case-control cohorts, and others in the cases-only subcohorts. Gene Ontology terms that were overrepresented included “immune response” and “defense response.” The cell types whose type-specific genes were overrepresented in modules (p < 0.05) included natural killer cells, dendritic cells, and neutrophils. Together, this is the largest investigation of gene blood expression in COPD with 469 cases in COPDGene, ECLIPSE and TESRA combined, with 6267 genes common to all data sets. Additional, we have 42 and 83 controls in COPDGene and ECLIPSE, respectively.
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Affiliation(s)
- Dominik Reinhold
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Denver, Aurora, Colorado, United States of America
- * E-mail:
| | - Jarrett D. Morrow
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, United States of America
| | - Sean Jacobson
- Department of Medicine, National Jewish Health, Denver, Colorado, United States of America
| | - Junxiao Hu
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Benjamin Ringel
- Center for Genes, Environment and Health, Department of Pediatrics, National Jewish Health, Denver, Colorado, United States of America
| | - Max A. Seibold
- Center for Genes, Environment and Health, Department of Pediatrics, National Jewish Health, Denver, Colorado, United States of America
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Craig P. Hersh
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, United States of America
| | - Katerina J. Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Russell P. Bowler
- Department of Medicine, National Jewish Health, Denver, Colorado, United States of America
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Shi L, Zhu B, Xu M, Wang X. Selection of AECOPD-specific immunomodulatory biomarkers by integrating genomics and proteomics with clinical informatics. Cell Biol Toxicol 2017; 34:109-123. [DOI: 10.1007/s10565-017-9405-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 07/06/2017] [Indexed: 12/14/2022]
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Bhattacharya S, Rosenberg AF, Peterson DR, Grzesik K, Baran AM, Ashton JM, Gill SR, Corbett AM, Holden-Wiltse J, Topham DJ, Walsh EE, Mariani TJ, Falsey AR. Transcriptomic Biomarkers to Discriminate Bacterial from Nonbacterial Infection in Adults Hospitalized with Respiratory Illness. Sci Rep 2017; 7:6548. [PMID: 28747714 PMCID: PMC5529430 DOI: 10.1038/s41598-017-06738-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 06/16/2017] [Indexed: 02/02/2023] Open
Abstract
Lower respiratory tract infection (LRTI) commonly causes hospitalization in adults. Because bacterial diagnostic tests are not accurate, antibiotics are frequently prescribed. Peripheral blood gene expression to identify subjects with bacterial infection is a promising strategy. We evaluated whole blood profiling using RNASeq to discriminate infectious agents in adults with microbiologically defined LRTI. Hospitalized adults with LRTI symptoms were recruited. Clinical data and blood was collected, and comprehensive microbiologic testing performed. Gene expression was measured using RNASeq and qPCR. Genes discriminatory for bacterial infection were identified using the Bonferroni-corrected Wilcoxon test. Constrained logistic models to predict bacterial infection were fit using screened LASSO. We enrolled 94 subjects who were microbiologically classified; 53 as “non-bacterial” and 41 as “bacterial”. RNAseq and qPCR confirmed significant differences in mean expression for 10 genes previously identified as discriminatory for bacterial LRTI. A novel dimension reduction strategy selected three pathways (lymphocyte, α-linoleic acid metabolism, IGF regulation) including eleven genes as optimal markers for discriminating bacterial infection (naïve AUC = 0.94; nested CV-AUC = 0.86). Using these genes, we constructed a classifier for bacterial LRTI with 90% (79% CV) sensitivity and 83% (76% CV) specificity. This novel, pathway-based gene set displays promise as a method to distinguish bacterial from nonbacterial LRTI.
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Affiliation(s)
- Soumyaroop Bhattacharya
- Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, Department of Pediatrics, University of Rochester School Medicine, Rochester, NY, USA
| | - Alex F Rosenberg
- Division of Allergy Immunology & Rheumatology, Department of Medicine, University of Rochester School Medicine, Rochester, NY, USA
| | - Derick R Peterson
- Department of Biostatistics and Computational Biology, University of Rochester School Medicine, Rochester, NY, USA
| | - Katherine Grzesik
- Department of Biostatistics and Computational Biology, University of Rochester School Medicine, Rochester, NY, USA
| | - Andrea M Baran
- Department of Biostatistics and Computational Biology, University of Rochester School Medicine, Rochester, NY, USA
| | - John M Ashton
- Genomics Research Center, University of Rochester School Medicine, Rochester, NY, USA
| | - Steven R Gill
- Genomics Research Center, University of Rochester School Medicine, Rochester, NY, USA
| | - Anthony M Corbett
- Department of Biostatistics and Computational Biology, University of Rochester School Medicine, Rochester, NY, USA
| | - Jeanne Holden-Wiltse
- Department of Biostatistics and Computational Biology, University of Rochester School Medicine, Rochester, NY, USA
| | - David J Topham
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester School Medicine, Rochester, NY, USA.,Department of Microbiology and Immunology, University of Rochester School Medicine, Rochester, NY, USA
| | - Edward E Walsh
- Division of Infectious Diseases, Department of Medicine, University of Rochester School Medicine and Rochester General Hospital, Rochester, NY, USA
| | - Thomas J Mariani
- Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, Department of Pediatrics, University of Rochester School Medicine, Rochester, NY, USA
| | - Ann R Falsey
- Division of Infectious Diseases, Department of Medicine, University of Rochester School Medicine and Rochester General Hospital, Rochester, NY, USA.
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MicroRNA expression profiling defines the impact of electronic cigarettes on human airway epithelial cells. Sci Rep 2017. [PMID: 28439113 DOI: 10.1038/s41598‐017‐01167‐8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
While all forms of tobacco exposure have negative health effects, the significance of exposure to electronic cigarettes (eCig) is not fully understood. Here, we studied the global effects of eCig on the micro RNA (miRNA) transcriptome in human lung epithelial cells. Primary human bronchial epithelial (NHBE) cells differentiated at air-liquid interface were exposed to eCig liquid. Exposure of NHBE to any eCig liquid resulted in the induction of oxidative stress-response genes including GCLM, GCLC, GPX2, NQO1 and HO-1. Vaporization of, and/or the presence of nicotine in, eCig liquid was associated with a greater response. We identified 578 miRNAs dysregulated by eCig exposure in NHBE, and 125 miRNA affected by vaporization of eCig liquid. Nicotine containing eCig vapor displayed the most profound effects upon miRNA expression. We selected 8 miRNAs (29A, 140, 126, 374A, 26A-2, 147B, 941 and 589) for further study. We validated increased expression of multiple miRNAs, including miR126, following eCig exposure. We also found significant reduction in the expression of two miR126 target genes, MYC and MRGPRX3, following exposure. These data demonstrated that eCig exposure has profound effects upon gene expression in human lung epithelial cells, some of which are epigenetically programmed at the level of miRNA regulation.
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12
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MicroRNA expression profiling defines the impact of electronic cigarettes on human airway epithelial cells. Sci Rep 2017; 7:1081. [PMID: 28439113 PMCID: PMC5430826 DOI: 10.1038/s41598-017-01167-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/27/2017] [Indexed: 01/18/2023] Open
Abstract
While all forms of tobacco exposure have negative health effects, the significance of exposure to electronic cigarettes (eCig) is not fully understood. Here, we studied the global effects of eCig on the micro RNA (miRNA) transcriptome in human lung epithelial cells. Primary human bronchial epithelial (NHBE) cells differentiated at air-liquid interface were exposed to eCig liquid. Exposure of NHBE to any eCig liquid resulted in the induction of oxidative stress-response genes including GCLM, GCLC, GPX2, NQO1 and HO-1. Vaporization of, and/or the presence of nicotine in, eCig liquid was associated with a greater response. We identified 578 miRNAs dysregulated by eCig exposure in NHBE, and 125 miRNA affected by vaporization of eCig liquid. Nicotine containing eCig vapor displayed the most profound effects upon miRNA expression. We selected 8 miRNAs (29A, 140, 126, 374A, 26A-2, 147B, 941 and 589) for further study. We validated increased expression of multiple miRNAs, including miR126, following eCig exposure. We also found significant reduction in the expression of two miR126 target genes, MYC and MRGPRX3, following exposure. These data demonstrated that eCig exposure has profound effects upon gene expression in human lung epithelial cells, some of which are epigenetically programmed at the level of miRNA regulation.
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Obeidat M, Nie Y, Chen V, Shannon CP, Andiappan AK, Lee B, Rotzschke O, Castaldi PJ, Hersh CP, Fishbane N, Ng RT, McManus B, Miller BE, Rennard S, Paré PD, Sin DD. Network-based analysis reveals novel gene signatures in peripheral blood of patients with chronic obstructive pulmonary disease. Respir Res 2017; 18:72. [PMID: 28438154 PMCID: PMC5404332 DOI: 10.1186/s12931-017-0558-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 04/20/2017] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) is currently the third leading cause of death and there is a huge unmet clinical need to identify disease biomarkers in peripheral blood. Compared to gene level differential expression approaches to identify gene signatures, network analyses provide a biologically intuitive approach which leverages the co-expression patterns in the transcriptome to identify modules of co-expressed genes. METHODS A weighted gene co-expression network analysis (WGCNA) was applied to peripheral blood transcriptome from 238 COPD subjects to discover co-expressed gene modules. We then determined the relationship between these modules and forced expiratory volume in 1 s (FEV1). In a second, independent cohort of 381 subjects, we determined the preservation of these modules and their relationship with FEV1. For those modules that were significantly related to FEV1, we determined the biological processes as well as the blood cell-specific gene expression that were over-represented using additional external datasets. RESULTS Using WGCNA, we identified 17 modules of co-expressed genes in the discovery cohort. Three of these modules were significantly correlated with FEV1 (FDR < 0.1). In the replication cohort, these modules were highly preserved and their FEV1 associations were reproducible (P < 0.05). Two of the three modules were negatively related to FEV1 and were enriched in IL8 and IL10 pathways and correlated with neutrophil-specific gene expression. The positively related module, on the other hand, was enriched in DNA transcription and translation and was strongly correlated to CD4+, CD8+ T cell-specific gene expression. CONCLUSIONS Network based approaches are promising tools to identify potential biomarkers for COPD. TRIAL REGISTRATION The ECLIPSE study was funded by GlaxoSmithKline, under ClinicalTrials.gov identifier NCT00292552 and GSK No. SCO104960.
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Affiliation(s)
- Ma'en Obeidat
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, 1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada.
| | - Yunlong Nie
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, 1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada
| | - Virginia Chen
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
| | - Casey P Shannon
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
| | | | - Bernett Lee
- Singapore Immunology Network, 8A Biomedical Grove, Singapore, Singapore
| | - Olaf Rotzschke
- Singapore Immunology Network, 8A Biomedical Grove, Singapore, Singapore
| | - Peter J Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, USA
- Division of General Internal Medicine and Primary Care, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, USA
- Pulmonary and Critical Care Division, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Nick Fishbane
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, 1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada
| | - Raymond T Ng
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
| | - Bruce McManus
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, 1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
| | | | - Stephen Rennard
- Division of Pulmonary and Critical Care Medicine, University of Nebraska Medical Center, Omaha, NE, USA
- Clinical Discovery Unit, Early Clinical Development, AstraZeneca, Cambridge, UK
| | - Peter D Paré
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, 1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Don D Sin
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, 1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
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Obeidat M, Ding X, Fishbane N, Hollander Z, Ng RT, McManus B, Tebbutt SJ, Miller BE, Rennard S, Paré PD, Sin DD. The Effect of Different Case Definitions of Current Smoking on the Discovery of Smoking-Related Blood Gene Expression Signatures in Chronic Obstructive Pulmonary Disease. Nicotine Tob Res 2016; 18:1903-9. [PMID: 27154971 PMCID: PMC4978988 DOI: 10.1093/ntr/ntw129] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/26/2016] [Indexed: 11/13/2022]
Abstract
INTRODUCTION Smoking is the number one modifiable environmental risk factor for chronic obstructive pulmonary disease (COPD). Clinical, epidemiological and increasingly "omics" studies assess or adjust for current smoking status using only self-report, which may be inaccurate. Objective measures such as exhaled carbon monoxide (eCO) may also be problematic owing to limitations in the measurements and the relatively short half life of the molecule. In this study, we determined the impact of different case definitions of current cigarette smoking on gene expression in peripheral blood of patients with COPD. METHODS Peripheral blood gene expression from 573 former- and current-smokers with COPD in the ECLIPSE study was used to find genes whose expression was associated with smoking status. Current smoking was defined using self-report, eCO concentrations, or both. Linear regression was used to determine the association of current smoking status with gene expression adjusting for age, sex and propensity score. Pathway enrichment analyses were performed on genes with P < .001. RESULT Using self-report or eCO, only two genes were differentially expressed between current and ex-smokers, with no enrichment in biological processes. When current smoking was defined using both eCO and self-report, four genes were differentially expressed (LRRN3, PID1, FUCA1, GPR15) with enrichment in 40 biological pathways related to metabolic processes, response to hypoxia and hormonal stimulus. Additionally, the combined definition provided better distributions of test statistics for differential gene expression. CONCLUSION A combined phenotype of eCO and self report allows for better discovery of genes and pathways related to current smoking. IMPLICATIONS Studies relying only on self report of smoking status to assess or adjust for the impact of smoking may not fully capture its effect and will lead to residual confounding of results.
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Affiliation(s)
- Ma'en Obeidat
- University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
| | - Xiaoting Ding
- University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
| | - Nick Fishbane
- University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
| | - Zsuzsanna Hollander
- University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada; Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
| | - Raymond T Ng
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada; Department of Computer Science, University of British Columbia Centre, Vancouver, BC, Canada
| | - Bruce McManus
- University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada; Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
| | - Scott J Tebbutt
- University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada; Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
| | | | - Stephen Rennard
- Division of Pulmonary and Critical Care Medicine, University of Nebraska Medical Center, Omaha, NE
| | - Peter D Paré
- University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada; Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Don D Sin
- University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada; Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
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Fratta Pasini AM, Ferrari M, Stranieri C, Vallerio P, Mozzini C, Garbin U, Zambon G, Cominacini L. Nrf2 expression is increased in peripheral blood mononuclear cells derived from mild-moderate ex-smoker COPD patients with persistent oxidative stress. Int J Chron Obstruct Pulmon Dis 2016; 11:1733-43. [PMID: 27555763 PMCID: PMC4968670 DOI: 10.2147/copd.s102218] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Inadequacy of antioxidant nuclear factor-E2-related factor 2 (Nrf2) and endoplasmic reticulum stress-mediated unfolded protein response has been implicated in severe chronic obstructive pulmonary disease (COPD) and cigarette smoking-induced emphysema. As evidence suggests that the ability to upregulate Nrf2 expression may influence the progression of COPD and no data exist up to now in ex-smokers with mild-moderate COPD, this study was first aimed to evaluate Nrf2 and unfolded protein response expression in peripheral blood mononuclear cells (PBMC) of mild-moderate ex-smokers with COPD compared to smoking habit-matched non-COPD subjects. Then, we tested whether oxidative stress persists after cigarette smoking cessation and whether the concentrations of oxidized phospholipids (oxidation products of the phospholipid 1-palmitoyl-2-arachidonyl-sn-glycero-3-phosphorylcholine [oxPAPC]) in the PBMC of the same subjects may have a causative role in determining the upregulation of Nrf2. The expression (mRNA and protein) of Nrf2 and of its related gene heme oxygenase-1 was significantly increased in COPD group without differences in the unfolded protein response. Plasma malondialdehyde, the circulating marker of oxidative stress, and oxPAPC in PBMC were significantly higher in COPD than in non-COPD subjects. The fact that the expression of p47phox, a subunit of NADPH oxidase, was increased in PBMC of COPD patients and that it was directly correlated with oxPAPC may indicate that oxPAPC may be one of the determinants of oxidative stress-induced Nrf2 upregulation. Finally, we also demonstrated that lung function inversely correlated with plasma malondialdehyde and with Nrf2 and heme oxygenase-1 mRNA expression in all subjects. Our results indicate that mild-moderate ex-smokers with COPD may be able to counteract oxidative stress by increasing the expression of Nrf2/antioxidant-response elements. Because Nrf2 failure significantly contributes to the development of COPD, our findings suggest that the possibility to prevent Nrf2 reduction may open a new scenario in helping to prevent the oxidative stress-associated lung function decline.
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Affiliation(s)
| | - Marcello Ferrari
- Department of Medicine, Unit of Respiratory Diseases, University of Verona, Verona, Italy
| | | | | | | | - Ulisse Garbin
- Department of Medicine, Section of Internal Medicine
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Grunig G, Baghdassarian A, Park SH, Pylawka S, Bleck B, Reibman J, Berman-Rosenzweig E, Durmus N. Challenges and Current Efforts in the Development of Biomarkers for Chronic Inflammatory and Remodeling Conditions of the Lungs. Biomark Insights 2016; 10:59-72. [PMID: 26917944 PMCID: PMC4756863 DOI: 10.4137/bmi.s29514] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 10/14/2015] [Accepted: 10/18/2015] [Indexed: 02/06/2023] Open
Abstract
This review discusses biomarkers that are being researched for their usefulness to phenotype chronic inflammatory lung diseases that cause remodeling of the lung's architecture. The review focuses on asthma, chronic obstructive pulmonary disease (COPD), and pulmonary hypertension. Bio-markers of environmental exposure and specific classes of biomarkers (noncoding RNA, metabolism, vitamin, coagulation, and microbiome related) are also discussed. Examples of biomarkers that are in clinical use, biomarkers that are under development, and biomarkers that are still in the research phase are discussed. We chose to present examples of the research in biomarker development by diseases, because asthma, COPD, and pulmonary hypertension are distinct entities, although they clearly share processes of inflammation and remodeling.
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Affiliation(s)
- Gabriele Grunig
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, USA.; Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Aram Baghdassarian
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, USA
| | - Sung-Hyun Park
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, USA
| | - Serhiy Pylawka
- College of Dental Medicine, Columbia University, New York, NY, USA
| | - Bertram Bleck
- Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Joan Reibman
- Department of Medicine, New York University School of Medicine, New York, NY, USA
| | | | - Nedim Durmus
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, USA
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Lysosome and Cytoskeleton Pathways Are Robustly Enriched in the Blood of Septic Patients: A Meta-Analysis of Transcriptomic Data. Mediators Inflamm 2015; 2015:984825. [PMID: 26063982 PMCID: PMC4430672 DOI: 10.1155/2015/984825] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 03/27/2015] [Accepted: 04/01/2015] [Indexed: 12/12/2022] Open
Abstract
Background. Sepsis is a leading cause of mortality in intensive care units worldwide. A better understanding of the blood systems response to sepsis should expedite the identification of biomarkers for early diagnosis and therapeutic interventions. Methods. We analyzed microarray studies whose data is available from the GEO repository and which were performed on the whole blood of septic patients and normal controls. Results. We identified 6 cohorts consisting of 450 individuals (sepsis = 323, control = 127) providing genome-wide messenger RNA (mRNA) expression data. Through meta-analysis we found the “Lysosome” and “Cytoskeleton” pathways were upregulated in human sepsis patients relative to controls, in addition to previously known signaling pathways (including MAPK, TLR). The key regulatory genes in the “Lysosome” pathway include lysosomal acid hydrolases (e.g., protease cathepsin A, D) as well as the major (LAMP1, 2) and minor (SORT1, LAPTM4B) membrane proteins. In contrast, pathways related to “Ribosome”, “Spliceosome” and “Cell adhesion molecules” were found to be downregulated, along with known pathways for immune dysfunction. Overall, our study revealed distinct mRNA activation profiles and protein-protein interaction networks in blood of human sepsis. Conclusions. Our findings suggest that aberrant mRNA expression in the lysosome and cytoskeleton pathways may play a pivotal role in the molecular pathobiology of human sepsis.
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Pniewska E, Sokolowska M, Kupryś-Lipińska I, Kacprzak D, Kuna P, Pawliczak R. Exacerbating factors induce different gene expression profiles in peripheral blood mononuclear cells from asthmatics, patients with chronic obstructive pulmonary disease and healthy subjects. Int Arch Allergy Immunol 2015; 165:229-43. [PMID: 25634111 DOI: 10.1159/000370067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 11/21/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Despite several common phenotypic features, chronic obstructive pulmonary disease (COPD) and severe asthma differ with regard to their causative factors and pathophysiology. Both diseases may be exacerbated by environmental factors, however, the molecular profiles of disease episodes have not been comprehensively studied. We identified differences in gene and protein expression profiles expressed by peripheral blood mononuclear cells (PBMC) of COPD patients, patients with atopic asthma and healthy subjects when challenged with exacerbating factors in vitro: lipopolysaccharide (LPS), house dust mite (HDM) and cat allergen. METHODS PBMC isolated from patients with severe atopic asthma and COPD, as well as healthy subjects were stimulated with rDer p 1 DG, rFel d 1 DG and LPS. The changes in the expression of 47 genes belonging to five groups (phospholipase A2, eicosanoids, transcription factors, cytokines and airway remodeling) were studied using TaqMan low density array cards. Immunoblotting was used to study relative protein expression. RESULTS rDer p 1 significantly up-regulated the expression of PLA2G4A, PLA2G6, PLA2G15, CYSLTR1, LB4R2, PTGS1, PTGS2, FOXP1, GATA3, HDAC2, IREB2, PPARG, STAT4, TSLP and CHI3L1 genes in asthmatics in comparison to healthy subjects. LPS induced significant expression of ANXA1 and LTA4H in asthmatics when compared to COPD patients and healthy subjects. SOX6,STAT4 and IL1RL1 were induced in COPD after LPS stimulation. Analysis of protein expression revealed a pattern similar to mRNA expression. CONCLUSIONS LPS-induced exacerbation of asthma and COPD is characterized by differential expression of selected genes in PBMC. HDM allergen changed the expression profile of inflammatory genes between patients with asthma of atopic origin and healthy controls.
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Affiliation(s)
- Ewa Pniewska
- Division of Allergology, Immunology and Dermatology, Department of Immunopathology, Faculty of Biomedical Sciences and Postgraduate Training, Medical University of Lodz, Lodz, Poland
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20
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Morrow JD, Qiu W, Chhabra D, Rennard SI, Belloni P, Belousov A, Pillai SG, Hersh CP. Identifying a gene expression signature of frequent COPD exacerbations in peripheral blood using network methods. BMC Med Genomics 2015; 8:1. [PMID: 25582225 PMCID: PMC4302028 DOI: 10.1186/s12920-014-0072-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 12/12/2014] [Indexed: 12/11/2022] Open
Abstract
Background Exacerbations of chronic obstructive pulmonary disease (COPD), characterized by acute deterioration in symptoms, may be due to bacterial or viral infections, environmental exposures, or unknown factors. Exacerbation frequency may be a stable trait in COPD patients, which could imply genetic susceptibility. Observing the genes, networks, and pathways that are up- and down-regulated in COPD patients with differing susceptibility to exacerbations will help to elucidate the molecular signature and pathogenesis of COPD exacerbations. Methods Gene expression array and plasma biomarker data were obtained using whole-blood samples from subjects enrolled in the Treatment of Emphysema With a Gamma-Selective Retinoid Agonist (TESRA) study. Linear regression, weighted gene co-expression network analysis (WGCNA), and pathway analysis were used to identify signatures and network sub-modules associated with the number of exacerbations within the previous year; other COPD-related phenotypes were also investigated. Results Individual genes were not found to be significantly associated with the number of exacerbations. However using network methods, a statistically significant gene module was identified, along with other modules showing moderate association. A diverse signature was observed across these modules using pathway analysis, marked by differences in B cell and NK cell activity, as well as cellular markers of viral infection. Within two modules, gene set enrichment analysis recapitulated the molecular signatures of two gene expression experiments; one involving sputum from asthma exacerbations and another involving viral lung infections. The plasma biomarker myeloperoxidase (MPO) was associated with the number of recent exacerbations. Conclusion A distinct signature of COPD exacerbations may be observed in peripheral blood months following the acute illness. While not predictive in this cross-sectional analysis, these results will be useful in uncovering the molecular pathogenesis of COPD exacerbations. Electronic supplementary material The online version of this article (doi:10.1186/s12920-014-0072-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jarrett D Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA.
| | - Weiliang Qiu
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA.
| | - Divya Chhabra
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA. .,Division of Biomedical Informatics, University of California, San Diego, CA, USA.
| | | | - Paula Belloni
- Genentech, Member of the Roche Group, South San Francisco, CA, USA.
| | | | - Sreekumar G Pillai
- Hoffman La Roche, Nutley, NJ, USA. .,Current address: Eli Lilly and Company, Indianapolis, IN, USA.
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA.
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Personalized Management of Pulmonary Disorders. TEXTBOOK OF PERSONALIZED MEDICINE 2015. [PMCID: PMC7121715 DOI: 10.1007/978-1-4939-2553-7_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
There are a large number of pulmonary disorders some of which present challenges in management. Role of genetic ancestry in lung function is under investigation. There is still limited information on pharmacogenomics and pharmacogenetics of pulmonary therapeutics. Personalized approaches to some pulmonary diseases will be described briefly as examples in this chapter.
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Wu X, Sun X, Chen C, Bai C, Wang X. Dynamic gene expressions of peripheral blood mononuclear cells in patients with acute exacerbation of chronic obstructive pulmonary disease: a preliminary study. Crit Care 2014; 18:508. [PMID: 25407108 PMCID: PMC4305227 DOI: 10.1186/s13054-014-0508-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 08/26/2014] [Indexed: 01/09/2023] Open
Abstract
INTRODUCTION Acute exacerbation of chronic obstructive pulmonary disease (AECOPD) is a serious event that is responsible for the progress of the disease, increases in medical costs and high mortality. METHODS The aim of the present study was to identify AECOPD-specific biomarkers by evaluating the dynamic gene expression profiling of peripheral blood mononuclear cells (PBMCs) from patients with AECOPD on days 1, 3 and 10 after hospital admission and to compare the derived data with data from healthy controls or patients with stable COPD. RESULTS We found that 14 genes were co-differentially upregulated and 2 downregulated greater than 10-fold in patients with COPD or AECOPD compared with the healthy individuals. Eight co-differentially upregulated genes and six downregulated genes were identified as a panel of AECOPD-specific genes. Downregulation of TCF7 in PBMCs was found to be associated with the severity of COPD. Dynamic changes of Aminolevulinate-delta-synthase 2 and carbonic anhydrase I had similar patterns of Digital Evaluation Score System scores and may serve as potential genes of interest during the course of AECOPD. CONCLUSION Thus, our findings indicate a panel of altered gene expression patterns in PBMCs that can be used as AECOPD-specific dynamic biomarkers to monitor the course of AECOPD.
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Affiliation(s)
- Xiaodan Wu
- Department of Respiratory Medicine, Zhongshan Hospital, Fudan University, Fenglin Rd. No180, 200032, Shanghai, China.
| | - Xiaoru Sun
- Department of Respiratory Medicine, Wenzhou Medical University and The First Hospital, Nanbaixiang, 325000, Wenzhou, China.
| | - Chengshui Chen
- Department of Respiratory Medicine, Wenzhou Medical University and The First Hospital, Nanbaixiang, 325000, Wenzhou, China.
| | - Chunxue Bai
- Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Clinical Bioinformatics, Shanghai Respiratory Research Medicine, Fenglin Rd. No 180, 200032, Shanghai, China.
| | - Xiangdong Wang
- Department of Respiratory Medicine, Wenzhou Medical University and The First Hospital, Nanbaixiang, 325000, Wenzhou, China.
- Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Clinical Bioinformatics, Shanghai Respiratory Research Medicine, Fenglin Rd. No 180, 200032, Shanghai, China.
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23
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Singh D, Fox SM, Tal-Singer R, Bates S, Riley JH, Celli B. Altered gene expression in blood and sputum in COPD frequent exacerbators in the ECLIPSE cohort. PLoS One 2014; 9:e107381. [PMID: 25265030 PMCID: PMC4179270 DOI: 10.1371/journal.pone.0107381] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 08/14/2014] [Indexed: 11/27/2022] Open
Abstract
Patients with chronic obstructive pulmonary disease (COPD) who are defined as frequent exacerbators suffer with 2 or more exacerbations every year. The molecular mechanisms responsible for this phenotype are poorly understood. We investigated gene expression profile patterns associated with frequent exacerbations in sputum and blood cells in a well-characterised cohort. Samples from subjects from the ECLIPSE COPD cohort were used; sputum and blood samples from 138 subjects were used for microarray gene expression analysis, while blood samples from 438 subjects were used for polymerase chain reaction (PCR) testing. Using microarray, 150 genes were differentially expressed in blood (>±1.5 fold change, p≤0.01) between frequent compared to non-exacerbators. In sputum cells, only 6 genes were differentially expressed. The differentially regulated genes in blood included downregulation of those involved in lymphocyte signalling and upregulation of pro-apoptotic signalling genes. Multivariate analysis of the microarray data followed by confirmatory PCR analysis identified 3 genes that predicted frequent exacerbations; B3GNT, LAF4 and ARHGEF10. The sensitivity and specificity of these 3 genes to predict the frequent exacerbator phenotype was 88% and 33% respectively. There are alterations in systemic immune function associated with frequent exacerbations; down-regulation of lymphocyte function and a shift towards pro-apoptosis mechanisms are apparent in patients with frequent exacerbations.
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Affiliation(s)
- Dave Singh
- University of Manchester, Medicines Evaluation Unit, Manchester, United Kingdom
- * E-mail:
| | - Steven M. Fox
- GlaxoSmithKline, Medicines Research Centre, Stevenage, United Kingdom
| | - Ruth Tal-Singer
- GlaxoSmithKline, King of Prussia, Pennsylvania, United States of America
| | - Stewart Bates
- GlaxoSmithKline, Medicines Research Centre, Stevenage, United Kingdom
| | - John H. Riley
- GlaxoSmithKline, Stockley Park, Uxbridge, United Kingdom
| | - Bartolome Celli
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
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24
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Hobbs BD, Hersh CP. Integrative genomics of chronic obstructive pulmonary disease. Biochem Biophys Res Commun 2014; 452:276-86. [PMID: 25078622 PMCID: PMC4172635 DOI: 10.1016/j.bbrc.2014.07.086] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 07/18/2014] [Indexed: 01/21/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is a complex disease with both environmental and genetic determinants, the most important of which is cigarette smoking. There is marked heterogeneity in the development of COPD among persons with similar cigarette smoking histories, which is likely partially explained by genetic variation. Genomic approaches such as genomewide association studies and gene expression studies have been used to discover genes and molecular pathways involved in COPD pathogenesis; however, these "first generation" omics studies have limitations. Integrative genomic studies are emerging which can combine genomic datasets to further examine the molecular underpinnings of COPD. Future research in COPD genetics will likely use network-based approaches to integrate multiple genomic data types in order to model the complex molecular interactions involved in COPD pathogenesis. This article reviews the genomic research to date and offers a vision for the future of integrative genomic research in COPD.
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Affiliation(s)
- Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, United States; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, United States; Harvard Medical School, Boston, MA, United States
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, United States; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, United States; Harvard Medical School, Boston, MA, United States.
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25
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Faner R, Gonzalez N, Cruz T, Kalko SG, Agustí A. Systemic inflammatory response to smoking in chronic obstructive pulmonary disease: evidence of a gender effect. PLoS One 2014; 9:e97491. [PMID: 24830457 PMCID: PMC4022517 DOI: 10.1371/journal.pone.0097491] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 04/18/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Tobacco smoking is the main risk factor of chronic obstructive pulmonary disease (COPD) but not all smokers develop the disease. An abnormal pulmonary and systemic inflammatory response to smoking is thought to play a major pathogenic role in COPD, but this has never been tested directly. METHODS We studied the systemic biomarker and leukocyte transcriptomic response (Affymetrix microarrays) to smoking exposure in 10 smokers with COPD and 10 smokers with normal spirometry. We also studied 10 healthy never smokers (not exposed to smoking) as controls. Because some aspects of COPD may differ in males and females, and the inflammatory response to other stressors (infection) might be different in man and women, we stratified participant recruitment by sex. Differentially expressed genes were validated by q-PCR. Ontology enrichment was evaluated and interaction networks inferred. RESULTS Principal component analysis identified sex differences in the leukocyte transcriptomic response to acute smoking. In both genders, we identified genes that were differentially expressed in response to smoking exclusively in COPD patients (COPD related signature) or smokers with normal spirometry (Smoking related signature), their ontologies and interaction networks. CONCLUSIONS The use of an experimental intervention (smoking exposure) to investigate the transcriptomic response of peripheral leukocytes in COPD is a step beyond the standard case-control transcriptomic profiling carried out so far, and has facilitated the identification of novel COPD and Smoking expression related signatures which differ in males and females.
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Affiliation(s)
- Rosa Faner
- Fundació Privada Clínic per a la Recerca Biomèdica, Barcelona, Spain
- Institut d'investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Barcelona, Spain
| | - Nuria Gonzalez
- Fundació Privada Clínic per a la Recerca Biomèdica, Barcelona, Spain
| | - Tamara Cruz
- Fundació Privada Clínic per a la Recerca Biomèdica, Barcelona, Spain
- Institut d'investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | - Alvar Agustí
- Fundació Privada Clínic per a la Recerca Biomèdica, Barcelona, Spain
- Institut d'investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Barcelona, Spain
- Thorax Institute, Hospital Clinic, University of Barcelona, Barcelona, Spain
- Fundació de Investigació Sanitaria Illes Balears (FISIB), Mallorca, Spain
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26
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Bahr TM, Hughes GJ, Armstrong M, Reisdorph R, Coldren CD, Edwards MG, Schnell C, Kedl R, LaFlamme DJ, Reisdorph N, Kechris KJ, Bowler RP. Peripheral blood mononuclear cell gene expression in chronic obstructive pulmonary disease. Am J Respir Cell Mol Biol 2013; 49:316-23. [PMID: 23590301 DOI: 10.1165/rcmb.2012-0230oc] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Although most cases of chronic obstructive pulmonary disease (COPD) occur in smokers, only a fraction of smokers develop the disease. We hypothesized distinct molecular signatures for COPD and emphysema in the peripheral blood mononuclear cells (PBMCs) of current and former smokers. To test this hypothesis, we identified and validated PBMC gene expression profiles in smokers with and without COPD. We generated expression data on 136 subjects from the COPDGene study, using Affymetrix U133 2.0 microarrays (Affymetrix, Santa Clara, CA). Multiple linear regression with adjustment for covariates (gender, age, body mass index, family history, smoking status, and pack-years) was used to identify candidate genes, and ingenuity pathway analysis was used to identify candidate pathways. Candidate genes were validated in 149 subjects according to multiplex quantitative real-time polymerase chain reaction, which included 75 subjects not previously profiled. Pathways that were differentially expressed in subjects with COPD and emphysema included those that play a role in the immune system, inflammatory responses, and sphingolipid (ceramide) metabolism. Twenty-six of the 46 candidate genes (e.g., FOXP1, TCF7, and ASAH1) were validated in the independent cohort. Plasma metabolomics was used to identify a novel glycoceramide (galabiosylceramide) as a biomarker of emphysema, supporting the genomic association between acid ceramidase (ASAH1) and emphysema. COPD is a systemic disease whose gene expression signatures in PBMCs could serve as novel diagnostic or therapeutic targets.
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Affiliation(s)
- Timothy M Bahr
- Department of Biostatistics and Informatics, University of Colorado at Denver, Aurora, CO, USA
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Mariani TJ, Martinez F. Chronic obstructive pulmonary disease genomics: yesterday, discovering population biomarkers; tomorrow, defining disease clusters. Am J Respir Crit Care Med 2013; 187:900-2. [PMID: 23634854 DOI: 10.1164/rccm.201302-0340ed] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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28
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Almansa R, Socias L, Sanchez-Garcia M, Martín-Loeches I, del Olmo M, Andaluz-Ojeda D, Bobillo F, Rico L, Herrero A, Roig V, San-Jose CA, Rosich S, Barbado J, Disdier C, de Lejarazu RO, Gallegos MC, Fernandez V, Bermejo-Martin JF. Critical COPD respiratory illness is linked to increased transcriptomic activity of neutrophil proteases genes. BMC Res Notes 2012; 5:401. [PMID: 22852767 PMCID: PMC3475085 DOI: 10.1186/1756-0500-5-401] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 07/24/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene expression profiling (GEP) in cells obtained from peripheral blood has shown that this is a very useful approach for biomarker discovery and for studying molecular pathogenesis of prevalent diseases. While there is limited literature available on gene expression markers associated with Chronic Obstructive Pulmonary Disease (COPD), the transcriptomic picture associated with critical respiratory illness in this disease is not known at the present moment. FINDINGS By using Agilent microarray chips, we have profiled gene expression signatures in the whole blood of 28 COPD patients hospitalized with different degrees of respiratory compromise.12 of them needed of admission to the ICU, whilst 16 were admitted to the Respiratory Medicine Service. GeneSpring GX 11.0 software was used for performing statistical comparisons of transcript levels between ICU and non-ICU patients. Ingenuity pathway analysis 8.5 (IPA) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to select, annotate and visualize genes by function and pathway (gene ontology). T-test showed evidence of 1501 genes differentially expressed between ICU and non-ICU patients. IPA and KEGG analysis of the most representative biological functions revealed that ICU patients had increased levels of neutrophil gene transcripts, being [cathepsin G (CTSG)], [elastase, neutrophil expressed (ELANE)], [proteinase 3 (PRTN3)], [myeloperoxidase (MPO)], [cathepsin D (CTSD)], [defensin, alpha 3, neutrophil-specific (DEFA3)], azurocidin 1 (AZU1)], and [bactericidal/permeability-increasing protein (BPI)] the most representative ones. Proteins codified by these genes form part of the azurophilic granules of neutrophils and are involved in both antimicrobial defence and tissue damage. This "neutrophil signature" was paralleled by the necessity of advanced respiratory and vital support, and the presence of bacterial infection. CONCLUSION Study of transcriptomic signatures in blood suggests an essential role of neutrophil proteases in COPD patients with critical respiratory illness. Measurement and modulation of the expression of these genes could present an option for clinical monitoring and treatment of severe COPD exacerbations.
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Affiliation(s)
- Raquel Almansa
- Investigación Biomédica del Clínico (ibC), Hospital Clínico Universitario de Valladolid, Avda Ramón y Cajal 3, 47005 Valladolid, Spain
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29
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Zheng Y, Bai C, Wang X. Potential significance of telocytes in the pathogenesis of lung diseases. Expert Rev Respir Med 2012; 6:45-9. [PMID: 22283578 DOI: 10.1586/ers.11.91] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Multiple cells play critical roles in the pathogenesis of lung diseases, even though the exact mechanisms are still not clear. Telocytes are characterized by telopodes, which are thin and long prolongations, and a small amount of cytoplasm rich with mitochondria, as shown by immune-positive staining against CD34, c-kit and vimentin. Telocytes have been found in many organs of mammals, including the trachea and lung. This report summarizes the latest findings associated with telocytes, with a special focus on the lung, and demonstrates that telocytes exist in the smooth muscle layer under cartilage and bronchiole in the lung, and also in the interstitial space of alveoli. Telocytes have a mediate connection with epithelial cells and direct connection with smooth muscle cells both in blood vessels and bronchiole in the lung. Telocytes also have a close relationship with other cell types, such as immune cells and stem cells. Telopodes appear with dichotomous branching and alternation of podom and podomer, forming a 3D network structure with complex homo- and hetero-cellular junctions. All characteristics of telocytes in lung tissue indicate that telocytes may play a potential, but important, role in the pathogenesis of lung diseases.
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Affiliation(s)
- Yonghua Zheng
- Zhongshan Hospital, Fudan University, Shanghai, China
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