{
  "abstract": "Introduction Sarcoidosis is a multisystem disorder with variable presentation and disease course. Diagnosis requires the exclusion of other causes of granulomatous inflammation. Current clinical management is often fraught with diagnostic uncertainy and the lack of tools to predict pulmonary disease progression. To address these challenges, we designed a study using data from bronchoalveolar lavage (BAL) fluid and cells to develop diagnostic and prognostic tools in patients with pulmonary sarcoidosis.Methods and Analysis This multicentre study will include discovery and validation cohorts of healthy controls, interstitial lung disease controls and pulmonary sarcoidosis cases from three study sites. Sarcoidosis participants will be grouped into progressive and non-progressive pulmonary disease based on changes in pulmonary function testing, chest radiographs or treatment requirements. The discovery cohort consists of participants with existing BAL fluid, BAL cells, and clinical datasets; the validation cohort will be prospectively enrolled and participants will consent for BAL collection from either a clinical or research bronchoscopy. Untargeted proteomic profiling of BALF along with statistical modelling with variable selection techniques will generate a classifier for diagnosis and prognosis. Targeted proteomics using parallel reaction monitoring–mass spectrometry will be used for internal and external validation. Additionally, BAL cell single-cell gene-expression analysis using Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) will be integrated with proteome-wide data to elucidate cell-specific pathways implicated in the development and progression of sarcoidosis.Ethics and Dissemination The study will be conducted in accordance with Good Clinical Practice and the Declaration of Helsinki. The protocol has been approved by the Biomedical Research Alliance of New York Institutional Review Board (IRB), which serves as the single IRB across all study sites. The findings of this study will be presented as abstracts at scientific meetings and summarised in peer-reviewed journal manuscripts.",
  "authors": [
    {
      "affiliations": [
        "Division of Pulmonary and Critical Care Medicine, The Ohio State University, Columbus, Ohio, USA",
        "Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Minnesota Medical School, Minneapolis, Minnesota, USA"
      ],
      "name": "Maneesh Bhargava"
    },
    {
      "affiliations": [
        "Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Minnesota Medical School, Minneapolis, Minnesota, USA",
        "Department of Biochemistry, Molecular Biology and Biophysics, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota, USA"
      ],
      "name": "Danielle O Weise"
    },
    {
      "affiliations": [
        "Division of Environmental and Occupational Health Sciences, National Jewish Health, Denver, Colorado, USA"
      ],
      "name": "Briana Q Barkes"
    },
    {
      "affiliations": [
        "Department of Biochemistry, Molecular Biology and Biophysics, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota, USA"
      ],
      "name": "Pratik D Jagtap"
    },
    {
      "affiliations": [
        "Department of Biochemistry, Molecular Biology and Biophysics, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota, USA"
      ],
      "name": "Subina Mehta"
    },
    {
      "affiliations": [
        "Division of Biostatistics and Health Data Science, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA"
      ],
      "name": "Eric F Lock"
    },
    {
      "affiliations": [
        "Division of Biostatistics and Health Data Science, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA"
      ],
      "name": "Bhargob Kakoty"
    },
    {
      "affiliations": [
        "Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Minnesota Medical School, Minneapolis, Minnesota, USA"
      ],
      "name": "David M Perlman"
    },
    {
      "affiliations": [
        "Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Minnesota Medical School, Minneapolis, Minnesota, USA"
      ],
      "name": "Erhan H Dincer"
    },
    {
      "affiliations": [
        "Division of Environmental and Occupational Health Sciences, National Jewish Health, Denver, Colorado, USA",
        "Division of Pulmonary and Critical Care Sciences, University of Colorado, Denver, Colorado, USA"
      ],
      "name": "Clara I Restrepo"
    },
    {
      "affiliations": [
        "Department of Biochemistry, Molecular Biology and Biophysics, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota, USA"
      ],
      "name": "Timothy J Griffin"
    },
    {
      "affiliations": [
        "Department of Immunology and Genomic Medicine, Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA",
        "Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado, USA"
      ],
      "name": "Tasha E Fingerlin"
    },
    {
      "affiliations": [
        "Division of Environmental and Occupational Health Sciences, National Jewish Health, Denver, Colorado, USA",
        "Division of Pulmonary and Critical Care Sciences, University of Colorado, Denver, Colorado, USA"
      ],
      "name": "Li Li"
    },
    {
      "affiliations": [
        "Health Partners Institute, Saint Paul, Minnesota, USA"
      ],
      "name": "Melissa King-Biggs"
    },
    {
      "affiliations": [
        "Division of Environmental and Occupational Health Sciences, National Jewish Health, Denver, Colorado, USA",
        "Department of Environmental and Occupational Health, Colorado School of Public Health, Aurora, Colorado, USA",
        "Division of Pulmonary and Critical Care Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA"
      ],
      "name": "Lisa A Maier"
    }
  ],
  "title": "Comprehensive proteomic classifier for molecular characterisation of pulmonary sarcoidosis: protocol for a longitudinal multi-centre study to evaluate bronchoalveolar fluid and cell diagnostic and prognostic biomarkers of pulmonary sarcoidosis",
  "uid": "ea69e930-22db-56ea-80bf-cb97a003baf8"
}