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Application of ‘omics technologies to biomarker discovery in inflammatory lung diseases

Craig E. Wheelock, Victoria M. Goss, David Balgoma, Ben Nicholas, Joost Brandsma, Paul J. Skipp, Stuart Snowden, Arnaldo D'Amico, Ildiko Horvath, Amphun Chaiboonchoe, Hassan Ahmed, Stéphane Ballereau, Christos Rossios, Kian Fan Chung, Paolo Montuschi, Stephen J. Fowler, Ian M. Adcock, Anthony D. Postle, Sven-Erik Dahlén, Anthony Rowe, Peter J. Sterk, Charles Auffray, Ratko Djukanović, the U-BIOPRED Study Group
European Respiratory Journal 2012; DOI: 10.1183/09031936.00078812
Craig E. Wheelock
*Dept of Medical Biochemistry and Biophysics, Division of Physiological Chemistry II, Karolinska Institutet, Stockholm, Sweden
#Centre for Allergy Research, Karolinska Institutet, Stockholm, Sweden;
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Victoria M. Goss
¶Clinical and Experimental Sciences, University of Southampton Faculty of Medicine and NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom;
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David Balgoma
*Dept of Medical Biochemistry and Biophysics, Division of Physiological Chemistry II, Karolinska Institutet, Stockholm, Sweden
#Centre for Allergy Research, Karolinska Institutet, Stockholm, Sweden;
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Ben Nicholas
¶Clinical and Experimental Sciences, University of Southampton Faculty of Medicine and NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom;
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Joost Brandsma
¶Clinical and Experimental Sciences, University of Southampton Faculty of Medicine and NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom;
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Paul J. Skipp
+Centre for Biological Sciences, University of Southampton Faculty of Natural and Environmental Sciences and Centre for Proteomic Research, Southampton, United Kingdom;
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Stuart Snowden
*Dept of Medical Biochemistry and Biophysics, Division of Physiological Chemistry II, Karolinska Institutet, Stockholm, Sweden
#Centre for Allergy Research, Karolinska Institutet, Stockholm, Sweden;
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Arnaldo D'Amico
§Dept of Electronic Engineering, University of Rome "Tor Vergata", Rome, Italy;
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Ildiko Horvath
fDept of Pulmonology, Semmelweis University, Budapest Dios arok 1/C, H-1125, Hungary;
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Amphun Chaiboonchoe
**CNRS Institute of Biological Sciences, European Institute for Systems Biology & Medicine, Claude Bernard University, Lyon, France;
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Hassan Ahmed
**CNRS Institute of Biological Sciences, European Institute for Systems Biology & Medicine, Claude Bernard University, Lyon, France;
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Stéphane Ballereau
**CNRS Institute of Biological Sciences, European Institute for Systems Biology & Medicine, Claude Bernard University, Lyon, France;
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Christos Rossios
##Airways Disease, National Heart & Lung Institute, Imperial College London, United Kingdom;
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Kian Fan Chung
##Airways Disease, National Heart & Lung Institute, Imperial College London, United Kingdom;
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Paolo Montuschi
¶¶Dept of Pharmacology, Faculty of Medicine, Catholic University of the Sacred Heart, Rome, Italy;
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Stephen J. Fowler
++Lecturer and Honorary Consultant in Respiratory Medicine, University of Manchester and Lancashire Teaching Hospitals NHS Foundation Trust, Respiratory Research Group, Education and Research Centre, Wythenshawe Hospital, Manchester, United Kingdom;
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Ian M. Adcock
##Airways Disease, National Heart & Lung Institute, Imperial College London, United Kingdom;
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Anthony D. Postle
¶Clinical and Experimental Sciences, University of Southampton Faculty of Medicine and NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom;
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Sven-Erik Dahlén
#Centre for Allergy Research, Karolinska Institutet, Stockholm, Sweden;
§§Unit for Experimental Asthma and Allergy Research, Karolinska Institutet, Stockholm, Sweden;
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Anthony Rowe
ffJanssen Research and Development Ltd, High Wycombe, UK
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Peter J. Sterk
***Dept of Respiratory Medicine, Academic Medical Center University of Amsterdam, Amsterdam, The Netherlands
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Charles Auffray
**CNRS Institute of Biological Sciences, European Institute for Systems Biology & Medicine, Claude Bernard University, Lyon, France;
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Ratko Djukanović
¶Clinical and Experimental Sciences, University of Southampton Faculty of Medicine and NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom;
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  • For correspondence: R.Djukanovic@soton.ac.uk
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Abstract

Inflammatory lung diseases are highly complex in respect of pathogenesis and relationships between inflammation, clinical disease and response to treatment. Sophisticated large-scale analytical methods to quantify gene expression (transcriptomics), proteins (proteomics), lipids (lipidomics) and metabolites (metabolomics) in the lungs, blood and urine are now available to identify biomarkers that define disease in terms of combined clinical, physiological and patho-biological abnormalities. The aspiration is that these approaches will improve diagnosis, i.e., define pathological phenotypes, and facilitate the monitoring of disease and therapy and, also, unravel underlying molecular pathways. Biomarker studies can either select pre-defined biomarker(s) measured by specific methods or apply an “unbiased” approach involving detection platforms that are indiscriminate in focus. This article reviews the technologies presently available to study biomarkers of lung disease within the ‘omics field. The contributions of the individual ‘omics analytical platforms to the field of respiratory diseases are summarised, with the goal of providing background on their respective abilities to contribute to systems medicine-based studies of lung disease.

  • Asthma
  • lipidomics
  • lung disease
  • metabolomics
  • proteomics
  • systems biology
  • systems medicine
  • transcriptomics
  • ERS
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Vol 62 Issue 5 Table of Contents
European Respiratory Journal: 62 (5)
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Application of ‘omics technologies to biomarker discovery in inflammatory lung diseases
Craig E. Wheelock, Victoria M. Goss, David Balgoma, Ben Nicholas, Joost Brandsma, Paul J. Skipp, Stuart Snowden, Arnaldo D'Amico, Ildiko Horvath, Amphun Chaiboonchoe, Hassan Ahmed, Stéphane Ballereau, Christos Rossios, Kian Fan Chung, Paolo Montuschi, Stephen J. Fowler, Ian M. Adcock, Anthony D. Postle, Sven-Erik Dahlén, Anthony Rowe, Peter J. Sterk, Charles Auffray, Ratko Djukanović, the U-BIOPRED Study Group
European Respiratory Journal Jan 2012, erj00788-2012; DOI: 10.1183/09031936.00078812

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Application of ‘omics technologies to biomarker discovery in inflammatory lung diseases
Craig E. Wheelock, Victoria M. Goss, David Balgoma, Ben Nicholas, Joost Brandsma, Paul J. Skipp, Stuart Snowden, Arnaldo D'Amico, Ildiko Horvath, Amphun Chaiboonchoe, Hassan Ahmed, Stéphane Ballereau, Christos Rossios, Kian Fan Chung, Paolo Montuschi, Stephen J. Fowler, Ian M. Adcock, Anthony D. Postle, Sven-Erik Dahlén, Anthony Rowe, Peter J. Sterk, Charles Auffray, Ratko Djukanović, the U-BIOPRED Study Group
European Respiratory Journal Jan 2012, erj00788-2012; DOI: 10.1183/09031936.00078812
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