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Fabbri L, Russell AM, Chaudhuri N, Adams W, Cowan K, Conway J, Dickinson W, Gibbons M, Hart S, Jones S, Lynch-Wilson J, McMillan T, Milward S, Ward M, Wright LE, Jenkins G. Research priorities for progressive pulmonary fibrosis in the UK. BMJ Open Respir Res 2024; 11:e002368. [PMID: 39231598 PMCID: PMC11428979 DOI: 10.1136/bmjresp-2024-002368] [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: 02/09/2024] [Accepted: 08/16/2024] [Indexed: 09/06/2024] Open
Abstract
INTRODUCTION Health research bodies recommend patient involvement and engagement in research and healthcare planning, although their implementation is not yet widespread. This deficiency extends to progressive pulmonary fibrosis (PPF), where crucial aspects remain unknown, including causal mechanisms, curative treatments and optimal symptom management. This study addresses these gaps by seeking stakeholders' perspectives to guide research and treatment directions. METHOD A priority-setting partnership was established to explore stakeholders' priorities in the diagnosis, treatment, management and care of PPF, including idiopathic pulmonary fibrosis which is the archetypal PPF. Stakeholders included people living with PPF, their carers, relatives and healthcare professionals involved in their management. RESULTS Through an online open-ended survey, 2542 responses were collected from 638 stakeholders. Thematic analysis identified 48 specific research questions, which were then cross-referenced with academic literature to pinpoint research gaps. Following the evidence check, 44 unanswered questions were shortlisted by 834 stakeholders in a second online survey. Ultimately, a top 10 priority list was established through consensus.The prioritised research questions include (1) improved diagnosis accuracy and timing, (2) development of new treatments, (3) enhanced accuracy in primary care, (4) optimal timing for drug and non-drug interventions, (5) effective cough treatment, (6) early intervention for PPF, (7) improved survival rates, (8) symptom reduction, (9) impact of interventions on life expectancy and (10) new treatments with reduced side effects. CONCLUSION Stakeholders' priorities can be summarised into five areas: early diagnosis, drug and non-drug treatments, survival and symptom management. Ideally, these topics should guide funding bodies and health policies.
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Affiliation(s)
- Laura Fabbri
- National Heart and Lung Institute, Imperial College London Department of Medicine, London, UK
- Department of Respiratory Medicine, Royal Brompton Hospital, London, UK
- Nottingham Biomedical Research Centre, National Institute for Health Research, Nottingham, UK
| | - Anne-Marie Russell
- College of Medical and Dental Sciences (MDS) University of Birmingham, Birmingham, UK
- University of Exeter, Exeter, UK
| | - Nazia Chaudhuri
- University of Ulster Faculty of Life and Health Sciences, Londonderry, UK
| | - Wendy Adams
- Action for Pulmonary Fibrosis, Peterborough, UK
| | - Katherine Cowan
- James Lind Alliance, Southampton, UK
- Katherine Cowan Consulting Limited, East Sussex, UK
| | | | | | - Michael Gibbons
- Respiratory Medicine, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
| | - Simon Hart
- Respiratory Research Group, Hull York Medical School/University of Hull, Cottingham, UK
| | - Steve Jones
- Action for Pulmonary Fibrosis, Peterborough, UK
| | | | | | | | | | | | - Gisli Jenkins
- National Heart and Lung Institute, Imperial College London Department of Medicine, London, UK
- Department of Respiratory Medicine, Royal Brompton Hospital, London, UK
- Nottingham Biomedical Research Centre, National Institute for Health Research, Nottingham, UK
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2
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Hata A, Aoyagi K, Hino T, Kawagishi M, Wada N, Song J, Wang X, Valtchinov VI, Nishino M, Muraguchi Y, Nakatsugawa M, Koga A, Sugihara N, Ozaki M, Hunninghake GM, Tomiyama N, Li Y, Christiani DC, Hatabu H. Automated Interstitial Lung Abnormality Probability Prediction at CT: A Stepwise Machine Learning Approach in the Boston Lung Cancer Study. Radiology 2024; 312:e233435. [PMID: 39225600 PMCID: PMC11419784 DOI: 10.1148/radiol.233435] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Background It is increasingly recognized that interstitial lung abnormalities (ILAs) detected at CT have potential clinical implications, but automated identification of ILAs has not yet been fully established. Purpose To develop and test automated ILA probability prediction models using machine learning techniques on CT images. Materials and Methods This secondary analysis of a retrospective study included CT scans from patients in the Boston Lung Cancer Study collected between February 2004 and June 2017. Visual assessment of ILAs by two radiologists and a pulmonologist served as the ground truth. Automated ILA probability prediction models were developed that used a stepwise approach involving section inference and case inference models. The section inference model produced an ILA probability for each CT section, and the case inference model integrated these probabilities to generate the case-level ILA probability. For indeterminate sections and cases, both two- and three-label methods were evaluated. For the case inference model, we tested three machine learning classifiers (support vector machine [SVM], random forest [RF], and convolutional neural network [CNN]). Receiver operating characteristic analysis was performed to calculate the area under the receiver operating characteristic curve (AUC). Results A total of 1382 CT scans (mean patient age, 67 years ± 11 [SD]; 759 women) were included. Of the 1382 CT scans, 104 (8%) were assessed as having ILA, 492 (36%) as indeterminate for ILA, and 786 (57%) as without ILA according to ground-truth labeling. The cohort was divided into a training set (n = 96; ILA, n = 48), a validation set (n = 24; ILA, n = 12), and a test set (n = 1262; ILA, n = 44). Among the models evaluated (two- and three-label section inference models; two- and three-label SVM, RF, and CNN case inference models), the model using the three-label method in the section inference model and the two-label method and RF in the case inference model achieved the highest AUC, at 0.87. Conclusion The model demonstrated substantial performance in estimating ILA probability, indicating its potential utility in clinical settings. © RSNA, 2024 Supplemental material is available for this article. See also the editorial by Zagurovskaya in this issue.
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Affiliation(s)
- Akinori Hata
- Center for Pulmonary Functional Imaging, Department of Radiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
- Diagnostic and Interventional Radiology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kota Aoyagi
- Canon Medical Systems Corporation, Tochigi, Japan
| | - Takuya Hino
- Center for Pulmonary Functional Imaging, Department of Radiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
- Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | | | - Noriaki Wada
- Center for Pulmonary Functional Imaging, Department of Radiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
- Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Jiyeon Song
- Department of Biostatistics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, USA
| | - Xinan Wang
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA
| | - Vladimir I. Valtchinov
- Center for Pulmonary Functional Imaging, Department of Radiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Mizuki Nishino
- Center for Pulmonary Functional Imaging, Department of Radiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
- Dana Farber Cancer Institute, Department of Imaging, Boston, MA
| | | | | | - Akihiro Koga
- Canon Medical Systems Corporation, Tochigi, Japan
| | | | | | - Gary M. Hunninghake
- Pulmonary and Critical Care Division, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Noriyuki Tomiyama
- Diagnostic and Interventional Radiology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yi Li
- Department of Biostatistics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, USA
| | - David C. Christiani
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA
| | - Hiroto Hatabu
- Center for Pulmonary Functional Imaging, Department of Radiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
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Ting C, Konopka K, Benedeck RE, Riches DWH, Redente EF, Oldham JM, Zemans RL. Biomarkers Unveil Insights into Pathology of Transitional Epithelial States in Pulmonary Fibrosis. Am J Respir Crit Care Med 2024; 210:687-690. [PMID: 38889340 PMCID: PMC11389567 DOI: 10.1164/rccm.202310-1839le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 06/17/2024] [Indexed: 06/20/2024] Open
Affiliation(s)
- Christopher Ting
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine
| | | | - Rachel E Benedeck
- Program in Cellular and Molecular Biology, School of Medicine, University of Michigan, Ann Arbor, Michigan
| | - David W H Riches
- Program in Cell Biology, Department of Pediatrics, National Jewish Health, Denver, Colorado
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado; and
- Department of Research, Veterans Affairs Eastern Colorado Health Care System, Denver, Colorado
| | - Elizabeth F Redente
- Program in Cell Biology, Department of Pediatrics, National Jewish Health, Denver, Colorado
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado; and
| | - Justin M Oldham
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine
| | - Rachel L Zemans
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine
- Program in Cellular and Molecular Biology, School of Medicine, University of Michigan, Ann Arbor, Michigan
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Huang Y, Ma SF, Oldham JM, Adegunsoye A, Zhu D, Murray S, Kim JS, Bonham C, Strickland E, Linderholm AL, Lee CT, Paul T, Mannem H, Maher TM, Molyneaux PL, Strek ME, Martinez FJ, Noth I. Machine Learning of Plasma Proteomics Classifies Diagnosis of Interstitial Lung Disease. Am J Respir Crit Care Med 2024; 210:444-454. [PMID: 38422478 PMCID: PMC11351805 DOI: 10.1164/rccm.202309-1692oc] [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: 09/27/2023] [Accepted: 02/29/2024] [Indexed: 03/02/2024] Open
Abstract
Rationale: Distinguishing connective tissue disease-associated interstitial lung disease (CTD-ILD) from idiopathic pulmonary fibrosis (IPF) can be clinically challenging. Objectives: To identify proteins that separate and classify patients with CTD-ILD and those with IPF. Methods: Four registries with 1,247 patients with IPF and 352 patients with CTD-ILD were included in analyses. Plasma samples were subjected to high-throughput proteomics assays. Protein features were prioritized using recursive feature elimination to construct a proteomic classifier. Multiple machine learning models, including support vector machine, LASSO (least absolute shrinkage and selection operator) regression, random forest, and imbalanced Random Forest, were trained and tested in independent cohorts. The validated models were used to classify each case iteratively in external datasets. Measurements and Main Results: A classifier with 37 proteins (proteomic classifier 37 [PC37]) was enriched in the biological process of bronchiole development and smooth muscle proliferation and immune responses. Four machine learning models used PC37 with sex and age score to generate continuous classification values. Receiver operating characteristic curve analyses of these scores demonstrated consistent areas under the curve of 0.85-0.90 in the test cohort and 0.94-0.96 in the single-sample dataset. Binary classification demonstrated 78.6-80.4% sensitivity and 76-84.4% specificity in the test cohort and 93.5-96.1% sensitivity and 69.5-77.6% specificity in the single-sample classification dataset. Composite analysis of all machine learning models confirmed 78.2% (194 of 248) accuracy in the test cohort and 82.9% (208 of 251) in the single-sample classification dataset. Conclusions: Multiple machine learning models trained with large cohort proteomic datasets consistently distinguished CTD-ILD from IPF. Many of the identified proteins are involved in immune pathways. We further developed a novel approach for single-sample classification, which could facilitate honing the differential diagnosis of ILD in challenging cases and improve clinical decision making.
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Affiliation(s)
- Yong Huang
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, Virginia
| | - Shwu-Fan Ma
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, Virginia
| | - Justin M. Oldham
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Ayodeji Adegunsoye
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois
| | - Daisy Zhu
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, Virginia
| | - Susan Murray
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - John S. Kim
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, Virginia
| | - Catherine Bonham
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, Virginia
| | - Emma Strickland
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, Virginia
| | - Angela L. Linderholm
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California, Davis, Davis, California
| | - Cathryn T. Lee
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois
| | - Tessy Paul
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, Virginia
| | - Hannah Mannem
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, Virginia
| | - Toby M. Maher
- National Heart and Lung Institute, Imperial College, London, United Kingdom
- Keck Medicine of the University of Southern California, Los Angeles, California; and
| | | | - Mary E. Strek
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois
| | | | - Imre Noth
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, Virginia
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Maddali MV, Kim JS, Oldham JM. Mapping the Proteomic Landscape of Radiological Lung Abnormalities. Am J Respir Crit Care Med 2024; 209:1052-1054. [PMID: 38442249 PMCID: PMC11092952 DOI: 10.1164/rccm.202402-0310ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 03/05/2024] [Indexed: 03/07/2024] Open
Affiliation(s)
- Manoj V Maddali
- Division of Pulmonary, Allergy, and Critical Care Medicine
- Department of Biomedical Data Science Stanford University Stanford, California
| | - John S Kim
- Division of Pulmonary and Critical Care Medicine University of Virginia Charlottesville, Virginia
| | - Justin M Oldham
- Division of Pulmonary and Critical Care Medicine
- Department of Epidemiology University of Michigan Ann Arbor, Michigan
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6
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Oldham JM, Huang Y, Bose S, Ma SF, Kim JS, Schwab A, Ting C, Mou K, Lee CT, Adegunsoye A, Ghodrati S, Pugashetti JV, Nazemi N, Strek ME, Linderholm AL, Chen CH, Murray S, Zemans RL, Flaherty KR, Martinez FJ, Noth I. Proteomic Biomarkers of Survival in Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med 2024; 209:1111-1120. [PMID: 37847691 PMCID: PMC11092951 DOI: 10.1164/rccm.202301-0117oc] [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: 01/18/2023] [Accepted: 10/16/2023] [Indexed: 10/19/2023] Open
Abstract
Rationale: Idiopathic pulmonary fibrosis (IPF) causes progressive lung scarring and high mortality. Reliable and accurate prognostic biomarkers are urgently needed. Objectives: To identify and validate circulating protein biomarkers of IPF survival. Methods: High-throughput proteomic data were generated using prospectively collected plasma samples from patients with IPF from the Pulmonary Fibrosis Foundation Patient Registry (discovery cohort) and the Universities of California, Davis; Chicago; and Virginia (validation cohort). Proteins associated with three-year transplant-free survival (TFS) were identified using multivariable Cox proportional hazards regression. Those associated with TFS after adjustment for false discovery in the discovery cohort were advanced for testing in the validation cohort, with proteins maintaining TFS association with consistent effect direction considered validated. After combining cohorts, functional analyses were performed, and machine learning was used to derive a proteomic signature of TFS. Measurements and Main Results: Of 2,921 proteins tested in the discovery cohort (n = 871), 231 were associated with differential TFS. Of these, 140 maintained TFS association with consistent effect direction in the validation cohort (n = 355). After cohorts were combined, the validated proteins with the strongest TFS association were latent-transforming growth factor β-binding protein 2 (hazard ratio [HR], 2.43; 95% confidence interval [CI] = 2.09-2.82), collagen α-1(XXIV) chain (HR, 2.21; 95% CI = 1.86-2.39), and keratin 19 (HR, 1.60; 95% CI = 1.47-1.74). In decision curve analysis, a proteomic signature of TFS outperformed a similarly derived clinical prediction model. Conclusions: In the largest proteomic investigation of IPF outcomes performed to date, we identified and validated 140 protein biomarkers of TFS. These results shed important light on potential drivers of IPF progression.
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Affiliation(s)
- Justin M. Oldham
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine
- Department of Epidemiology, and
| | - Yong Huang
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, Virginia
| | - Swaraj Bose
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan
| | - Shwu-Fan Ma
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, Virginia
| | - John S. Kim
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, Virginia
| | - Alexandra Schwab
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, Virginia
| | - Christopher Ting
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine
| | - Kaniz Mou
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine
| | - Cathryn T. Lee
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois
| | - Ayodeji Adegunsoye
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois
| | - Sahand Ghodrati
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California, Davis, Davis, California
| | | | - Nazanin Nazemi
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine
| | - Mary E. Strek
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois
| | - Angela L. Linderholm
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California, Davis, Davis, California
| | - Ching-Hsien Chen
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California, Davis, Davis, California
| | - Susan Murray
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan
| | - Rachel L. Zemans
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine
| | - Kevin R. Flaherty
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine
- Pulmonary Fibrosis Foundation, Chicago, Illinois; and
| | | | - Imre Noth
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, Virginia
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7
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Choi B, Liu GY, Sheng Q, Amancherla K, Perry A, Huang X, San José Estépar R, Ash SY, Guan W, Jacobs DR, Martinez FJ, Rosas IO, Bowler RP, Kropski JA, Banovich NE, Khan SS, San José Estépar R, Shah R, Thyagarajan B, Kalhan R, Washko GR. Proteomic Biomarkers of Quantitative Interstitial Abnormalities in COPDGene and CARDIA Lung Study. Am J Respir Crit Care Med 2024; 209:1091-1100. [PMID: 38285918 PMCID: PMC11092953 DOI: 10.1164/rccm.202307-1129oc] [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: 07/03/2023] [Accepted: 01/29/2024] [Indexed: 01/31/2024] Open
Abstract
Rationale: Quantitative interstitial abnormalities (QIAs) are early measures of lung injury automatically detected on chest computed tomography scans. QIAs are associated with impaired respiratory health and share features with advanced lung diseases, but their biological underpinnings are not well understood. Objectives: To identify novel protein biomarkers of QIAs using high-throughput plasma proteomic panels within two multicenter cohorts. Methods: We measured the plasma proteomics of 4,383 participants in an older, ever-smoker cohort (COPDGene [Genetic Epidemiology of Chronic Obstructive Pulmonary Disease]) and 2,925 participants in a younger population cohort (CARDIA [Coronary Artery Disease Risk in Young Adults]) using the SomaLogic SomaScan assays. We measured QIAs using a local density histogram method. We assessed the associations between proteomic biomarker concentrations and QIAs using multivariable linear regression models adjusted for age, sex, body mass index, smoking status, and study center (Benjamini-Hochberg false discovery rate-corrected P ⩽ 0.05). Measurements and Main Results: In total, 852 proteins were significantly associated with QIAs in COPDGene and 185 in CARDIA. Of the 144 proteins that overlapped between COPDGene and CARDIA, all but one shared directionalities and magnitudes. These proteins were enriched for 49 Gene Ontology pathways, including biological processes in inflammatory response, cell adhesion, immune response, ERK1/2 regulation, and signaling; cellular components in extracellular regions; and molecular functions including calcium ion and heparin binding. Conclusions: We identified the proteomic biomarkers of QIAs in an older, smoking population with a higher prevalence of pulmonary disease and in a younger, healthier community cohort. These proteomics features may be markers of early precursors of advanced lung diseases.
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Affiliation(s)
- Bina Choi
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
- Applied Chest Imaging Laboratory, and
| | - Gabrielle Y. Liu
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California Davis, Sacramento, California
| | | | | | | | - Xiaoning Huang
- Division of Cardiology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Ruben San José Estépar
- Applied Chest Imaging Laboratory, and
- Department of Radiology, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Samuel Y. Ash
- Department of Critical Care, South Shore Hospital, South Weymouth, Massachusetts
| | | | - David R. Jacobs
- Division of Epidemiology and Community Health, School of Public Health, and
| | - Fernando J. Martinez
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Ivan O. Rosas
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Russell P. Bowler
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, National Jewish Health, Denver, Colorado
| | - Jonathan A. Kropski
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Sadiya S. Khan
- Division of Cardiology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Raúl San José Estépar
- Applied Chest Imaging Laboratory, and
- Department of Radiology, Brigham and Women’s Hospital, Boston, Massachusetts
| | | | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | - Ravi Kalhan
- Division of Pulmonary and Critical Care Medicine and
| | - George R. Washko
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
- Applied Chest Imaging Laboratory, and
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Puiu R, Motoc NS, Lucaciu S, Ruta MV, Rajnoveanu RM, Todea DA, Man MA. The Role of Lung Microbiome in Fibrotic Interstitial Lung Disease-A Systematic Review. Biomolecules 2024; 14:247. [PMID: 38540667 PMCID: PMC10968628 DOI: 10.3390/biom14030247] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 02/11/2024] [Accepted: 02/13/2024] [Indexed: 07/23/2024] Open
Abstract
Interstitial Lung Disease (ILD) involves lung disorders marked by chronic inflammation and fibrosis. ILDs include pathologies like idiopathic pulmonary fibrosis (IPF), connective tissue disease-associated ILD (CTD-ILD), hypersensitivity pneumonitis (HP) or sarcoidosis. Existing data covers pathogenesis, diagnosis (especially using high-resolution computed tomography), and treatments like antifibrotic agents. Despite progress, ILD diagnosis and management remains challenging with significant morbidity and mortality. Recent focus is on Progressive Fibrosing ILD (PF-ILD), characterized by worsening symptoms and fibrosis on HRCT. Prevalence is around 30%, excluding IPF, with a poor prognosis. Early diagnosis is crucial for optimizing outcomes in PF-ILD individuals. The lung microbiome comprises all the microorganisms that are in the respiratory tract. Relatively recent research try to evaluate its role in respiratory disease. Healthy lungs have a diverse microbial community. An imbalance in bacterial composition, changes in bacterial metabolic activities, or changes in bacterial distribution within the lung termed dysbiosis is linked to conditions like COPD, asthma and ILDs. We conducted a systematic review of three important scientific data base using a focused search strategy to see how the lung microbiome is involved in the progression of ILDs. Results showed that some differences in the composition and quality of the lung microbiome exist in ILDs that show progressive fibrosing phenotype. The results seem to suggest that the lung microbiota could be involved in ILD progression, but more studies showing its exact pathophysiological mechanisms are needed.
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Affiliation(s)
- Ruxandra Puiu
- Department of Medical Sciences, Pulmonology, Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania or (R.P.); (S.L.); (D.A.T.); (M.A.M.)
| | - Nicoleta Stefania Motoc
- Department of Medical Sciences, Pulmonology, Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania or (R.P.); (S.L.); (D.A.T.); (M.A.M.)
| | - Sergiu Lucaciu
- Department of Medical Sciences, Pulmonology, Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania or (R.P.); (S.L.); (D.A.T.); (M.A.M.)
| | - Maria Victoria Ruta
- I Department of Pulmonology, “Leon Daniello” Clinical Hospital of Pulmonology, 400371 Cluj-Napoca, Romania;
| | - Ruxandra-Mioara Rajnoveanu
- Department of Palliative Medicine, Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania;
| | - Doina Adina Todea
- Department of Medical Sciences, Pulmonology, Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania or (R.P.); (S.L.); (D.A.T.); (M.A.M.)
| | - Milena Adina Man
- Department of Medical Sciences, Pulmonology, Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania or (R.P.); (S.L.); (D.A.T.); (M.A.M.)
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9
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Kim JS, Montesi SB, Adegunsoye A, Humphries SM, Salisbury ML, Hariri LP, Kropski JA, Richeldi L, Wells AU, Walsh S, Jenkins RG, Rosas I, Noth I, Hunninghake GM, Martinez FJ, Podolanczuk AJ. Approach to Clinical Trials for the Prevention of Pulmonary Fibrosis. Ann Am Thorac Soc 2023; 20:1683-1693. [PMID: 37703509 PMCID: PMC10704236 DOI: 10.1513/annalsats.202303-188ps] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 09/13/2023] [Indexed: 09/15/2023] Open
Affiliation(s)
- John S. Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, Virginia
- Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | | | - Ayodeji Adegunsoye
- Department of Medicine, The University of Chicago Medicine, Chicago, Illinois
| | | | - Margaret L. Salisbury
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Lida P. Hariri
- Division of Pulmonary and Critical Care Medicine, and
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jonathan A. Kropski
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Luca Richeldi
- Fondazione Policlinico Universitario Agostino Gemelli Istituto di Ricovero e Cura a Carattere Scientifico, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Athol U. Wells
- Department of Radiology, and
- Interstitial Lung Disease Service, Royal Brompton Hospital, London, United Kingdom
| | - Simon Walsh
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - R. Gisli Jenkins
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Ivan Rosas
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Imre Noth
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, Virginia
| | - Gary M. Hunninghake
- Pulmonary and Critical Care Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts; and
| | - Fernando J. Martinez
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Anna J. Podolanczuk
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medicine, New York, New York
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10
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Moll M, Peljto AL, Kim JS, Xu H, Debban CL, Chen X, Menon A, Putman RK, Ghosh AJ, Saferali A, Nishino M, Hatabu H, Hobbs BD, Hecker J, McDermott G, Sparks JA, Wain LV, Allen RJ, Tobin MD, Raby BA, Chun S, Silverman EK, Zamora AC, Ortega VE, Garcia CK, Barr RG, Bleecker ER, Meyers DA, Kaner RJ, Rich SS, Manichaikul A, Rotter JI, Dupuis J, O’Connor GT, Fingerlin TE, Hunninghake GM, Schwartz DA, Cho MH. A Polygenic Risk Score for Idiopathic Pulmonary Fibrosis and Interstitial Lung Abnormalities. Am J Respir Crit Care Med 2023; 208:791-801. [PMID: 37523715 PMCID: PMC10563194 DOI: 10.1164/rccm.202212-2257oc] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 07/31/2023] [Indexed: 08/02/2023] Open
Abstract
Rationale: In addition to rare genetic variants and the MUC5B locus, common genetic variants contribute to idiopathic pulmonary fibrosis (IPF) risk. The predictive power of common variants outside the MUC5B locus for IPF and interstitial lung abnormalities (ILAs) is unknown. Objectives: We tested the predictive value of IPF polygenic risk scores (PRSs) with and without the MUC5B region on IPF, ILA, and ILA progression. Methods: We developed PRSs that included (PRS-M5B) and excluded (PRS-NO-M5B) the MUC5B region (500-kb window around rs35705950-T) using an IPF genome-wide association study. We assessed PRS associations with area under the receiver operating characteristic curve (AUC) metrics for IPF, ILA, and ILA progression. Measurements and Main Results: We included 14,650 participants (1,970 IPF; 1,068 ILA) from six multi-ancestry population-based and case-control cohorts. In cases excluded from genome-wide association study, the PRS-M5B (odds ratio [OR] per SD of the score, 3.1; P = 7.1 × 10-95) and PRS-NO-M5B (OR per SD, 2.8; P = 2.5 × 10-87) were associated with IPF. Participants in the top PRS-NO-M5B quintile had ∼sevenfold odds for IPF compared with those in the first quintile. A clinical model predicted IPF (AUC, 0.61); rs35705950-T and PRS-NO-M5B demonstrated higher AUCs (0.73 and 0.7, respectively), and adding both genetic predictors to a clinical model yielded the highest performance (AUC, 0.81). The PRS-NO-M5B was associated with ILA (OR, 1.25) and ILA progression (OR, 1.16) in European ancestry participants. Conclusions: A common genetic variant risk score complements the MUC5B variant to identify individuals at high risk of interstitial lung abnormalities and pulmonary fibrosis.
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Affiliation(s)
- Matthew Moll
- Division of Pulmonary and Critical Care Medicine, and
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Anna L. Peljto
- Department of Medicine and
- Department of Immunology, Division of Pulmonary Medicine, University of Colorado, Aurora, Colorado
| | - John S. Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, Virginia
| | - Hanfei Xu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Catherine L. Debban
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Xianfeng Chen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Mayo Clinic, Phoenix, Arizona
| | - Aravind Menon
- Division of Pulmonary and Critical Care Medicine, and
| | | | - Auyon J. Ghosh
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, State University of New York Upstate Medical Center, Syracuse, New York
| | - Aabida Saferali
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Mizuki Nishino
- Center for Pulmonary Functional Imaging, Department of Radiology
| | - Hiroto Hatabu
- Center for Pulmonary Functional Imaging, Department of Radiology
| | - Brian D. Hobbs
- Division of Pulmonary and Critical Care Medicine, and
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Julian Hecker
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Gregory McDermott
- Division of Rheumatology, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Jeffrey A. Sparks
- Division of Rheumatology, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Louise V. Wain
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Richard J. Allen
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Martin D. Tobin
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Benjamin A. Raby
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Pediatrics
- Division of Pulmonary Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Sung Chun
- Division of Pulmonary Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Edwin K. Silverman
- Division of Pulmonary and Critical Care Medicine, and
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ana C. Zamora
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Mayo Clinic, Phoenix, Arizona
| | - Victor E. Ortega
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Mayo Clinic, Phoenix, Arizona
| | - Christine K. Garcia
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - R. Graham Barr
- Department of Medicine and
- Division of General Medicine, Department of Epidemiology, Columbia University Medical Center, New York, New York
| | - Eugene R. Bleecker
- Division of Genetics, Genomics, and Precision Medicine, Department of Medicine, University of Arizona, Tucson, Arizona
| | - Deborah A. Meyers
- Division of Genetics, Genomics, and Precision Medicine, Department of Medicine, University of Arizona, Tucson, Arizona
| | - Robert J. Kaner
- Division of Pulmonary Medicine, Weill Cornell School of Medicine, New York, New York
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-University of California, Los Angeles Medical Center, Torrance, California
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
- Department of Epidemiology, Biostatistics and Occupational Health, School of Population and Global Health, McGill University Faculty of Medicine and Health Sciences, Montreal, Quebec, Canada
| | - George T. O’Connor
- Department of Medicine, Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts; and
| | - Tasha E. Fingerlin
- The National Jewish Health Cohen Family Asthma Institute, Division of Allergy and Immunology, National Jewish Health, Denver, Colorado
| | | | - David A. Schwartz
- Department of Medicine and
- Department of Immunology, Division of Pulmonary Medicine, University of Colorado, Aurora, Colorado
| | - Michael H. Cho
- Division of Pulmonary and Critical Care Medicine, and
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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11
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Exarchos KP, Gkrepi G, Kostikas K, Gogali A. Recent Advances of Artificial Intelligence Applications in Interstitial Lung Diseases. Diagnostics (Basel) 2023; 13:2303. [PMID: 37443696 DOI: 10.3390/diagnostics13132303] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/02/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023] Open
Abstract
Interstitial lung diseases (ILDs) comprise a rather heterogeneous group of diseases varying in pathophysiology, presentation, epidemiology, diagnosis, treatment and prognosis. Even though they have been recognized for several years, there are still areas of research debate. In the majority of ILDs, imaging modalities and especially high-resolution Computed Tomography (CT) scans have been the cornerstone in patient diagnostic approach and follow-up. The intricate nature of ILDs and the accompanying data have led to an increasing adoption of artificial intelligence (AI) techniques, primarily on imaging data but also in genetic data, spirometry and lung diffusion, among others. In this literature review, we describe the most prominent applications of AI in ILDs presented approximately within the last five years. We roughly stratify these studies in three categories, namely: (i) screening, (ii) diagnosis and classification, (iii) prognosis.
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Affiliation(s)
- Konstantinos P Exarchos
- Respiratory Medicine Department, University of Ioannina School of Medicine, 45110 Ioannina, Greece
| | - Georgia Gkrepi
- Respiratory Medicine Department, University of Ioannina School of Medicine, 45110 Ioannina, Greece
| | - Konstantinos Kostikas
- Respiratory Medicine Department, University of Ioannina School of Medicine, 45110 Ioannina, Greece
| | - Athena Gogali
- Respiratory Medicine Department, University of Ioannina School of Medicine, 45110 Ioannina, Greece
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12
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Lasky JA, Thannickal VJ. NOTCH-ing up Surface Tension in the Fibrotic Lung. Am J Respir Crit Care Med 2023; 207:235-236. [PMID: 36351003 PMCID: PMC9896643 DOI: 10.1164/rccm.202210-1901ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Joseph A Lasky
- School of Medicine Tulane University New Orleans, Louisiana
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13
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Maher TM. Biomarkers for Interstitial Lung Abnormalities: A Stepping-stone Toward Idiopathic Pulmonary Fibrosis Prevention? Am J Respir Crit Care Med 2022; 206:244-246. [PMID: 35580066 PMCID: PMC9890254 DOI: 10.1164/rccm.202205-0839ed] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Toby M. Maher
- Keck School of MedicineUniversity of Southern CaliforniaLos Angeles, California,Royal Brompton and Harefield HospitalsGuy’s and St Thomas’ NHS Foundation TrustLondon, United Kingdom,National Heart and Lung InstituteImperial College LondonLondon, United Kingdom
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