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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 DOI: 10.1164/rccm.202402-0310ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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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 DOI: 10.1164/rccm.202301-0117oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Adegunsoye A, Kropski JA, Behr J, Blackwell TS, Corte TJ, Cottin V, Glanville A, Glassberg MK, Griese M, Hunninghake GM, Johannson KA, Keane MP, Kim JS, Kolb M, Maher TM, Oldham JM, Podolanczuk AJ, Rosas IO, Martinez FJ, Noth I, Schwartz DA. Genetics and Genomics of Pulmonary Fibrosis: Charting the Molecular Landscape and Shaping Precision Medicine. Am J Respir Crit Care Med 2024. [PMID: 38573068 DOI: 10.1164/rccm.202401-0238so] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/03/2024] [Indexed: 04/05/2024] Open
Abstract
Recent genetic and genomic advancements have elucidated the complex etiology of idiopathic pulmonary fibrosis (IPF) and other progressive fibrotic interstitial lung diseases (ILDs), emphasizing the contribution of heritable factors. This state-of-the-art review synthesizes evidence on significant genetic contributors to pulmonary fibrosis (PF), including rare genetic variants and common single nucleotide polymorphisms (SNPs). The MUC5B promoter variant is unusual, a common SNP that markedly elevates the risk of early and established PF. We address the utility of genetic variation in enhancing understanding of disease pathogenesis, clinical phenotypes, improving disease definitions, and informing prognosis and treatment response. Critical research gaps are highlighted, particularly the underrepresentation of non-European ancestries in PF genetic studies and the exploration of PF phenotypes beyond usual interstitial pneumonia (UIP)/IPF. We discuss the role of telomere length, often critically short in PF, and its link to progression and mortality, underscoring the genetic complexity involving telomere biology genes (TERT, TERC) and others like SFTPC and MUC5B. Additionally, we address the potential of gene-by-environment interactions to modulate disease manifestation, advocating for precision medicine in PF. Insights from gene expression profiling studies and multi-omic analyses highlight the promise for understanding disease pathogenesis and offer new approaches to clinical care, therapeutic drug development, and biomarker discovery. Finally, we discuss the ethical, legal, and social implications of genomic research and therapies in PF, stressing the need for sound practices and informed clinical genetic discussions. Looking forward, we advocate for comprehensive genetic testing panels and polygenic risk scores to improve the management of PF and related ILDs across diverse populations.
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Affiliation(s)
- Ayodeji Adegunsoye
- University of Chicago, Section of Pulmonary and Critical Care, Dept. of Medicine, Chicago, Illinois, United States;
| | - Jonathan A Kropski
- Vanderbilt University Medical Center, 12328, Nashville, Tennessee, United States
| | - Juergen Behr
- University of Munich, Department of Internal Medicine V, Munich, Germany
| | | | - Tamera J Corte
- Royal Prince Alfred Hospital, Department of Respiratory Medicine, Sydney, New South Wales, Australia
- University of Sydney, 4334, Medical School, Sydney, New South Wales, Australia
| | - Vincent Cottin
- Louis Pradel University Hospital, Respiratory Medicine, Lyon, France
| | - Allan Glanville
- St Vincent's Hospital, Respiratory and Sleep Medicine, Sydney, New South Wales, Australia
| | - Marilyn K Glassberg
- Loyola University Chicago Stritch School of Medicine, 12248, Medicine, Maywood, Illinois, United States
| | | | - Gary M Hunninghake
- Brigham and Women's Hospital, 1861, Medicine, Boston, Massachusetts, United States
| | | | | | - John S Kim
- University of Virginia, 2358, Medicine, Charlottesville, Virginia, United States
| | - Martin Kolb
- McMaster University, Hamilton, Ontario, Canada
| | - Toby M Maher
- University of Southern California Keck School of Medicine, 12223, PCCSM, Los Angeles, California, United States
| | - Justin M Oldham
- University of California Davis, 8789, Pulmonary and Critical Care Medicine, Davis, California, United States
| | - Anna J Podolanczuk
- Weill Cornell Medical College, 12295, Department of Medicine, New York, New York, United States
| | - Ivan O Rosas
- Brigham and Women's Hospital, 1861, Department of Medicine, Division of Pulmonary and Critical Care Medicine, Boston, Massachusetts, United States
| | | | - Imre Noth
- University of Virginia, 2358, Division of Pulmonary and Critical Care Medicine, Charlottesville, Virginia, United States
| | - David A Schwartz
- University of Colorado, School of Medicine, Department of Medicine, Aurora, Colorado, United States
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Pugashetti JV, Kim JS, Combs MP, Ma SF, Adegunsoye A, Linderholm AL, Strek ME, Chen CH, Dilling DF, Whelan TPM, Flaherty KR, Martinez FJ, Noth I, Oldham JM. A multidimensional classifier to support lung transplant referral in patients with pulmonary fibrosis. J Heart Lung Transplant 2024:S1053-2498(24)01560-2. [PMID: 38556070 DOI: 10.1016/j.healun.2024.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/13/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Lung transplantation remains the sole curative option for patients with idiopathic pulmonary fibrosis (IPF), but donor organs remain scarce, and many eligible patients die before transplant. Tools to optimize the timing of transplant referrals are urgently needed. METHODS Least absolute shrinkage and selection operator was applied to clinical and proteomic data generated as part of a prospective cohort study of interstitial lung disease (ILD) to derive clinical, proteomic, and multidimensional logit models of near-term death or lung transplant within 18 months of blood draw. Model-fitted values were dichotomized at the point of maximal sensitivity and specificity, and decision curve analysis was used to select the best-performing classifier. We then applied this classifier to independent IPF and non-IPF ILD cohorts to determine test performance characteristics. Cohorts were restricted to patients aged ≤72 years with body mass index 18 to 32 to increase the likelihood of transplant eligibility. RESULTS IPF derivation, IPF validation, and non-IPF ILD validation cohorts consisted of 314, 105, and 295 patients, respectively. A multidimensional model comprising 2 clinical variables and 20 proteins outperformed stand-alone clinical and proteomic models. Following dichotomization, the multidimensional classifier predicted near-term outcome with 70% sensitivity and 92% specificity in the IPF validation cohort and 70% sensitivity and 80% specificity in the non-IPF ILD validation cohort. CONCLUSIONS A multidimensional classifier of near-term outcomes accurately discriminated this end-point with good test performance across independent IPF and non-IPF ILD cohorts. These findings support refinement and prospective validation of this classifier in transplant-eligible individuals.
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Affiliation(s)
- Janelle Vu Pugashetti
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan
| | - John S Kim
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, Virginia
| | - Michael P Combs
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan
| | - Shwu-Fan Ma
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, Virginia
| | - Ayodeji Adegunsoye
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois
| | - Angela L Linderholm
- Department of Internal Medicine, University of California Davis, Davis, California
| | - Mary E Strek
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois
| | - Ching-Hsien Chen
- Department of Internal Medicine, University of California Davis, Davis, California
| | - Daniel F Dilling
- Division of Pulmonary and Critical Care Medicine, Loyola University Chicago, Stritch School of Medicine, Chicago, Illinois
| | - Timothy P M Whelan
- Division of Pulmonary and Critical Care, Medical University of South Carolina, Charleston, South Carolina; Pulmonary Fibrosis Foundation, Chicago, Illinois
| | - Kevin R Flaherty
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan; Pulmonary Fibrosis Foundation, Chicago, Illinois
| | - Fernando J Martinez
- Division of Pulmonary and Critical Care, Weill Cornell Medical Center, New York, New York
| | - Imre Noth
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, Virginia
| | - Justin M Oldham
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan; Department of Epidemiology, University of Michigan, Ann Arbor, Michigan.
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Carter H, Costa RM, Adams TS, Gilchrist T, Emch CE, Bame M, Oldham JM, Linderholm AL, Noth I, Kaminski N, Moore BB, Gurczynski SJ. Dendritic Cell - Fibroblast Crosstalk via TLR9 and AHR Signaling Drives Lung Fibrogenesis. bioRxiv 2024:2024.03.15.584457. [PMID: 38559175 PMCID: PMC10980010 DOI: 10.1101/2024.03.15.584457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Idiopathic pulmonary fibrosis (IPF) is characterized by progressive scarring and loss of lung function. With limited treatment options, patients succumb to the disease within 2-5 years. The molecular pathogenesis of IPF regarding the immunologic changes that occur is poorly understood. We characterize a role for non-canonical aryl-hydrocarbon receptor signaling (ncAHR) in dendritic cells (DCs) that leads to production of IL-6 and IL-17, promoting fibrosis. TLR9 signaling in myofibroblasts is shown to regulate production of TDO2 which converts tryptophan into the endogenous AHR ligand kynurenine. Mice with augmented ncAHR signaling were created by crossing floxed AHR exon-2 deletion mice (AHR Δex2 ) with mice harboring a CD11c-Cre. Bleomycin was used to study fibrotic pathogenesis. Isolated CD11c+ cells and primary fibroblasts were treated ex-vivo with relevant TLR agonists and AHR modulating compounds to study how AHR signaling influenced inflammatory cytokine production. Human datasets were also interrogated. Inhibition of all AHR signaling rescued fibrosis, however, AHR Δex2 mice treated with bleomycin developed more fibrosis and DCs from these mice were hyperinflammatory and profibrotic upon adoptive transfer. Treatment of fibrotic fibroblasts with TLR9 agonist increased expression of TDO2. Study of human samples corroborate the relevance of these findings in IPF patients. We also, for the first time, identify that AHR exon-2 floxed mice retain capacity for ncAHR signaling.
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Behr J, Salisbury ML, Walsh SLF, Podolanczuk AJ, Hariri LP, Hunninghake GM, Kolb M, Ryerson CJ, Cottin V, Beasley MB, Corte T, Glanville AR, Adegunsoye A, Hogaboam C, Wuyts WA, Noth I, Oldham JM, Richeldi L, Raghu G, Wells AU. The Role of Inflammation and Fibrosis in ILD Treatment Decisions. Am J Respir Crit Care Med 2024. [PMID: 38484133 DOI: 10.1164/rccm.202401-0048pp] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 03/13/2024] [Indexed: 03/20/2024] Open
Affiliation(s)
- Juergen Behr
- University of Munich, Department of Medicine V, LMU University Hospital, LMU Munich, Comprehensive Pneumology Center, Member of the German Center for Lung Research, Munich, Germany;
| | - Margaret L Salisbury
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Simon L F Walsh
- Imperial College London, 4615, National Heart and Lung Institute, London, United Kingdom of Great Britain and Northern Ireland
| | - Anna J Podolanczuk
- Weill Cornell Medical College, 12295, Department of Medicine, New York, New York, United States
| | - Lida P Hariri
- Massachusetts General Hospital, Pathology, Boston, Massachusetts, United States
| | - Gary M Hunninghake
- Brigham and Women's Hospital, 1861, Medicine, Boston, Massachusetts, United States
| | - Martin Kolb
- McMaster University, Hamilton, Ontario, Canada
| | | | - Vincent Cottin
- Louis Pradel University Hospital, Respiratory Medicine, Lyon, France
| | - Mary B Beasley
- Mount Sinai Medical Center, 5944, Department of Pathology, New York, New York, United States
| | - Tamera Corte
- Royal Prince Alfred Hospital, Department of Respiratory Medicine, Sydney, New South Wales, Australia
- University of Sydney, 4334, Medical School, Sydney, New South Wales, Australia
| | - Allan R Glanville
- St Vincent's Hospital, Respiratory and Sleep Medicine, Sydney, New South Wales, Australia
| | - Ayodeji Adegunsoye
- University of Chicago, Section of Pulmonary and Critical Care, Dept. of Medicine, Chicago, Illinois, United States
| | - Cory Hogaboam
- Cedars Sinai Medical Center, Department of Medicine, Los Angeles, California, United States
| | - Wim A Wuyts
- K U Leuven, respiratory medicine, Leuven, Belgium
| | - Imre Noth
- University of Virginia, 2358, Division of Pulmonary and Critical Care Medicine, Charlottesville, Virginia, United States
| | - Justin M Oldham
- University of California Davis, 8789, Pulmonary and Critical Care Medicine, Davis, California, United States
| | - Luca Richeldi
- Universita Cattolica del Sacro Cuore Sede di Roma, 96983, Pulmonary Medicine, Roma, Lazio, Italy
| | - Ganesh Raghu
- University of Washington Medical Center, 21617, Division of Pulmonary and Critical Care Medicine, Seattle, Washington, United States
| | - Athol U Wells
- Royal Brompton Hospital, Interstitial Lung Disease Unit, London, United Kingdom of Great Britain and Northern Ireland
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Thillai M, Oldham JM, Ruggiero A, Kanavati F, McLellan T, Saini G, Johnson SR, Ble FX, Azim A, Ostridge K, Platt A, Belvisi M, Maher TM, Molyneaux PL. Deep Learning-based Segmentation of CT Scans Predicts Disease Progression and Mortality in IPF. Am J Respir Crit Care Med 2024. [PMID: 38452227 DOI: 10.1164/rccm.202311-2185oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/06/2024] [Indexed: 03/09/2024] Open
Abstract
RATIONALE Despite evidence demonstrating a prognostic role for CT scans in IPF, image-based biomarkers are not routinely used in clinical practice or trials. OBJECTIVES Develop automated imaging biomarkers using deep learning based segmentation of CT scans. METHODS We developed segmentation processes for four anatomical biomarkers which were applied to a unique cohort of treatment-naive IPF patients enrolled in the PROFILE study and tested against a further UK cohort. The relationship between CT biomarkers, lung function, disease progression and mortality were assessed. MEASUREMENTS AND MAIN RESULTS Data was analysed from 446 PROFILE patients. Median follow-up was 39.1 months (IQR 18.1-66.4) with cumulative incidence of death of 277 over 5 years (62.1%). Segmentation was successful on 97.8% of all scans, across multiple imaging vendors at slice thicknesses 0.5-5mm. Of 4 segmentations, lung volume showed strongest correlation with FVC (r=0.82, p<0.001). Lung, vascular and fibrosis volumes were consistently associated across cohorts with differential five-year survival, which persisted after adjustment for baseline GAP score. Lower lung volume (HR 0.98, CI 0.96-0.99, p=0.001), increased vascular volume (HR 1.30, CI 1.12-1.51, p=0.001) and increased fibrosis volume (HR 1.17, CI 1.12-1.22, p=<0.001) were associated with reduced two-year progression-free survival in the pooled PROFILE cohort. Longitudinally, decreasing lung volume (HR 3.41; 95% CI 1.36-8.54; p=0.009) and increasing fibrosis volume (HR 2.23; 95% CI 1.22-4.08; p=0.009) were associated with differential survival. CONCLUSIONS Automated models can rapidly segment IPF CT scans, providing prognostic near and long-term information, which could be used in routine clinical practice or as key trial endpoints. This article is open access and distributed under the terms of the Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/).
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Affiliation(s)
- Muhunthan Thillai
- Royal Papworth Hospital, 2144, Cambridge, United Kingdom of Great Britain and Northern Ireland
- Qureight, Cambridge, United Kingdom of Great Britain and Northern Ireland
| | - Justin M Oldham
- University of California Davis, 8789, Pulmonary and Critical Care Medicine, Davis, California, United States
| | - Alessandro Ruggiero
- Royal Papworth Hospital, 2144, Cambridge, United Kingdom of Great Britain and Northern Ireland
- Qureight, Cambridge, United Kingdom of Great Britain and Northern Ireland
| | - Fahdi Kanavati
- Qureight, Cambridge, United Kingdom of Great Britain and Northern Ireland
| | - Tom McLellan
- Royal Papworth Hospital, 2144, Cambridge, United Kingdom of Great Britain and Northern Ireland
| | - Gauri Saini
- University of Nottingham, Translational Medical Sciences, NIHR Biomedical Research Centre, Nottingham, United Kingdom of Great Britain and Northern Ireland
| | - Simon R Johnson
- University of Nottingham, Translational Medical Sciences, NIHR Biomedical Research Centre, Nottingham, United Kingdom of Great Britain and Northern Ireland
| | - Francois-Xavier Ble
- Translational Science and Experimental Medicine, Respiratory, Inflammation, and Autoimmune (RIA), BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom of Great Britain and Northern Ireland
| | - Adnan Azim
- Translational Science and Experimental Medicine, Respiratory, Inflammation, and Autoimmune (RIA), BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom of Great Britain and Northern Ireland
| | - Kristoffer Ostridge
- AstraZeneca R&D Gothenburg, 128698, Clinical Development, Research and Early Development, Respiratory & Immunology, Goteborg, Sweden
| | - Adam Platt
- AstraZeneca UK Ltd, 4978, Translational Science and Experimental Medicine, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, Cambridge, Cambridgeshire, United Kingdom of Great Britain and Northern Ireland
| | - Maria Belvisi
- Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
- Imperial College London, 4615, National Heart & Lung Institute, London, United Kingdom of Great Britain and Northern Ireland
| | - Toby M Maher
- University of Southern California Keck School of Medicine, 12223, PCCSM, Los Angeles, California, United States
- Imperial College London, 4615, National Heart & Lung Institute, London, United Kingdom of Great Britain and Northern Ireland
| | - Philip L Molyneaux
- Imperial College London, 4615, National Heart & Lung Institute, London, United Kingdom of Great Britain and Northern Ireland
- Royal Brompton and Harefield Hospitals, 4964, London, United Kingdom of Great Britain and Northern Ireland;
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Kim JS, Ma SF, Ma JZ, Huang Y, Bonham CA, Oldham JM, Adegunsoye A, Strek ME, Flaherty KR, Strickland E, Udofia I, Mooney JJ, Ghosh S, Maddipati K, Noth I. Associations of Plasma Omega-3 Fatty Acids With Progression and Survival in Pulmonary Fibrosis. Chest 2024; 165:621-631. [PMID: 37866772 PMCID: PMC10925547 DOI: 10.1016/j.chest.2023.09.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/22/2023] [Accepted: 09/22/2023] [Indexed: 10/24/2023] Open
Abstract
BACKGROUND Preclinical experiments suggest protective effects of omega-3 fatty acids and their metabolites in lung injury and fibrosis. Whether higher intake of omega-3 fatty acids is associated with disease progression and survival in humans with pulmonary fibrosis is unknown. RESEARCH QUESTION What are the associations of plasma omega-3 fatty acid levels (a validated marker of omega-3 nutritional intake) with disease progression and transplant-free survival in pulmonary fibrosis? STUDY DESIGN AND METHODS Omega-3 fatty acid levels were measured from plasma samples of patients with clinically diagnosed pulmonary fibrosis from the Pulmonary Fibrosis Foundation Patient Registry (n = 150), University of Virginia (n = 58), and University of Chicago (n = 101) cohorts. The N-3 index (docosahexaenoic acid + eicosapentaenoic acid) was the primary exposure variable of interest. Linear-mixed effects models with random intercept and slope were used to examine associations of plasma omega-3 fatty acid levels with changes in FVC and diffusing capacity for carbon monoxide over a period of 12 months. Cox proportional hazards models were used to examine transplant-free survival. Stratified analyses by telomere length were performed in the University of Chicago cohort. RESULTS Most of the cohort were patients with idiopathic pulmonary fibrosis (88%) and male patients (74%). One-unit increment in log-transformed N-3 index plasma level was associated with a change in diffusing capacity for carbon monoxide of 1.43 mL/min/mm Hg per 12 months (95% CI, 0.46-2.41) and a hazard ratio for transplant-free survival of 0.44 (95% CI, 0.24-0.83). Cardiovascular disease history, smoking, and antifibrotic usage did not significantly modify associations. Omega-3 fatty acid levels were not significantly associated with changes in FVC. Higher eicosapentaenoic acid plasma levels were associated with longer transplant-free survival among University of Chicago participants with shorter telomere length (P value for interaction = .02). INTERPRETATION Further research is needed to investigate underlying biological mechanisms and whether omega-3 fatty acids are a potential disease-modifying therapy.
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Affiliation(s)
- John S Kim
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA; Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY.
| | - Shwu-Fan Ma
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA
| | - Jennie Z Ma
- Department of Public Health, University of Virginia School of Medicine, Charlottesville, VA
| | - Yong Huang
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA
| | - Catherine A Bonham
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA
| | - Justin M Oldham
- Department of Medicine, University of Michigan, Ann Arbor, MI
| | | | - Mary E Strek
- Department of Medicine, University of Chicago, Chicago, IL
| | | | - Emma Strickland
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA
| | | | | | - Shrestha Ghosh
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA; Department of Immunology, Harvard Medical School, Boston, MA
| | | | - Imre Noth
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA
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9
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Hatt C, Chung JH, Oldham JM. Response. Chest 2024; 165:e89-e90. [PMID: 38461028 DOI: 10.1016/j.chest.2023.10.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 03/11/2024] Open
Affiliation(s)
| | - Jonathan H Chung
- Department of Radiology, University of California at San Diego, San Diego, CA
| | - Justin M Oldham
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI; Department of Epidemiology, University of Michigan, Ann Arbor, MI.
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10
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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. [PMID: 38422478 DOI: 10.1164/rccm.202309-1692oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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 Identify proteins that separate and classify CTD-ILD from IPF patients. METHODS Four registries with 1247 IPF and 352 CTD-ILD patients were included in analyses. Plasma samples were subjected to high-throughput proteomics assays. Protein features were prioritized using Recursive Feature Elimination (RFE) to construct a proteomic classifier. Multiple machine learning models, including Support Vector Machine, LASSO regression, Random Forest (RF), and imbalanced-RF, were trained and tested in independent cohorts. The validated models were used to classify each case iteratively in external datasets. MEASUREMENT AND MAIN RESULTS A classifier with 37 proteins (PC37) was enriched in 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 Area-Under-Curve 0.85-0.90 in 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 test cohort, 93.5%-96.1% sensitivity and 69.5%-77.6% specificity in single-sample classification dataset. Composite analysis of all machine learning models confirmed 78.2% (194/248) accuracy in test cohort and 82.9% (208/251) in single-sample classification dataset. CONCLUSIONS Multiple machine learning models trained with large cohort proteomic datasets consistently distinguished CTD-ILD from IPF. Identified proteins 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
- University of Virginia School of Medicine, 12349, Charlottesville, Virginia, United States
| | - Shwu-Fan Ma
- University of Virginia School of Medicine, 12349, Division of Pulmonary & Critical Care Medicine, Charlottesville, Virginia, United States
- University of Virginia
| | - Justin M Oldham
- University of California Davis, 8789, Pulmonary and Critical Care Medicine, Davis, California, United States
| | - Ayodeji Adegunsoye
- University of Chicago, Section of Pulmonary and Critical Care, Dept. of Medicine, Chicago, Illinois, United States
| | - Daisy Zhu
- University of Virginia School of Medicine, 12349, Medicine, Charlottesville, Virginia, United States
| | - Susan Murray
- University of Michigan, 1259, Ann Arbor, Michigan, United States
| | - John S Kim
- University of Virginia, 2358, Medicine, Charlottesville, Virginia, United States
- Charlottesville, Virginia, United States
| | - Catherine Bonham
- University of Virginia, 2358, Pulmonary & Critical Care Medicine, Charlottesville, Virginia, United States
| | - Emma Strickland
- University of Virginia, 2358, Charlottesville, Virginia, United States
| | | | - Cathryn T Lee
- The University of Chicago, 2462, Department of Medicine, Chicago, Illinois, United States
| | - Tessy Paul
- University of Virginia, 2358, Medicine, Charlottesville, Virginia, United States
| | - Hannah Mannem
- University of Virginia, Medicine, Charlottesville, Virginia, United States
| | - Toby M Maher
- University of Southern California Keck School of Medicine, 12223, PCCSM, Los Angeles, California, United States
| | - Philip L Molyneaux
- Imperial College London, National Heart and Lung Institute, London, United Kingdom of Great Britain and Northern Ireland
| | - Mary E Strek
- University of Chicago Hosp, Department of Medicine, Chicago, Illinois, United States
| | | | - Imre Noth
- University of Virginia, Division of Pulmonary & Critical Care & Sleep Medicine, Department of Medicine, , Charlottesville, Virginia, United States;
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11
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Chung JH, Chelala L, Pugashetti JV, Wang JM, Adegunsoye A, Matyga AW, Keith L, Ludwig K, Zafari S, Ghodrati S, Ghasemiesfe A, Guo H, Soo E, Lyen S, Sayer C, Hatt C, Oldham JM. A Deep Learning-Based Radiomic Classifier for Usual Interstitial Pneumonia. Chest 2024; 165:371-380. [PMID: 37844797 PMCID: PMC11026174 DOI: 10.1016/j.chest.2023.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/09/2023] [Accepted: 10/05/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND Because chest CT scan has largely supplanted surgical lung biopsy for diagnosing most cases of interstitial lung disease (ILD), tools to standardize CT scan interpretation are urgently needed. RESEARCH QUESTION Does a deep learning (DL)-based classifier for usual interstitial pneumonia (UIP) derived using CT scan features accurately discriminate radiologist-determined visual UIP? STUDY DESIGN AND METHODS A retrospective cohort study was performed. Chest CT scans acquired in individuals with and without ILD were drawn from a variety of public and private data sources. Using radiologist-determined visual UIP as ground truth, a convolutional neural network was used to learn discrete CT scan features of UIP, with outputs used to predict the likelihood of UIP using a linear support vector machine. Test performance characteristics were assessed in an independent performance cohort and multicenter ILD clinical cohort. Transplant-free survival was compared between UIP classification approaches using the Kaplan-Meier estimator and Cox proportional hazards regression. RESULTS A total of 2,907 chest CT scans were included in the training (n = 1,934), validation (n = 408), and performance (n = 565) data sets. The prevalence of radiologist-determined visual UIP was 12.4% and 37.1% in the performance and ILD clinical cohorts, respectively. The DL-based UIP classifier predicted visual UIP in the performance cohort with sensitivity and specificity of 93% and 86%, respectively, and in the multicenter ILD clinical cohort with 81% and 77%, respectively. DL-based and visual UIP classification similarly discriminated survival, and outcomes were consistent among cases with positive DL-based UIP classification irrespective of visual classification. INTERPRETATION A DL-based classifier for UIP demonstrated good test performance across a wide range of UIP prevalence and similarly discriminated survival when compared with radiologist-determined UIP. This automated tool could efficiently screen for UIP in patients undergoing chest CT scan and identify a high-risk phenotype among those with known ILD.
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Affiliation(s)
| | - Lydia Chelala
- Department of Radiology, University of Chicago, Chicago, IL
| | - Janelle Vu Pugashetti
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI
| | - Jennifer M Wang
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI
| | - Ayodeji Adegunsoye
- Division of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, IL
| | | | | | | | | | - Sahand Ghodrati
- Department of Radiology, University of California at Davis, Sacramento, CA
| | | | - Henry Guo
- Department of Radiology, Stanford University, Palo Alto, CA
| | - Eleanor Soo
- Heart and Lung Imaging, Ltd, London, England
| | | | | | | | - Justin M Oldham
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI; Department of Epidemiology, University of Michigan, Ann Arbor, MI.
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12
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O'Dwyer D, Noth I, Oldham JM. Reply to: Leveraging Microbiome Composition Variability for Precision Medicine in Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med 2024. [PMID: 38271703 DOI: 10.1164/rccm.202312-2262le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/25/2024] [Indexed: 01/27/2024] Open
Affiliation(s)
- David O'Dwyer
- University of Michigan Hospital, 166144, Internal Medicine, Ann Arbor, Michigan, United States
| | - Imre Noth
- University of Virginia, 2358, Division of Pulmonary and Critical Care Medicine, Charlottesville, Virginia, United States
| | - Justin M Oldham
- University of California Davis, 8789, Pulmonary and Critical Care Medicine, Davis, California, United States;
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13
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Leavy OC, Goemans AF, Stockwell AD, Allen RJ, Guillen-Guio B, Hernandez-Beeftink T, Adegunsoye A, Booth HL, Cullinan P, Fahy WA, Fingerlin TE, Virk HS, Hall IP, Hart SP, Hill MR, Hirani N, Hubbard RB, Kaminski N, Ma SF, McAnulty RJ, Sheng XR, Millar AB, Molina-Molina M, Navaratnam V, Neighbors M, Parfrey H, Saini G, Sayers I, Strek ME, Tobin MD, Whyte MK, Zhang Y, Maher TM, Molyneaux PL, Oldham JM, Yaspan BL, Flores C, Martinez F, Reynolds CJ, Schwartz DA, Noth I, Jenkins RG, Wain LV. Genome-wide SNP-sex interaction analysis of susceptibility to idiopathic pulmonary fibrosis. medRxiv 2024:2024.01.12.24301204. [PMID: 38293162 PMCID: PMC10827242 DOI: 10.1101/2024.01.12.24301204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Background Idiopathic pulmonary fibrosis (IPF) is a chronic lung condition that is more prevalent in males than females. The reasons for this are not fully understood, with differing environmental exposures due to historically sex-biased occupations, or diagnostic bias, being possible explanations. To date, over 20 independent genetic variants have been identified to be associated with IPF susceptibility, but these have been discovered when combining males and females. Our aim was to test for the presence of sex-specific associations with IPF susceptibility and assess whether there is a need to consider sex-specific effects when evaluating genetic risk in clinical prediction models for IPF. Methods We performed genome-wide single nucleotide polymorphism (SNP)-by-sex interaction studies of IPF risk in six independent IPF case-control studies and combined them using inverse-variance weighted fixed effect meta-analysis. In total, 4,561 cases (1,280 females and 2,281 males) and 23,500 controls (8,360 females and 14,528 males) of European genetic ancestry were analysed. We used polygenic risk scores (PRS) to assess differences in genetic risk prediction between males and females. Findings Three independent genetic association signals were identified. All showed a consistent direction of effect across all individual IPF studies and an opposite direction of effect in IPF susceptibility between females and males. None had been previously identified in IPF susceptibility genome-wide association studies (GWAS). The predictive accuracy of the PRSs were similar between males and females, regardless of whether using combined or sex-specific GWAS results. Interpretation We prioritised three genetic variants whose effect on IPF risk may be modified by sex, however these require further study. We found no evidence that the predictive accuracy of common SNP-based PRSs varies significantly between males and females.
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Affiliation(s)
- Olivia C Leavy
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Anne F Goemans
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | | | - Richard J Allen
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Beatriz Guillen-Guio
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Tamara Hernandez-Beeftink
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | | | | | | | | | | | | | - Ian P Hall
- University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham, UK
| | | | | | | | - Richard B Hubbard
- University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham, UK
| | | | | | | | | | | | - Maria Molina-Molina
- Servei de Pneumologia, Laboratori de Pneumologia Experimental, Instituto de Investigación Biomédica de Bellvitge (IDIBELL), Barcelona, Spain
- Campus de Bellvitge, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Vidya Navaratnam
- Department of Respiratory Medicine, Sir Charles Gardiner Hospital, Perth, Australia
- Centre for Respiratory Research, University of Western Australia, Perth, Australia
| | | | - Helen Parfrey
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | | | - Ian Sayers
- Centre for Respiratory Research, NIHR Nottingham Biomedical Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | | | - Martin D Tobin
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | | | | | - Toby M Maher
- NIHR Imperial Biomedical Research Unit, National Heart and Lung Institute, Imperial College London, London, UK
- Division of Pulmonary and Critical Care Medicine, University of Southern California, Los Angeles, USA
| | - Philip L Molyneaux
- National Institute for Health Research Respiratory Clinical Research Facility, Royal Brompton Hospital, London, UK
- NIHR Imperial Biomedical Research Unit, National Heart and Lung Institute, Imperial College London, London, UK
| | | | | | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- Genomics Division, Instituto Tecnologico y de Energias Renovables, Santa Cruz de Tenerife, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | | | | | | | - Imre Noth
- University of Virginia, Virginia, USA
| | - R Gisli Jenkins
- NIHR Imperial Biomedical Research Unit, National Heart and Lung Institute, Imperial College London, London, UK
| | - Louise V Wain
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
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14
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Zhang D, Adegunsoye A, Oldham JM, Wolters PJ, Garcia CK, Newton CA. Reply: Telomere length and immunosuppression in non-idiopathic pulmonary fibrosis interstitial lung disease. Eur Respir J 2024; 63:2302146. [PMID: 38237997 PMCID: PMC11002962 DOI: 10.1183/13993003.02146-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 01/23/2024]
Affiliation(s)
- David Zhang
- Division of Pulmonary and Critical Care Medicine, Columbia University, New York, NY, USA
| | - Ayodeji Adegunsoye
- Section of Pulmonary and Critical Care, University of Chicago, Chicago, IL, USA
| | - Justin M Oldham
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Paul J Wolters
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Christine Kim Garcia
- Division of Pulmonary and Critical Care Medicine, Columbia University, New York, NY, USA
| | - Chad A Newton
- Division of Pulmonary and Critical Care Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
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15
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Guillen-Guio B, Paynton ML, Allen RJ, Chin DP, Donoghue LJ, Stockwell A, Leavy OC, Hernandez-Beeftink T, Reynolds C, Cullinan P, Martinez F, Booth HL, Fahy WA, Hall IP, Hart SP, Hill MR, Hirani N, Hubbard RB, McAnulty RJ, Millar AB, Navaratnam V, Oballa E, Parfrey H, Saini G, Sayers I, Tobin MD, Whyte MK, Adegunsoye A, Kaminski N, Ma SF, Strek ME, Zhang Y, Fingerlin TE, Molina-Molina M, Neighbors M, Sheng XR, Oldham JM, Maher TM, Molyneaux PL, Flores C, Noth I, Schwartz DA, Yaspan BL, Jenkins RG, Wain LV, Hollox EJ. Association study of human leukocyte antigen variants and idiopathic pulmonary fibrosis. ERJ Open Res 2024; 10:00553-2023. [PMID: 38375425 PMCID: PMC10875457 DOI: 10.1183/23120541.00553-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/05/2023] [Indexed: 02/21/2024] Open
Abstract
Introduction Idiopathic pulmonary fibrosis (IPF) is a chronic interstitial pneumonia marked by progressive lung fibrosis and a poor prognosis. Recent studies have highlighted the potential role of infection in the pathogenesis of IPF, and a prior association of the HLA-DQB1 gene with idiopathic fibrotic interstitial pneumonia (including IPF) has been reported. Owing to the important role that the human leukocyte antigen (HLA) region plays in the immune response, here we evaluated if HLA genetic variation was associated specifically with IPF risk. Methods We performed a meta-analysis of associations of the HLA region with IPF risk in individuals of European ancestry from seven independent case-control studies of IPF (comprising 5159 cases and 27 459 controls, including a prior study of fibrotic interstitial pneumonia). Single nucleotide polymorphisms, classical HLA alleles and amino acids were analysed and signals meeting a region-wide association threshold of p<4.5×10-4 and a posterior probability of replication >90% were considered significant. We sought to replicate the previously reported HLA-DQB1 association in the subset of studies independent of the original report. Results The meta-analysis of all seven studies identified four significant independent single nucleotide polymorphisms associated with IPF risk. However, none met the posterior probability for replication criterion. The HLA-DQB1 association was not replicated in the independent IPF studies. Conclusion Variation in the HLA region was not consistently associated with risk in studies of IPF. However, this does not preclude the possibility that other genomic regions linked to the immune response may be involved in the aetiology of IPF.
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Affiliation(s)
- Beatriz Guillen-Guio
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
- Joint first authors
| | - Megan L. Paynton
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- Joint first authors
| | - Richard J. Allen
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Daniel P.W. Chin
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | | | | | - Olivia C. Leavy
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Tamara Hernandez-Beeftink
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Carl Reynolds
- National Heart & Lung Institute, Imperial College London, London, UK
| | - Paul Cullinan
- National Heart & Lung Institute, Imperial College London, London, UK
| | | | - Helen L. Booth
- University College Hospital, University College London, London, UK
| | | | - Ian P. Hall
- School of Medicine, University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham, UK
| | - Simon P. Hart
- Hull York Medical School, University of Hull, Hull, UK
| | - Mike R. Hill
- MRC Population Health Unit, University of Oxford, Oxford, UK
| | - Nik Hirani
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Richard B. Hubbard
- School of Medicine, University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham, UK
| | | | - Ann B. Millar
- Bristol Medical School, University of Bristol, Bristol, UK
| | - Vidya Navaratnam
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK
- Queensland Lung Transplant Service, The Prince Charles Hospital, Brisbane, QLD, Australia
| | | | - Helen Parfrey
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | - Gauri Saini
- School of Medicine, University of Nottingham, Nottingham, UK
| | - Ian Sayers
- Centre for Respiratory Research, NIHR Nottingham Biomedical Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Martin D. Tobin
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Moira K.B. Whyte
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | | | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Shwu-Fan Ma
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Mary E. Strek
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tasha E. Fingerlin
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, USA
| | - Maria Molina-Molina
- Servei de Pneumologia, Laboratori de Pneumologia Experimental, Instituto de Investigación Biomédica de Bellvitge (IDIBELL), Barcelona, Spain
- Campus de Bellvitge, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | | | | | - Justin M. Oldham
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Toby M. Maher
- National Heart and Lung Institute, Imperial College London, London, UK
- Division of Pulmonary and Critical Care Medicine, University of Southern California, Los Angeles, USA
| | - Philip L. Molyneaux
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas’ NHS Foundation Trust, London, UK
| | - Carlos Flores
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- Genomics Division, Instituto Tecnologico y de Energias Renovables, Santa Cruz de Tenerife, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Imre Noth
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | | | | | - R. Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Louise V. Wain
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
- Joint senior authors
| | - Edward J. Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Joint senior authors
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16
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Saleem F, Ryerson CJ, Sarma N, Johannson K, Marcoux V, Fisher J, Assayag D, Manganas H, Khalil N, Morisset J, Glaspole IN, Goh N, Oldham JM, Cox G, Fell C, Gershon AS, Halayko A, Hambly N, Lok SD, Shapera S, To T, Wilcox PG, Wong AW, Kolb M, Khor YH. Predicting New-onset Exertional and Resting Hypoxemia in Fibrotic Interstitial Lung Disease. Ann Am Thorac Soc 2023; 20:1726-1734. [PMID: 37676933 DOI: 10.1513/annalsats.202303-208oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 09/07/2023] [Indexed: 09/09/2023] Open
Abstract
Rationale: Hypoxemia in fibrotic interstitial lung disease (ILD) indicates disease progression and is of prognostic significance. The onset of hypoxemia signifies disease progression and predicts mortality in fibrotic ILD. Accurately predicting new-onset exertional and resting hypoxemia prompts appropriate patient discussion and timely consideration of home oxygen. Objectives: We derived and externally validated a risk prediction tool for both new-onset exertional and new-onset resting hypoxemia. Methods: This study used ILD registries from Canada for the derivation cohort and from Australia and the United States for the validation cohort. New-onset exertional and resting hypoxemia were defined as nadir oxyhemoglobin saturation < 88% during 6-minute-walk tests, resting oxyhemoglobin saturation < 88%, or the initiation of ambulatory or continuous oxygen. Candidate predictors included patient demographics, ILD subtypes, and pulmonary function. Time-varying Cox regression was used to identify the top-performing prediction model according to Akaike information criterion and clinical usability. Model performance was assessed using Harrell's C-index and goodness-of-fit (GoF) likelihood ratio test. A categorized risk prediction tool was developed. Results: The best-performing prediction model for both new-onset exertional and new-onset resting hypoxemia included age, body mass index, a diagnosis of idiopathic pulmonary fibrosis, and percent predicted forced vital capacity and diffusing capacity of carbon monoxide. The risk prediction tool exhibited good performance for exertional hypoxemia (C-index, 0.70; GoF, P = 0.85) and resting hypoxemia (C-index, 0.77; GoF, P = 0.27) in the derivation cohort, with similar performance in the validation cohort except calibration for resting hypoxemia (GoF, P = 0.001). Conclusions: This clinically applicable risk prediction tool predicted new-onset exertional and resting hypoxemia at 6 months in the derivation cohort and a diverse validation cohort. Suboptimal GoF in the validation cohort likely reflected overestimation of hypoxemia risk and indicated that the model is not flawed because of underestimation of hypoxemia.
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Affiliation(s)
- Ferhan Saleem
- Department of Medicine and
- Department of Medicine, St. Martinus University, Willemstad, Curaçao, Netherlands Antilles
| | - Christopher J Ryerson
- Department of Medicine and
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nandini Sarma
- Department of Pulmonary and Critical Care Medicine, Oregon Health and Science University, Portland, Oregon
| | - Kerri Johannson
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Veronica Marcoux
- Department of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | | | - Deborah Assayag
- Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Helene Manganas
- Département de Médecine, Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
| | | | - Julie Morisset
- Département de Médecine, Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
| | - Ian N Glaspole
- Department of Respiratory Medicine, Alfred Health, Melbourne, Victoria, Australia
| | - Nicole Goh
- Department of Respiratory and Sleep Medicine, Austin Health, Heidelberg, Victoria, Australia
| | - Justin M Oldham
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan
| | - Gerard Cox
- Firestone Institute for Respiratory Health, McMaster University, Hamilton, Ontario, Canada
| | - Charlene Fell
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Andrea S Gershon
- Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada
| | - Andrew Halayko
- Departmentof Physiology and Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Nathan Hambly
- Firestone Institute for Respiratory Health, McMaster University, Hamilton, Ontario, Canada
| | - Stacey D Lok
- Department of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | | | - Teresa To
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Alyson W Wong
- Department of Medicine and
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada
| | - Martin Kolb
- Firestone Institute for Respiratory Health, McMaster University, Hamilton, Ontario, Canada
| | - Yet H Khor
- Department of Respiratory Medicine, Alfred Health, Melbourne, Victoria, Australia
- Department of Respiratory and Sleep Medicine, Austin Health, Heidelberg, Victoria, Australia
- Respiratory Research@Alfred, Central Clinical School, Monash University, Melbourne, Victoria, Australia; and
- Institute for Breathing and Sleep, Heidelberg, Victoria, Australia
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17
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Zhang D, Adegunsoye A, Oldham JM, Kozlitina J, Garcia N, Poonawalla M, Strykowski R, Linderholm AL, Ley B, Ma SF, Noth I, Strek ME, Wolters PJ, Garcia CK, Newton CA. Telomere length and immunosuppression in non-idiopathic pulmonary fibrosis interstitial lung disease. Eur Respir J 2023; 62:2300441. [PMID: 37591536 PMCID: PMC10695771 DOI: 10.1183/13993003.00441-2023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/26/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND Studies suggest a harmful pharmacogenomic interaction exists between short leukocyte telomere length (LTL) and immunosuppressants in idiopathic pulmonary fibrosis (IPF). It remains unknown if a similar interaction exists in non-IPF interstitial lung disease (ILD). METHODS A retrospective, multicentre cohort analysis was performed in fibrotic hypersensitivity pneumonitis (fHP), unclassifiable ILD (uILD) and connective tissue disease (CTD)-ILD patients from five centres. LTL was measured by quantitative PCR for discovery and replication cohorts and expressed as age-adjusted percentiles of normal. Inverse probability of treatment weights based on propensity scores were used to assess the association between mycophenolate or azathioprine exposure and age-adjusted LTL on 2-year transplant-free survival using weighted Cox proportional hazards regression incorporating time-dependent immunosuppressant exposure. RESULTS The discovery and replication cohorts included 613 and 325 patients, respectively. In total, 40% of patients were exposed to immunosuppression and 22% had LTL <10th percentile of normal. fHP and uILD patients with LTL <10th percentile experienced reduced survival when exposed to either mycophenolate or azathioprine in the discovery cohort (mortality hazard ratio (HR) 4.97, 95% CI 2.26-10.92; p<0.001) and replication cohort (mortality HR 4.90, 95% CI 1.74-13.77; p=0.003). Immunosuppressant exposure was not associated with differential survival in patients with LTL ≥10th percentile. There was a significant interaction between LTL <10th percentile and immunosuppressant exposure (discovery pinteraction=0.013; replication pinteraction=0.011). Low event rate and prevalence of LTL <10th percentile precluded subgroup analyses for CTD-ILD. CONCLUSION Similar to IPF, fHP and uILD patients with age-adjusted LTL <10th percentile may experience reduced survival when exposed to immunosuppression.
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Affiliation(s)
- David Zhang
- Division of Pulmonary and Critical Care Medicine, Columbia University, New York, NY, USA
- These two authors contributed equally to this work
| | - Ayodeji Adegunsoye
- Section of Pulmonary and Critical Care, Department of Medicine, University of Chicago, Chicago, IL, USA
- These two authors contributed equally to this work
| | - Justin M Oldham
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Julia Kozlitina
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nicole Garcia
- Section of Pulmonary and Critical Care, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Maria Poonawalla
- Section of Pulmonary and Critical Care, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Rachel Strykowski
- Section of Pulmonary and Critical Care, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Angela L Linderholm
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of California Davis, Sacramento, CA, USA
| | - Brett Ley
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Shwu-Fan Ma
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, VA, USA
| | - Imre Noth
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, VA, USA
| | - Mary E Strek
- Section of Pulmonary and Critical Care, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Paul J Wolters
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Christine Kim Garcia
- Division of Pulmonary and Critical Care Medicine, Columbia University, New York, NY, USA
| | - Chad A Newton
- Division of Pulmonary and Critical Care Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
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18
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Amati F, Spagnolo P, Ryerson CJ, Oldham JM, Gramegna A, Stainer A, Mantero M, Sverzellati N, Lacedonia D, Richeldi L, Blasi F, Aliberti S. Walking the path of treatable traits in interstitial lung diseases. Respir Res 2023; 24:251. [PMID: 37872563 PMCID: PMC10594881 DOI: 10.1186/s12931-023-02554-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/05/2023] [Indexed: 10/25/2023] Open
Abstract
Interstitial lung diseases (ILDs) are complex and heterogeneous diseases. The use of traditional diagnostic classification in ILD can lead to suboptimal management, which is worsened by not considering the molecular pathways, biological complexity, and disease phenotypes. The identification of specific "treatable traits" in ILDs, which are clinically relevant and modifiable disease characteristics, may improve patient's outcomes. Treatable traits in ILDs may be classified into four different domains (pulmonary, aetiological, comorbidities, and lifestyle), which will facilitate identification of related assessment tools, treatment options, and expected benefits. A multidisciplinary care team model is a potential way to implement a "treatable traits" strategy into clinical practice with the aim of improving patients' outcomes. Multidisciplinary models of care, international registries, and the use of artificial intelligence may facilitate the implementation of the "treatable traits" approach into clinical practice. Prospective studies are needed to test potential therapies for a variety of treatable traits to further advance care of patients with ILD.
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Affiliation(s)
- Francesco Amati
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072, Pieve Emanuele, Milan, Italy
- IRCCS Humanitas Research Hospital, Respiratory Unit, Via Manzoni 56, 20089, Rozzano, Milan, Italy
| | - Paolo Spagnolo
- Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padua, Italy
| | - Christopher J Ryerson
- Department of Medicine, University of British Columbia and Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, Canada
| | - Justin M Oldham
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Andrea Gramegna
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Respiratory Unit and Cystic Fibrosis Adult Center, Milan, Italy
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Anna Stainer
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072, Pieve Emanuele, Milan, Italy
- IRCCS Humanitas Research Hospital, Respiratory Unit, Via Manzoni 56, 20089, Rozzano, Milan, Italy
| | - Marco Mantero
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Respiratory Unit and Cystic Fibrosis Adult Center, Milan, Italy
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Nicola Sverzellati
- Unit of Scienze Radiologiche, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Donato Lacedonia
- Department of Medical and Occupational Sciences, Institute of Respiratory Disease, Università degli Studi di Foggia, Foggia, Italy
| | - Luca Richeldi
- Fondazione Policlinico A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Francesco Blasi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Respiratory Unit and Cystic Fibrosis Adult Center, Milan, Italy
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Stefano Aliberti
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072, Pieve Emanuele, Milan, Italy.
- IRCCS Humanitas Research Hospital, Respiratory Unit, Via Manzoni 56, 20089, Rozzano, Milan, Italy.
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19
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Maher TM, Assassi S, Azuma A, Cottin V, Hoffmann-Vold AM, Kreuter M, Oldham JM, Richeldi L, Valenzuela C, Wijsenbeek MS, Coeck C, Schlecker C, Voss F, Wachtlin D, Martinez FJ. Design of a phase III, double-blind, randomised, placebo-controlled trial of BI 1015550 in patients with progressive pulmonary fibrosis (FIBRONEER-ILD). BMJ Open Respir Res 2023; 10:e001580. [PMID: 37709661 PMCID: PMC10503394 DOI: 10.1136/bmjresp-2022-001580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 08/22/2023] [Indexed: 09/16/2023] Open
Abstract
INTRODUCTION Progressive pulmonary fibrosis (PPF) includes any diagnosis of progressive fibrotic interstitial lung disease (ILD) other than idiopathic pulmonary fibrosis (IPF). However, disease progression appears comparable between PPF and IPF, suggesting a similar underlying pathology relating to pulmonary fibrosis. Following positive results in a phase II study in IPF, this phase III study will investigate the efficacy and safety of BI 1015550 in patients with PPF (FIBRONEER-ILD). METHODS AND ANALYSIS In this phase III, double-blind, placebo-controlled trial, patients are being randomised 1:1:1 to receive BI 1015550 (9 mg or 18 mg) or placebo twice daily over at least 52 weeks, stratified by background nintedanib use. Patients must be diagnosed with pulmonary fibrosis other than IPF that is progressive, based on predefined criteria. Patients must have forced vital capacity (FVC) ≥45% predicted and haemoglobin-corrected diffusing capacity of the lung for carbon monoxide ≥25% predicted. Patients must be receiving nintedanib for at least 12 weeks, or not receiving nintedanib for at least 8 weeks, prior to screening. Patients on stable treatment with permitted immunosuppressives (eg, methotrexate, azathioprine) may continue their treatment throughout the trial. Patients with clinically significant airway obstruction or other pulmonary abnormalities, and those using immunosuppressives that may confound FVC results (cyclophosphamide, tocilizumab, mycophenolate, rituximab) or high-dose steroids will be excluded. The primary endpoint is absolute change from baseline in FVC (mL) at week 52. The key secondary endpoint is time to the first occurrence of any acute ILD exacerbation, hospitalisation for respiratory cause or death, over the duration of the trial. ETHICS AND DISSEMINATION The trial is being carried out in accordance with the ethical principles of the Declaration of Helsinki, the International Council on Harmonisation Guideline for Good Clinical Practice and other local ethics committees. The study results will be disseminated at scientific congresses and in peer-reviewed publications. TRIAL REGISTRATION NUMBER NCT05321082.
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Affiliation(s)
- Toby M Maher
- Department of Pulmonary, Critical Care and Sleep Medicine, University of Southern California Keck School of Medicine, Los Angeles, California, USA
- Section of Inflammation, Repair and Development, Imperial College London National Heart and Lung Institute, London, UK
| | - Shervin Assassi
- Division of Rheumatology, University of Texas McGovern Medical School, Houston, Texas, USA
| | - Arata Azuma
- Pulmonary Medicine and Oncology, Nippon Medical School, Tokyo, Japan
- Respiratory Medicine and Clinical Research Centre, Meisei Hospital, Saitama, Japan
| | - Vincent Cottin
- Service de pneumologie, Hôpital Louis Pradel, Centre de Référence des Maladies Pulmonaires Rares, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, iNRAE, member of ERN-LUNG, Lyon, France
| | | | - Michael Kreuter
- Center for Interstitial and Rare Lung Diseases, Department of Pneumology, Thoraxklinik, University of Heidelberg, Member of the German Center for Lung Research, Heidelberg, Germany
| | - Justin M Oldham
- Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Luca Richeldi
- Unità Operativa Complessa di Pneumologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Claudia Valenzuela
- ILD Unit, Pulmonology Department, Hospital Universitario de la Princesa, University Autonomade Madrid, Madrid, Spain
| | - Marlies S Wijsenbeek
- Department of Respiratory Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Carl Coeck
- Boehringer Ingelheim SComm, Brussels, Belgium
| | | | - Florian Voss
- Boehringer Ingelheim Pharma GmbH & Co. KG, Ingelheim am Rhein, Germany
| | - Daniel Wachtlin
- Boehringer Ingelheim Pharma GmbH & Co. KG, Ingelheim am Rhein, Germany
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20
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Neely ML, Hellkamp AS, Bender S, Todd JL, Liesching T, Luckhardt TR, Oldham JM, Raj R, White ES, Palmer SM. Lung function trajectories in patients with idiopathic pulmonary fibrosis. Respir Res 2023; 24:209. [PMID: 37612608 PMCID: PMC10463468 DOI: 10.1186/s12931-023-02503-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 08/01/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is a progressive fibrosing interstitial lung disease characterised by decline in lung function. We evaluated trajectories of forced vital capacity (FVC) and diffusing capacity (DLco) in a cohort of patients with IPF. METHODS Patients with IPF that was diagnosed or confirmed at the enrolling centre in the previous 6 months were enrolled into the IPF-PRO Registry between June 2014 and October 2018. Patients were followed prospectively, with lung function data collected as part of routine clinical care. Mean trajectories of FVC and DLco % predicted in all patients and in subgroups by characteristics assessed at enrolment were estimated using a joint model that accounted for factors such as disease severity and visit patterns. RESULTS Of 1002 patients in the registry, 941 had ≥ 1 FVC and/or DLco measurement after enrolment. The median (Q1, Q3) follow-up period was 35.1 (18.9, 47.2) months. Overall, mean estimated declines in FVC and DLco % predicted were 2.8% and 2.9% per year, respectively. There was no evidence that the mean trajectories of FVC or DLco had a non-linear relationship with time at the population level. Patients who were male, white, had a family history of ILD, were using oxygen, or had prior/current use of antifibrotic therapy at enrolment had greater rates of decline in FVC % predicted. Patients who were male or white had greater rates of decline in DLco % predicted. CONCLUSIONS Data from the IPF-PRO Registry suggest a constant rate of decline in lung function over a prolonged period, supporting the inexorably progressive nature of IPF. A graphical abstract summarising the data in this manuscript is available at: https://www.usscicomms.com/respiratory/IPF-PRORegistry_LungFunctionTrajectories . TRIAL REGISTRATION NCT01915511.
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Affiliation(s)
- Megan L Neely
- Duke Clinical Research Institute, Durham, NC, USA.
- Duke University Medical Center, Durham, NC, USA.
| | - Anne S Hellkamp
- Duke Clinical Research Institute, Durham, NC, USA
- Duke University Medical Center, Durham, NC, USA
| | - Shaun Bender
- Boehringer Ingelheim Pharmaceuticals, Inc, Ridgefield, CT, USA
| | - Jamie L Todd
- Duke Clinical Research Institute, Durham, NC, USA
- Duke University Medical Center, Durham, NC, USA
| | | | - Tracy R Luckhardt
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Justin M Oldham
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Rishi Raj
- Stanford University School of Medicine, Stanford, CA, USA
| | - Eric S White
- Boehringer Ingelheim Pharmaceuticals, Inc, Ridgefield, CT, USA
| | - Scott M Palmer
- Duke Clinical Research Institute, Durham, NC, USA
- Duke University Medical Center, Durham, NC, USA
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21
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Richeldi L, Azuma A, Cottin V, Kreuter M, Maher TM, Martinez FJ, Oldham JM, Valenzuela C, Gordat M, Liu Y, Stowasser S, Zoz DF, Wijsenbeek MS. Design of a phase III, double-blind, randomised, placebo-controlled trial of BI 1015550 in patients with idiopathic pulmonary fibrosis (FIBRONEER-IPF). BMJ Open Respir Res 2023; 10:e001563. [PMID: 37597969 PMCID: PMC10441083 DOI: 10.1136/bmjresp-2022-001563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 07/31/2023] [Indexed: 08/21/2023] Open
Abstract
IntroductionThere is an unmet need for new treatments for idiopathic pulmonary fibrosis (IPF). The oral preferential phosphodiesterase 4B inhibitor, BI 1015550, prevented a decline in forced vital capacity (FVC) in a phase II study in patients with IPF. This study design describes the subsequent pivotal phase III study of BI 1015550 in patients with IPF (FIBRONEER-IPF). METHODS AND ANALYSIS In this placebo-controlled, double-blind, phase III trial, patients are being randomised in a 1:1:1 ratio to receive 9 mg or 18 mg of BI 1015550 or placebo two times per day over at least 52 weeks, stratified by use of background antifibrotics (nintedanib/pirfenidone vs neither). The primary endpoint is the absolute change in FVC at week 52. The key secondary endpoint is a composite of time to first acute IPF exacerbation, hospitalisation due to respiratory cause or death over the duration of the trial. ETHICS AND DISSEMINATION The trial is being carried out in compliance with the ethical principles of the Declaration of Helsinki, in accordance with the International Council on Harmonisation Guideline for Good Clinical Practice and other local ethics committees. The results of the study will be disseminated at scientific congresses and in peer-reviewed publications. TRIAL REGISTRATION NUMBER NCT05321069.
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Affiliation(s)
- Luca Richeldi
- Unità Operativa Complessa di Pneumologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Arata Azuma
- Pulmonary Medicine and Oncology, Nippon Medical School, Tokyo, Japan
- Respiratory Medicine and Clinical Research Centre, Meisei Hospital, Saitama, Japan
| | - Vincent Cottin
- Hôpital Louis Pradel, Centre Coordonnateur National de référence des Maladies Pulmonaires Rares, Hospices Civils de Lyon, UMR754, INRAE, Université Claude Bernard Lyon 1, Member of ERN-LUNG, Lyon, France
| | - Michael Kreuter
- Centre for Interstitial and Rare Lung Diseases, Department of Pneumology, Thoraxklinik, University of Heidelberg, German Center for Lung Research, Heidelberg, Germany
- Department of Pneumology, RKH Clinic Ludwigsburg, Ludwigsburg, Germany
| | - Toby M Maher
- Department of Pulmonary, Critical Care and Sleep Medicine, USC Keck School of Medicine, Los Angeles, California, USA
- Section of Inflammation, Repair and Development, National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Justin M Oldham
- Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Claudia Valenzuela
- ILD Unit, Pulmonology Department, Hospital Universitario de la Princesa, Universidad Autónoma de Madrid, Madrid, Spain
| | - Maud Gordat
- Clinical Development & Operation Department, Boehringer Ingelheim, Reims, France
| | - Yi Liu
- Department of Biostatistics and Data Sciences, Boehringer Ingelheim Pharmaceuticals Inc, Ridgefield, Connecticut, USA
| | - Susanne Stowasser
- TA Inflammation Med, Boehringer Ingelheim International GmbH, Ingelheim am Rhein, Germany
| | - Donald F Zoz
- Global Clinical Development and Medical Affairs, Boehringer Ingelheim Pharmaceuticals Inc, Ridgefield, Connecticut, USA
| | - Marlies S Wijsenbeek
- Centre for Interstitial Lung Diseases and Sarcoidosis, Department of Respiratory Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
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22
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Guillen-Guio B, Paynton ML, Allen RJ, Chin DP, Donoghue LJ, Stockwell A, Leavy OC, Hernandez-Beeftink T, Reynolds C, Cullinan P, Martinez F, Booth HL, Fahy WA, Hall IP, Hart SP, Hill MR, Hirani N, Hubbard RB, McAnulty RJ, Millar AB, Navaratnam V, Oballa E, Parfrey H, Saini G, Sayers I, Tobin MD, Whyte MKB, Adegunsoye A, Kaminski N, Shwu-Fan M, Strek ME, Zhang Y, Fingerlin TE, Molina-Molina M, Neighbors M, Sheng XR, Oldham JM, Maher TM, Molyneaux PL, Flores C, Noth I, Schwartz DA, Yaspan BL, Jenkins RG, Wain LV, Hollox EJ. Association study of human leukocyte antigen (HLA) variants and idiopathic pulmonary fibrosis. medRxiv 2023:2023.07.20.23292940. [PMID: 37546732 PMCID: PMC10402235 DOI: 10.1101/2023.07.20.23292940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Introduction Idiopathic pulmonary fibrosis (IPF) is a chronic interstitial pneumonia marked by progressive lung fibrosis and a poor prognosis. Recent studies have highlighted the potential role of infection in the pathogenesis of IPF and a prior association of the HLA-DQB1 gene with idiopathic fibrotic interstitial pneumonia (including IPF) has been reported. Due to the important role that the Human Leukocyte Antigen (HLA) region plays in the immune response, here we evaluated if HLA genetic variation was associated specifically with IPF risk. Methods We performed a meta-analysis of associations of the HLA region with IPF risk in individuals of European ancestry from seven independent case-control studies of IPF (comprising a total of 5,159 cases and 27,459 controls, including the prior study of fibrotic interstitial pneumonia). Single nucleotide polymorphisms, classical HLA alleles and amino acids were analysed and signals meeting a region-wide association threshold p<4.5×10-4 and a posterior probability of replication >90% were considered significant. We sought to replicate the previously reported HLA-DQB1 association in the subset of studies independent of the original report. Results The meta-analysis of all seven studies identified four significant independent single nucleotide polymorphisms associated with IPF risk. However, none met the posterior probability for replication criterion. The HLA-DQB1 association was not replicated in the independent IPF studies. Conclusion Variation in the HLA region was not consistently associated with risk in studies of IPF. However, this does not preclude the possibility that other genomic regions linked to the immune response may be involved in the aetiology of IPF.
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Affiliation(s)
- Beatriz Guillen-Guio
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Megan L. Paynton
- Department of Population Health Sciences, University of Leicester, UK
| | - Richard J. Allen
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Daniel P.W. Chin
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | | | | | - Olivia C. Leavy
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Tamara Hernandez-Beeftink
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | | | | | | | | | | | | | - Ian P. Hall
- University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham, UK
| | | | | | | | - Richard B. Hubbard
- University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham, UK
| | | | | | - Vidya Navaratnam
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK
- Queensland Lung Transplant Service, The Prince Charles Hospital, Brisbane, QLD, Australia
| | | | - Helen Parfrey
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | | | - Ian Sayers
- Centre for Respiratory Research, NIHR Nottingham Biomedical Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Martin D. Tobin
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | | | | | | | | | | | | | | | - Maria Molina-Molina
- Servei de Pneumologia, Laboratori de Pneumologia Experimental, Instituto de Investigación Biomédica de Bellvitge (IDIBELL), Barcelona, Spain
- Campus de Bellvitge, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigacion Biomedica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | | | | | | | - Toby M. Maher
- National Heart and Lung Institute, Imperial College London, London, UK
- Division of Pulmonary and Critical Care Medicine, University of Southern California, Los Angeles, USA
| | - Philip L. Molyneaux
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy’s and St Thomas’ NHS Foundation Trust, London, UK
| | - Carlos Flores
- Centro de Investigacion Biomedica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- Genomics Division, Instituto Tecnologico y de Energias Renovables, Santa Cruz de Tenerife, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Imre Noth
- University of Virginia, Virginia, USA
| | | | | | - R. Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Louise V. Wain
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Edward J. Hollox
- Department of Genetics and Genome Biology, University of Leicester, UK
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23
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Oldham JM, Johnson KW, Albers GJ, Calamita E, Mah J, Ghai P, Hewitt RJ, Maher TM, Molyneaux PL, Huang M, Byrne AJ. Airway soluble CSF1R predicts progression in patients with idiopathic pulmonary fibrosis. ERJ Open Res 2023; 9:00690-2022. [PMID: 37465557 PMCID: PMC10350676 DOI: 10.1183/23120541.00690-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/03/2023] [Indexed: 07/20/2023] Open
Abstract
This study provides the first evidence for a role of airway sCSF1R in IPF https://bit.ly/3KTBrCA.
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Affiliation(s)
- Justin M. Oldham
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Gesa J. Albers
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Emily Calamita
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Jordina Mah
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Poonam Ghai
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Richard J. Hewitt
- National Heart and Lung Institute, Imperial College London, London, UK
- Interstitial Lung Disease Unit, Royal Brompton and Harefield Clinical Group, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Toby M. Maher
- National Heart and Lung Institute, Imperial College London, London, UK
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Philip L. Molyneaux
- National Heart and Lung Institute, Imperial College London, London, UK
- Interstitial Lung Disease Unit, Royal Brompton and Harefield Clinical Group, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | | | - Adam J. Byrne
- National Heart and Lung Institute, Imperial College London, London, UK
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Oldham JM, Allen RJ, Lorenzo-Salazar JM, Flores C, Wain LV, Noth I. Reply to Spek and Duitman. Am J Respir Crit Care Med 2023; 207:1644-1645. [PMID: 36927480 PMCID: PMC10273109 DOI: 10.1164/rccm.202303-0402le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Affiliation(s)
- Justin M. Oldham
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan
| | - Richard J. Allen
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - Jose M. Lorenzo-Salazar
- División Genómica, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, España, Spain
| | - Carlos Flores
- División Genómica, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, España, Spain
- Unidad de investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, España, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, España, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, España, Spain
| | - 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; and
| | - Imre Noth
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, Virginia
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Oldham JM, Allen RJ, Lorenzo-Salazar JM, Molyneaux PL, Ma SF, Joseph C, Kim JS, Guillen-Guio B, Hernández-Beeftink T, Kropski JA, Huang Y, Lee CT, Adegunsoye A, Pugashetti JV, Linderholm AL, Vo V, Strek ME, Jou J, Muñoz-Barrera A, Rubio-Rodriguez LA, Hubbard R, Hirani N, Whyte MKB, Hart S, Nicholson AG, Lancaster L, Parfrey H, Rassl D, Wallace W, Valenzi E, Zhang Y, Mychaleckyj J, Stockwell A, Kaminski N, Wolters PJ, Molina-Molina M, Banovich NE, Fahy WA, Martinez FJ, Hall IP, Tobin MD, Maher TM, Blackwell TS, Yaspan BL, Jenkins RG, Flores C, Wain LV, Noth I. PCSK6 and Survival in Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med 2023; 207:1515-1524. [PMID: 36780644 PMCID: PMC10263132 DOI: 10.1164/rccm.202205-0845oc] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 02/13/2023] [Indexed: 02/15/2023] Open
Abstract
Rationale: Idiopathic pulmonary fibrosis (IPF) is a devastating disease characterized by limited treatment options and high mortality. A better understanding of the molecular drivers of IPF progression is needed. Objectives: To identify and validate molecular determinants of IPF survival. Methods: A staged genome-wide association study was performed using paired genomic and survival data. Stage I cases were drawn from centers across the United States and Europe and stage II cases from Vanderbilt University. Cox proportional hazards regression was used to identify gene variants associated with differential transplantation-free survival (TFS). Stage I variants with nominal significance (P < 5 × 10-5) were advanced for stage II testing and meta-analyzed to identify those reaching genome-wide significance (P < 5 × 10-8). Downstream analyses were performed for genes and proteins associated with variants reaching genome-wide significance. Measurements and Main Results: After quality controls, 1,481 stage I cases and 397 stage II cases were included in the analysis. After filtering, 9,075,629 variants were tested in stage I, with 158 meeting advancement criteria. Four variants associated with TFS with consistent effect direction were identified in stage II, including one in an intron of PCSK6 (proprotein convertase subtilisin/kexin type 6) reaching genome-wide significance (hazard ratio, 4.11 [95% confidence interval, 2.54-6.67]; P = 9.45 × 10-9). PCSK6 protein was highly expressed in IPF lung parenchyma. PCSK6 lung staining intensity, peripheral blood gene expression, and plasma concentration were associated with reduced TFS. Conclusions: We identified four novel variants associated with IPF survival, including one in PCSK6 that reached genome-wide significance. Downstream analyses suggested that PCSK6 protein plays a potentially important role in IPF progression.
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Affiliation(s)
- Justin M. Oldham
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan
| | - Richard J. Allen
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - Jose M. Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | - Philip L. Molyneaux
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Shwu-Fan Ma
- Division of Pulmonary and Critical Care Medicine and
| | | | - John S. Kim
- Division of Pulmonary and Critical Care Medicine and
| | - Beatriz Guillen-Guio
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Tamara Hernández-Beeftink
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
| | - Jonathan A. Kropski
- Division of Pulmonary and Critical Care Medicine, Vanderbilt University, Nashville, Tennessee
| | - Yong Huang
- Division of Pulmonary and Critical Care Medicine and
| | - 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
| | - Janelle Vu Pugashetti
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California, Davis, Davis, California
| | - Angela L. Linderholm
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California, Davis, Davis, California
| | - Vivian Vo
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California, Davis, Davis, California
| | - Mary E. Strek
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois
| | - Jonathan Jou
- Department of Surgery, College of Medicine, University of Illinois, Peoria, Illinois
| | - Adrian Muñoz-Barrera
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | - Luis A. Rubio-Rodriguez
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | - Richard Hubbard
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, United Kingdom
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Nik Hirani
- Medical Research Council Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Moira K. B. Whyte
- Medical Research Council Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Simon Hart
- Respiratory Research Group, Hull York Medical School, Castle Hill Hospital, Cottingham, United Kingdom
| | - Andrew G. Nicholson
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Lisa Lancaster
- Division of Pulmonary and Critical Care Medicine, Vanderbilt University, Nashville, Tennessee
| | - Helen Parfrey
- Cambridge Interstitial Lung Disease Service, Royal Papworth Hospital, Cambridge, United Kingdom
| | - Doris Rassl
- Cambridge Interstitial Lung Disease Service, Royal Papworth Hospital, Cambridge, United Kingdom
| | - William Wallace
- Medical Research Council Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Eleanor Valenzi
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Josyf Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | | | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, School of Medicine, Yale University, New Haven, Connecticut
| | - Paul J. Wolters
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, California
| | - Maria Molina-Molina
- Servei de Pneumologia, Laboratori de Pneumologia Experimental, Instituto de Investigación Biomédica de Bellvitge, Campus de Bellvitge, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | | | - William A. Fahy
- Discovery Medicine, GlaxoSmithKline, Stevenage, United Kingdom
| | | | - Ian P. Hall
- Division of Respiratory Medicine and
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, 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
| | - Toby M. Maher
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Division of Pulmonary and Critical Care Medicine, University of Southern California, Los Angeles, California; and
| | - Timothy S. Blackwell
- Division of Pulmonary and Critical Care Medicine, Vanderbilt University, Nashville, Tennessee
| | | | - R. Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - 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
| | - Imre Noth
- Division of Pulmonary and Critical Care Medicine and
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Peljto AL, Blumhagen RZ, Walts AD, Cardwell J, Powers J, Corte TJ, Dickinson JL, Glaspole I, Moodley YP, Vasakova MK, Bendstrup E, Davidsen JR, Borie R, Crestani B, Dieude P, Bonella F, Costabel U, Gudmundsson G, Donnelly SC, Egan J, Henry MT, Keane MP, Kennedy MP, McCarthy C, McElroy AN, Olaniyi JA, O’Reilly KMA, Richeldi L, Leone PM, Poletti V, Puppo F, Tomassetti S, Luzzi V, Kokturk N, Mogulkoc N, Fiddler CA, Hirani N, Jenkins RG, Maher TM, Molyneaux PL, Parfrey H, Braybrooke R, Blackwell TS, Jackson PD, Nathan SD, Porteous MK, Brown KK, Christie JD, Collard HR, Eickelberg O, Foster EE, Gibson KF, Glassberg M, Kass DJ, Kropski JA, Lederer D, Linderholm AL, Loyd J, Mathai SK, Montesi SB, Noth I, Oldham JM, Palmisciano AJ, Reichner CA, Rojas M, Roman J, Schluger N, Shea BS, Swigris JJ, Wolters PJ, Zhang Y, Prele CMA, Enghelmayer JI, Otaola M, Ryerson CJ, Salinas M, Sterclova M, Gebremariam TH, Myllärniemi M, Carbone RG, Furusawa H, Hirose M, Inoue Y, Miyazaki Y, Ohta K, Ohta S, Okamoto T, Kim DS, Pardo A, Selman M, Aranda AU, Park MS, Park JS, Song JW, Molina-Molina M, Planas-Cerezales L, Westergren-Thorsson G, Smith AV, Manichaikul AW, Kim JS, Rich SS, Oelsner EC, Barr RG, Rotter JI, Dupuis J, O’Connor G, Vasan RS, Cho MH, Silverman EK, Schwarz MI, Steele MP, Lee JS, Yang IV, Fingerlin TE, Schwartz DA. Idiopathic Pulmonary Fibrosis Is Associated with Common Genetic Variants and Limited Rare Variants. Am J Respir Crit Care Med 2023; 207:1194-1202. [PMID: 36602845 PMCID: PMC10161752 DOI: 10.1164/rccm.202207-1331oc] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 01/04/2023] [Indexed: 01/06/2023] Open
Abstract
Rationale: Idiopathic pulmonary fibrosis (IPF) is a rare, irreversible, and progressive disease of the lungs. Common genetic variants, in addition to nongenetic factors, have been consistently associated with IPF. Rare variants identified by candidate gene, family-based, and exome studies have also been reported to associate with IPF. However, the extent to which rare variants, genome-wide, may contribute to the risk of IPF remains unknown. Objectives: We used whole-genome sequencing to investigate the role of rare variants, genome-wide, on IPF risk. Methods: As part of the Trans-Omics for Precision Medicine Program, we sequenced 2,180 cases of IPF. Association testing focused on the aggregated effect of rare variants (minor allele frequency ⩽0.01) within genes or regions. We also identified individual rare variants that are influential within genes and estimated the heritability of IPF on the basis of rare and common variants. Measurements and Main Results: Rare variants in both TERT and RTEL1 were significantly associated with IPF. A single rare variant in each of the TERT and RTEL1 genes was found to consistently influence the aggregated test statistics. There was no significant evidence of association with other previously reported rare variants. The SNP heritability of IPF was estimated to be 32% (SE = 3%). Conclusions: Rare variants within the TERT and RTEL1 genes and well-established common variants have the largest contribution to IPF risk overall. Efforts in risk profiling or the development of therapies for IPF that focus on TERT, RTEL1, common variants, and environmental risk factors are likely to have the largest impact on this complex disease.
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Affiliation(s)
- Anna L. Peljto
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Rachel Z. Blumhagen
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
- National Jewish Health, Denver, Colorado
| | | | - Jonathan Cardwell
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Julia Powers
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Tamera J. Corte
- Royal Prince Alfred Hospital, University of Sydney, Sydney, Australia
| | - Joanne L. Dickinson
- Menzies Institute of Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Ian Glaspole
- Allergy, Asthma and Clinical Immunology Clinic, Alfred Health, Sydney, Australia
| | - Yuben P. Moodley
- Department of Respiratory Medicine, University of Western Australia, Perth, Australia
| | | | - Elisabeth Bendstrup
- Center for Rare Lung Diseases, Department of Respiratory Diseases and Allergy, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Jesper R. Davidsen
- South Danish Center for Interstitial Lung Diseases, Department of Respiratory Medicine, Odense University Hospital, Odense, Denmark
| | | | - Bruno Crestani
- Service de Pneumologie A and
- Université Paris Cité, INSERM, Physiopathologie et Épidémiologie des Maladies Respiratoires, Paris, France
| | | | - Francesco Bonella
- Center for Interstitial and Rare Lung Diseases, Ruhrlandklinik University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Ulrich Costabel
- Center for Interstitial and Rare Lung Diseases, Ruhrlandklinik University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Gunnar Gudmundsson
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Department of Respiratory Medicine and Sleep, Landspitali University Hospital, Reykjavik, Iceland
| | | | - Jim Egan
- National Lung Transplantation Centre, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Michael T. Henry
- Department of Respiratory Medicine, Cork University Hospital, Cork, Ireland
| | - Michael P. Keane
- St. Vincent’s University Hospital, University College Dublin, Dublin, Ireland
| | - Marcus P. Kennedy
- Department of Respiratory Medicine, Cork University Hospital, Cork, Ireland
| | - Cormac McCarthy
- St. Vincent’s University Hospital, University College Dublin, Dublin, Ireland
| | | | | | | | - Luca Richeldi
- Fondazione Policlinico A. Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Paolo M. Leone
- Fondazione Policlinico A. Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Venerino Poletti
- Department of Diseases of the Thorax, G. B. Morgagni Hospital, Forlì, Italy
- Department of Medical and Surgical Sciences, DIMES University of Bologna, Bologna, Italy
| | - Francesco Puppo
- Department of Internal Medicine, University of Genoa, Genoa, Italy
| | - Sara Tomassetti
- Department of Clinical and Experimental Medicine, Interventional Pulmonology Unit, Careggi University Hospital, Florence, Italy
| | - Valentina Luzzi
- Interventional Pulmonology Unit, Careggi University Hospital, Florence, Italy
| | | | - Nesrin Mogulkoc
- Department of Pulmonology, Ege University Hospital, Izmir, Turkey
| | | | | | - R. Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Toby M. Maher
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Keck Medicine of USC, University of Southern California, Los Angeles, California
| | - Philip L. Molyneaux
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Helen Parfrey
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - Rebecca Braybrooke
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
| | | | - Peter D. Jackson
- Department of Pulmonary and Critical Care Medicine, Virginia Commonwealth University, Richmond, Virginia
| | | | - Mary K. Porteous
- Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Jason D. Christie
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Harold R. Collard
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Oliver Eickelberg
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Elena E. Foster
- Division of Pulmonary, Critical Care, and Sleep Medicine, School of Medicine, University of California, Davis, Sacramento, California
| | - Kevin F. Gibson
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Marilyn Glassberg
- Division of Pulmonary, Critical Care and Sleep Medicine, College of Medicine, University of Arizona, Phoenix, Arizona
| | - Daniel J. Kass
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - David Lederer
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York
| | - Angela L. Linderholm
- Department of Internal Medicine, University of California, Davis, Davis, California
| | - Jim Loyd
- Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Sydney B. Montesi
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | | | | | - Amy J. Palmisciano
- Division of Pulmonary, Critical Care and Sleep Medicine, Alpert Medical School, Brown University, Providence, Rhode Island
| | - Cristina A. Reichner
- Division of Pulmonary, Critical Care and Sleep Medicine, MedStar Georgetown University Hospital, Washington, DC
| | - Mauricio Rojas
- Division of Pulmonary, Critical Care, and Sleep Medicine, Ohio State University, Columbus, Ohio
| | - Jesse Roman
- Division of Pulmonary, Allergy, and Critical Care, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Neil Schluger
- Columbia University Medical Center, New York, New York
| | - Barry S. Shea
- Division of Pulmonary, Critical Care and Sleep Medicine, Alpert Medical School, Brown University, Providence, Rhode Island
| | | | - Paul J. Wolters
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Yingze Zhang
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Cecilia M. A. Prele
- Institute for Respiratory Health, University of Western Australia, Perth, Australia
| | - Juan I. Enghelmayer
- Brown University, Providence, Rhode Island
- Hospital de Clínicas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Maria Otaola
- Instituto de Rehabilitación Psicofísica de Buenos Aires, Buenos Aires, Argentina
| | - Christopher J. Ryerson
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Martina Sterclova
- Center for Rare Lung Diseases, Department of Respiratory Diseases and Allergy, Aarhus University Hospital, Aarhus, Denmark
| | | | - Marjukka Myllärniemi
- Department of Pulmonary Medicine, Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
| | | | - Haruhiko Furusawa
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masaki Hirose
- National Hospital Organization Kinki-Chuo Chest Medical Center, Osaka, Japan
| | - Yoshikazu Inoue
- National Hospital Organization Kinki-Chuo Chest Medical Center, Osaka, Japan
| | - Yasunari Miyazaki
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ken Ohta
- National Hospital Organization Tokyo National Hospital, Tokyo, Japan
| | - Shin Ohta
- Department of Medicine, Showa University, Tokyo, Japan
| | - Tsukasa Okamoto
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Dong Soon Kim
- Asan Medical Center, University of Ulsan, Seoul, Republic of Korea
| | - Annie Pardo
- Faculty of Sciences, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Moises Selman
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Alvaro U. Aranda
- Cardiopulmonary Research Center, Alliance Pulmonary Group, Guaynabo, Puerto Rico
| | - Moo Suk Park
- Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Sun Park
- Seoul National University Bundang Hospital, Seoul National University, Seongnam, Republic of Korea
| | - Jin Woo Song
- Asan Medical Center, University of Ulsan, Seoul, Republic of Korea
| | | | - Lurdes Planas-Cerezales
- Interstitial Lung Disease Multidisciplinary Unit, University Hospital of Bellvitge, University of Barcelona, Barcelona, Spain
| | | | - Albert V. Smith
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan
| | | | | | - Stephen S. Rich
- Center for Public Health Genomics, and
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia
| | - Elizabeth C. Oelsner
- Department of Medicine and Department of Epidemiology, Columbia University Medical Center, New York, New York
| | - R. Graham Barr
- Department of Medicine and Department of Epidemiology, Columbia University Medical Center, New York, New York
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, California
| | - Josee Dupuis
- Department of Biostatistics, School of Public Health, Boston University, Boston, Massachusetts
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Quebec, Canada
| | - George O’Connor
- Pulmonary Center, School of Medicine, Boston University, Boston, Massachusetts
| | - Ramachandran S. Vasan
- Boston University and National Heart, Lung, and Blood Institute Framingham Heart Study, Boston, Massachusetts; and
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Marvin I. Schwarz
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Mark P. Steele
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Joyce S. Lee
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Ivana V. Yang
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | | | - David A. Schwartz
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
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Reynolds CJ, Del Greco M F, Allen RJ, Flores C, Jenkins RG, Maher TM, Molyneaux PL, Noth I, Oldham JM, Wain LV, An J, Ong JS, MacGregor S, Yates TA, Cullinan P, Minelli C. The causal relationship between gastro-oesophageal reflux disease and idiopathic pulmonary fibrosis: a bidirectional two-sample Mendelian randomisation study. Eur Respir J 2023; 61:2201585. [PMID: 37080571 PMCID: PMC10209472 DOI: 10.1183/13993003.01585-2022] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 03/07/2023] [Indexed: 04/22/2023]
Abstract
BACKGROUND Gastro-oesophageal reflux disease (GORD) is associated with idiopathic pulmonary fibrosis (IPF) in observational studies. It is not known if this association arises because GORD causes IPF or because IPF causes GORD, or because of confounding by factors, such as smoking, associated with both GORD and IPF. We used bidirectional Mendelian randomisation (MR), where genetic variants are used as instrumental variables to address issues of confounding and reverse causation, to examine how, if at all, GORD and IPF are causally related. METHODS A bidirectional two-sample MR was performed to estimate the causal effect of GORD on IPF risk and of IPF on GORD risk, using genetic data from the largest GORD (78 707 cases and 288 734 controls) and IPF (4125 cases and 20 464 controls) genome-wide association meta-analyses currently available. RESULTS GORD increased the risk of IPF, with an OR of 1.6 (95% CI 1.04-2.49; p=0.032). There was no evidence of a causal effect of IPF on the risk of GORD, with an OR of 0.999 (95% CI 0.997-1.000; p=0.245). CONCLUSIONS We found that GORD increases the risk of IPF, but found no evidence that IPF increases the risk of GORD. GORD should be considered in future studies of IPF risk and interest in it as a potential therapeutic target should be renewed. The mechanisms underlying the effect of GORD on IPF should also be investigated.
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Affiliation(s)
- Carl J Reynolds
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Richard J Allen
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - R Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Toby M Maher
- National Heart and Lung Institute, Imperial College London, London, UK
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Imre Noth
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, VA, USA
| | - Justin M Oldham
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Louise V Wain
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Jiyuan An
- Centre for Agriculture and the Bioeconomy, Faculty of Science, Queensland University of Technology, Brisbane, Australia
| | - Jue-Sheng Ong
- Population Health Department, QIMR Berghofer Medical Research Institute, Herston, Australia
| | - Stuart MacGregor
- Population Health Department, QIMR Berghofer Medical Research Institute, Herston, Australia
| | - Tom A Yates
- Division of Infection and Immunity, Faculty of Medicine, University College London, London, UK
| | - Paul Cullinan
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Cosetta Minelli
- National Heart and Lung Institute, Imperial College London, London, UK
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Chaudhary S, Weigt SS, Ribeiro Neto ML, Benn BS, Pugashetti JV, Keith R, Chand A, Oh S, Kheir F, Ramalingam V, Solomon JJ, Harper R, Lasky JA, Oldham JM. Interstitial lung disease progression after genomic usual interstitial pneumonia testing. Eur Respir J 2023; 61:2201245. [PMID: 36549706 PMCID: PMC10288658 DOI: 10.1183/13993003.01245-2022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND A genomic classifier for usual interstitial pneumonia (gUIP) has been shown to predict histological UIP with high specificity, increasing diagnostic confidence for idiopathic pulmonary fibrosis (IPF). Whether those with positive gUIP classification exhibit a progressive, IPF-like phenotype remains unknown. METHODS A pooled, retrospective analysis of patients who underwent clinically indicated diagnostic bronchoscopy with gUIP testing at seven academic medical centres across the USA was performed. We assessed the association between gUIP classification and 18-month progression-free survival (PFS) using Cox proportional hazards regression. PFS was defined as the time from gUIP testing to death from any cause, lung transplant, ≥10% relative decline in forced vital capacity (FVC) or censoring at the time of last available FVC measure. Longitudinal change in FVC was then compared between gUIP classification groups using a joint regression model. RESULTS Of 238 consecutive patients who underwent gUIP testing, 192 had available follow-up data and were included in the analysis, including 104 with positive gUIP classification and 88 with negative classification. In multivariable analysis, positive gUIP classification was associated with reduced PFS (hazard ratio 1.58, 95% CI 0.86-2.92; p=0.14), but this did not reach statistical significance. Mean annual change in FVC was -101.8 mL (95% CI -142.7- -60.9 mL; p<0.001) for those with positive gUIP classification and -73.2 mL (95% CI -115.2- -31.1 mL; p<0.001) for those with negative classification (difference 28.7 mL, 95% CI -83.2-25.9 mL; p=0.30). CONCLUSIONS gUIP classification was not associated with differential rates of PFS or longitudinal FVC decline in a multicentre interstitial lung disease cohort undergoing bronchoscopy as part of the diagnostic evaluation.
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Affiliation(s)
- Sachin Chaudhary
- Division of Pulmonary and Critical Care Medicine, University of Arizona, Tucson, AZ, USA
| | - S Sam Weigt
- Division of Pulmonary and Critical Care Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | | | - Bryan S Benn
- Division of Pulmonary and Critical Care Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Janelle Vu Pugashetti
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California at Davis, Sacramento, CA, USA
| | - Rebecca Keith
- Division of Pulmonary and Critical Care and Sleep Medicine, National Jewish Health, Denver, CO, USA
| | - Arista Chand
- Division of Pulmonary and Critical Care Medicine, University of Arizona, Tucson, AZ, USA
| | - Scott Oh
- Division of Pulmonary and Critical Care Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Fayez Kheir
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Vijaya Ramalingam
- Division of Pulmonary and Critical Care Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
- Northeast Georgia Physicians Group
| | - Joshua J Solomon
- Division of Pulmonary and Critical Care and Sleep Medicine, National Jewish Health, Denver, CO, USA
| | - Richart Harper
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California at Davis, Sacramento, CA, USA
| | - Joseph A Lasky
- Division of Pulmonary and Critical Care Medicine, Tulane University, New Orleans, LA, USA
| | - Justin M Oldham
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
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Alqalyoobi S, Little BB, Oldham JM, Obi ON. The prognostic value of gastroesophageal reflux disorder in interstitial lung disease related hospitalizations. Respir Res 2023; 24:97. [PMID: 36998050 PMCID: PMC10061884 DOI: 10.1186/s12931-023-02407-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/23/2023] [Indexed: 03/31/2023] Open
Abstract
Abstract
Background
Gastroesophageal reflux disease (GERD) is a common comorbidity in patients with interstitial lung disease (ILD). We built and validated a model using the national inpatient sample (NIS) database to assess the contributory role of GERD in ILD-related hospitalizations mortality.
Methods
In this retrospective analysis, we extracted ILD-related hospitalizations data between 2007 and 2019 from the NIS database. Univariable logistic regression was used for predictor selection. Data were split into the training and validation cohorts (0.6 and 0.4, respectively). We used decision tree analysis (classification and regression tree, CART) to create a predictive model to explore the role of GERD in ILD-related hospitalizations mortality. Different metrics were used to evaluate our model. A bootstrap-based technique was implemented to balance our training data outcome to improve our model metrics in the validation cohort. We conducted a variance-based sensitivity analysis to evaluate GERD's importance in our model.
Findings
The model had a sensitivity of 73.43%, specificity of 66.15%, precision of 0.27, negative predictive value (NPV) of 93.62%, accuracy of 67.2%, Matthews Correlation Coefficient (MCC) of 0.3, F1 score of 0.4, and area under the curve (AUC) for the receiver operating characteristic (ROC) curve of 0.76. GERD did not predict survival in our cohort. GERD contribution to the model was ranked the eleventh among twenty-nine variables included in this analysis (importance of 0.003, normalized importance of 5%). GERD was the best predictor in ILD-related hospitalizations who didn’t receive mechanical ventilation.
Interpretations
GERD is associated with mild ILD-related hospitalization. Our model-performance measures suggest overall an acceptable discrimination. Our model showed that GERD does not have a prognostic value in ILD-related hospitalization, indicating that GERD per se might not have any impact on mortality in hospitalized ILD patients.
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Adegunsoye A, Newton CA, Oldham JM, Ley B, Lee CT, Linderholm AL, Chung JH, Garcia N, Zhang D, Vij R, Guzy R, Jablonski R, Bag R, Voogt RS, Ma SF, Sperling AI, Raghu G, Martinez FJ, Strek ME, Wolters PJ, Garcia CK, Pierce BL, Noth I. Telomere length associates with chronological age and mortality across racially diverse pulmonary fibrosis cohorts. Nat Commun 2023; 14:1489. [PMID: 36932145 PMCID: PMC10023792 DOI: 10.1038/s41467-023-37193-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
Pulmonary fibrosis (PF) is characterized by profound scarring and poor survival. We investigated the association of leukocyte telomere length (LTL) with chronological age and mortality across racially diverse PF cohorts. LTL measurements among participants with PF stratified by race/ethnicity were assessed in relation to age and all-cause mortality, and compared to controls. Generalized linear models were used to evaluate the age-LTL relationship, Cox proportional hazards models were used for hazard ratio estimation, and the Cochran-Armitage test was used to assess quartiles of LTL. Standardized LTL shortened with increasing chronological age; this association in controls was strengthened in PF (R = -0.28; P < 0.0001). In PF, age- and sex-adjusted LTL below the median consistently predicted worse mortality across all racial groups (White, HR = 2.21, 95% CI = 1.79-2.72; Black, HR = 2.22, 95% CI = 1.05-4.66; Hispanic, HR = 3.40, 95% CI = 1.88-6.14; and Asian, HR = 2.11, 95% CI = 0.55-8.23). LTL associates uniformly with chronological age and is a biomarker predictive of mortality in PF across racial groups.
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Affiliation(s)
- Ayodeji Adegunsoye
- Section of Pulmonary & Critical Care, Department of Medicine, The University of Chicago, Chicago, IL, USA.
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA.
| | - Chad A Newton
- Division of Pulmonary & Critical Care Medicine, Department of Internal Medicine, University of Texas Southwestern, Dallas, TX, USA
| | - Justin M Oldham
- Division of Pulmonary, Critical Care & Sleep Medicine, Department of Medicine, University of California, Davis, Sacramento, CA, USA
| | - Brett Ley
- Section of Pulmonary & Critical Care Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Cathryn T Lee
- Section of Pulmonary & Critical Care, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Angela L Linderholm
- Division of Pulmonary, Critical Care & Sleep Medicine, Department of Medicine, University of California, Davis, Sacramento, CA, USA
| | - Jonathan H Chung
- Department of Radiology, The University of Chicago, Chicago, IL, USA
| | - Nicole Garcia
- Section of Pulmonary & Critical Care, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Da Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, Columbia University Medical Center, New York, NY, USA
| | - Rekha Vij
- Section of Pulmonary & Critical Care, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Robert Guzy
- Section of Pulmonary & Critical Care, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Renea Jablonski
- Section of Pulmonary & Critical Care, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Remzi Bag
- Section of Pulmonary & Critical Care, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Rebecca S Voogt
- Section of Pulmonary & Critical Care, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Shwu-Fan Ma
- Division of Pulmonary & Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Anne I Sperling
- Section of Pulmonary & Critical Care, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Ganesh Raghu
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington Medical Center, Seattle, WA, USA
| | - Fernando J Martinez
- Pulmonary Critical Care Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Mary E Strek
- Section of Pulmonary & Critical Care, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Paul J Wolters
- Section of Pulmonary & Critical Care Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Christine Kim Garcia
- Division of Pulmonary, Allergy and Critical Care Medicine, Columbia University Medical Center, New York, NY, USA
| | - Brandon L Pierce
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Imre Noth
- Division of Pulmonary & Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
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Wang BR, Oldham JM. Clinical Trial Enrichment in Systemic Sclerosis-Associated Interstitial Lung Disease: The Search Continues. Chest 2023; 163:475-476. [PMID: 36894257 DOI: 10.1016/j.chest.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 11/01/2022] [Indexed: 03/09/2023] Open
Affiliation(s)
- Bonnie R Wang
- Division of Pulmonary and Critical Care, Department of Internal Medicine, University of Michigan, Ann Arbor, MI.
| | - Justin M Oldham
- Division of Pulmonary and Critical Care, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
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Adegunsoye A, Freiheit E, White EN, Kaul B, Newton CA, Oldham JM, Lee CT, Chung J, Garcia N, Ghodrati S, Vij R, Jablonski R, Flaherty KR, Wolters PJ, Garcia CK, Strek ME. Evaluation of Pulmonary Fibrosis Outcomes by Race and Ethnicity in US Adults. JAMA Netw Open 2023; 6:e232427. [PMID: 36897590 PMCID: PMC10984340 DOI: 10.1001/jamanetworkopen.2023.2427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
Importance Pulmonary fibrosis (PF) is characterized by progressive scarring of lung tissue and poor survival. Racial and ethnic minority populations face the greatest risk of morbidity and mortality from disparities impacting respiratory health, but the pattern of age at clinically relevant outcomes across diverse racial and ethnic populations with PF is unknown. Objective To compare the age at PF-related outcomes and the heterogeneity in survival patterns among Hispanic, non-Hispanic Black, and non-Hispanic White participants. Design, Setting, and Participants This cohort study included adult patients with a PF diagnosis and used data from prospective clinical registries: the Pulmonary Fibrosis Foundation Registry (PFFR) for the primary cohort and registries from 4 geographically distinct tertiary hospitals in the US for the external multicenter validation (EMV) cohort. Patients were followed between January 2003 and April 2021. Exposures Race and ethnicity comparisons between Black, Hispanic, and White participants with PF. Main Outcomes and Measures Age and sex distribution of participants were measured at the time of study enrollment. All-cause mortality and age at PF diagnosis, hospitalization, lung transplant, and death were assessed in participants over 14 389 person-years. Differences between racial and ethnic groups were compared using Wilcoxon rank sum tests, Bartlett 1-way analysis of variance, and χ2 tests, and crude mortality rates and rate ratios were assessed across racial and ethnic categories using Cox proportional hazards regression models. Results In total, 4792 participants with PF were assessed (mean [SD] age, 66.1 [11.2] years; 2779 [58.0%] male; 488 [10.2%] Black, 319 [6.7%] Hispanic, and 3985 [83.2%] White); 1904 were in the PFFR and 2888 in the EMV cohort. Black patients with PF were consistently younger than White patients (mean [SD] age at baseline, 57.9 [12.0] vs 68.6 [9.6] years; P < .001). Hispanic and White patients were predominantly male (Hispanic: PFFR, 73 of 124 [58.9%] and EMV, 109 of 195 [55.9%]; and White: PFFR, 1090 of 1675 [65.1%] and EMV, 1373 of 2310 [59.4%]), while Black patients were less likely to be male (PFFR, 32 of 105 [30.5%] and EMV, 102 of 383 [26.6%]). Compared with White patients, Black patients had a lower crude mortality rate ratio (0.57 [95% CI, 0.31-0.97), but for Hispanic patients, the mortality rate ratio was similar to that of White patients (0.89; 95% CI, 0.57-1.35). Mean (SD) hospitalization events per person were highest among Black patients compared with Hispanic and White patients (Black: 3.6 [5.0]; Hispanic, 1.8 [1.4]; and White, 1.7 [1.3]; P < .001). Black patients were consistently younger than Hispanic and White patients at first hospitalization (mean [SD] age: Black, 59.4 [11.7] years; Hispanic, 67.5 [9.8] years; and White, 70.0 [9.3] years; P < .001), lung transplant (Black, 58.6 [8.6] years; Hispanic, 60.5 [6.1] years; and White, 66.9 [6.7] years; P < .001), and death (Black, 68.7 [8.4] years; Hispanic, 72.9 [7.6] years; and White, 73.5 [8.7] years; P < .001). These findings remained consistent in the replication cohort and in sensitivity analyses within prespecified deciles of age groups. Conclusions and Relevance In this cohort study of participants with PF, racial and ethnic disparities, especially among Black patients, were found in PF-related outcomes, including earlier onset of death. Further research is essential to identify and mitigate the underlying responsible factors.
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Affiliation(s)
- Ayodeji Adegunsoye
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Elizabeth Freiheit
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor
| | - Emily N White
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor
| | - Bhavika Kaul
- Section of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco
| | - Chad A Newton
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Texas Southwestern, Dallas
| | - Justin M Oldham
- Division of Pulmonary & Critical Care Medicine, Department of Medicine, University of Michigan, Ann Arbor
| | - Cathryn T Lee
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Jonathan Chung
- Department of Radiology, The University of Chicago, Chicago, Illinois
| | - Nicole Garcia
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Sahand Ghodrati
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of California, Davis, Sacramento
| | - Rekha Vij
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Renea Jablonski
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Kevin R Flaherty
- Division of Pulmonary & Critical Care Medicine, Department of Medicine, University of Michigan, Ann Arbor
| | - Paul J Wolters
- Section of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco
| | - Christine Kim Garcia
- Division of Pulmonary, Allergy and Critical Care Medicine, Columbia University, New York, New York
| | - Mary E Strek
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Chicago, Chicago, Illinois
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Vu Pugashetti J, Newton CA, Molyneaux PL, Oldham JM. Reply to Noboa-Sevilla et al.. Am J Respir Crit Care Med 2023; 207:369-370. [PMID: 36174209 PMCID: PMC9896651 DOI: 10.1164/rccm.202209-1807le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
| | - Chad A Newton
- University of Texas Southwestern Medical Center Dallas, Texas
| | - Philip L Molyneaux
- Imperial College London London, United Kingdom and.,Guy's and St Thomas' National Health Service Foundation Trust London, United Kingdom
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34
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Amati F, Spagnolo P, Oldham JM, Ryerson CJ, Stainer A, Gramegna A, Mantero M, Lacedonia D, Sverzellati N, Richeldi L, Blasi F, Aliberti S. Treatable traits in interstitial lung diseases: a call to action. Lancet Respir Med 2023; 11:125-128. [PMID: 36646100 DOI: 10.1016/s2213-2600(23)00002-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/03/2022] [Accepted: 12/21/2022] [Indexed: 01/15/2023]
Affiliation(s)
- Francesco Amati
- Department of Biomedical Sciences, Humanitas University, Milan 20072, Italy; IRCCS Humanitas Research Hospital, Respiratory Unit, Milan, Italy
| | - Paolo Spagnolo
- Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health; University of Padua, Padua, Italy
| | - Justin M Oldham
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California Davis, Sacramento, CA, USA
| | - Christopher J Ryerson
- Department of Medicine, University of British Columbia and Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
| | - Anna Stainer
- Department of Biomedical Sciences, Humanitas University, Milan 20072, Italy; IRCCS Humanitas Research Hospital, Respiratory Unit, Milan, Italy
| | - Andrea Gramegna
- Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Marco Mantero
- Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Donato Lacedonia
- Department of Medical and Surgical Sciences, Università di Foggia, Institute of Respiratory Disease, Foggia, Italy
| | - Nicola Sverzellati
- Unit of Radiological Science, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Luca Richeldi
- Fondazione Policlinico A Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Francesco Blasi
- Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Stefano Aliberti
- Department of Biomedical Sciences, Humanitas University, Milan 20072, Italy; IRCCS Humanitas Research Hospital, Respiratory Unit, Milan, Italy.
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Allen RJ, Oldham JM, Jenkins DA, Leavy OC, Guillen-Guio B, Melbourne CA, Ma SF, Jou J, Kim JS, Fahy WA, Oballa E, Hubbard RB, Navaratnam V, Braybrooke R, Saini G, Roach KM, Tobin MD, Hirani N, Whyte MKB, Kaminski N, Zhang Y, Martinez FJ, Linderholm AL, Adegunsoye A, Strek ME, Maher TM, Molyneaux PL, Flores C, Noth I, Gisli Jenkins R, Wain LV. Longitudinal lung function and gas transfer in individuals with idiopathic pulmonary fibrosis: a genome-wide association study. Lancet Respir Med 2023; 11:65-73. [PMID: 35985358 PMCID: PMC10077113 DOI: 10.1016/s2213-2600(22)00251-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/17/2022] [Accepted: 06/22/2022] [Indexed: 01/21/2023]
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is an incurable lung disease characterised by progressive scarring leading to alveolar stiffness, reduced lung capacity, and impeded gas transfer. We aimed to identify genetic variants associated with declining lung capacity or declining gas transfer after diagnosis of IPF. METHODS We did a genome-wide meta-analysis of longitudinal measures of forced vital capacity (FVC) and diffusing capacity of the lung for carbon monoxide (DLCO) in individuals diagnosed with IPF. Individuals were recruited to three studies between June, 1996, and August, 2017, from across centres in the US, UK, and Spain. Suggestively significant variants were investigated further in an additional independent study (CleanUP-IPF). All four studies diagnosed cases following American Thoracic Society/European Respiratory Society guidelines. Variants were defined as significantly associated if they had a meta-analysis p<5 × 10-8 when meta-analysing across all discovery and follow-up studies, had consistent direction of effects across all four studies, and were nominally significant (p<0·05) in each study. FINDINGS 1329 individuals with a total of 5216 measures were included in the FVC analysis. 975 individuals with a total of 3361 measures were included in the DLCO analysis. For the discovery genome-wide analyses, 7 611 174 genetic variants were included in the FVC analysis and 7 536 843 in the DLCO analysis. One variant (rs115982800) located in an antisense RNA gene for protein kinase N2 (PKN2) showed a genome-wide significant association with FVC decline (-140 mL/year per risk allele [95% CI -180 to -100]; p=9·14 × 10-12). INTERPRETATION Our analysis identifies a genetic variant associated with disease progression, which might highlight a new biological mechanism for IPF. We found that PKN2, a Rho and Rac effector protein, is the most likely gene of interest from this analysis. PKN2 inhibitors are currently in development and signify a potential novel therapeutic approach for IPF. FUNDING Action for Pulmonary Fibrosis, Medical Research Council, Wellcome Trust, and National Institutes of Health National Heart, Lung, and Blood Institute.
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Affiliation(s)
- Richard J Allen
- Department of Health Sciences, University of Leicester, Leicester, UK.
| | - Justin M Oldham
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, USA
| | - David A Jenkins
- Division of Informatics, Imaging & Data Sciences, University of Manchester, Manchester, UK
| | - Olivia C Leavy
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Carl A Melbourne
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Shwu-Fan Ma
- Division of Pulmonary & Critical Care Medicine, University of Virginia, Charlottesville, VA, USA
| | - Jonathan Jou
- Department of Surgery, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | - John S Kim
- Division of Pulmonary & Critical Care Medicine, University of Virginia, Charlottesville, VA, USA
| | | | | | - Richard B Hubbard
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, UK; National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Vidya Navaratnam
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, UK; National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK; Queensland Lung Transplant Service, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Rebecca Braybrooke
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, UK; National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Gauri Saini
- Respiratory Medicine, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Katy M Roach
- Department of Respiratory Sciences, University of Leicester, Glenfield Hospital, Leicester, UK
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Nik Hirani
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Moira K B Whyte
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, The University of Pittsburgh, Pittsburgh, PA, USA
| | - Fernando J Martinez
- Division of Pulmonary and Critical Care Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Angela L Linderholm
- Department of Internal Medicine, University of California Davis, Davis, CA, USA
| | - Ayodeji Adegunsoye
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, IL, USA
| | - Mary E Strek
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, IL, USA
| | - Toby M Maher
- National Heart and Lung Institute, Imperial College London, London, UK; Royal Brompton and Harefield Hospitals, London, UK; Division of Pulmonary and Critical Care Medicine, University of Southern California, Los Angeles, CA, USA
| | - Philip L Molyneaux
- National Heart and Lung Institute, Imperial College London, London, UK; Royal Brompton and Harefield Hospitals, London, UK
| | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain; CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain; Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | - Imre Noth
- Division of Pulmonary & Critical Care Medicine, University of Virginia, Charlottesville, VA, USA
| | - R Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK; National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
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Pugashetti JV, Adegunsoye A, Wu Z, Lee CT, Srikrishnan A, Ghodrati S, Vo V, Renzoni EA, Wells AU, Garcia CK, Chua F, Newton CA, Molyneaux PL, Oldham JM. Validation of Proposed Criteria for Progressive Pulmonary Fibrosis. Am J Respir Crit Care Med 2023; 207:69-76. [PMID: 35943866 PMCID: PMC9952866 DOI: 10.1164/rccm.202201-0124oc] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 08/09/2022] [Indexed: 02/03/2023] Open
Abstract
Rationale: Criteria for progressive pulmonary fibrosis (PPF) have been proposed, but their prognostic value beyond categorical decline in FVC remains unclear. Objectives: To determine whether proposed PPF criteria predict transplant-free survival (TFS) in patients with non-idiopathic pulmonary fibrosis (IPF) forms of interstitial lung disease (ILD). Methods: A retrospective, multicenter cohort analysis was performed. Patients with diagnoses of fibrotic connective tissue disease-associated ILD, fibrotic hypersensitivity pneumonitis, and non-IPF idiopathic interstitial pneumonia from three U.S. centers and one UK center constituted the test and validation cohorts, respectively. Cox proportional hazards regression was used to test the association between 5-year TFS and ⩾10% FVC decline, followed by 13 additional PPF criteria satisfied in the absence of ⩾10% FVC decline. Measurements and Main Results: One thousand three hundred forty-one patients met the inclusion criteria. A ⩾10% relative FVC decline was the strongest predictor of reduced TFS and showed consistent TFS association across cohorts, ILD subtypes, and treatment groups, resulting in a phenotype that closely resembled IPF. Ten additional PPF criteria satisfied in the absence of 10% relative FVC decline were also associated with reduced TFS in the U.S. test cohort, with 6 maintaining TFS associations in the UK validation cohort. Validated PPF criteria requiring a combination of physiologic, radiologic, and symptomatic worsening performed similarly to their stand-alone components but captured a smaller number of patients. Conclusions: An FVC decline of ⩾10% and six additional PPF criteria satisfied in the absence of such decline identify patients with non-IPF ILD at increased risk for death or lung transplantation.
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Affiliation(s)
- Janelle Vu Pugashetti
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California, Davis, Davis, California
| | - Ayodeji Adegunsoye
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois
| | - Zhe Wu
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Cathryn T. Lee
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois
| | - Anand Srikrishnan
- Division of Pulmonary and Critical Care Medicine, University of Texas Southwestern Medical Center, Dallas, Texas; and
| | - Sahand Ghodrati
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California, Davis, Davis, California
| | - Vivian Vo
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California, Davis, Davis, California
| | - Elisabetta A. Renzoni
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Athol U. Wells
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Christine Kim Garcia
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Columbia University, New York, New York
| | - Felix Chua
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Chad A. Newton
- Division of Pulmonary and Critical Care Medicine, University of Texas Southwestern Medical Center, Dallas, Texas; and
| | - Philip L. Molyneaux
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Justin M. Oldham
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
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Fainberg HP, Oldham JM, Molyneau PL, Allen RJ, Kraven LM, Fahy WA, Porte J, Braybrooke R, Saini G, Karsdal MA, Leeming DJ, Sand JMB, Triguero I, Oballa E, Wells AU, Renzoni E, Wain LV, Noth I, Maher TM, Stewart ID, Jenkins RG. Forced vital capacity trajectories in patients with idiopathic pulmonary fibrosis: a secondary analysis of a multicentre, prospective, observational cohort. Lancet Digit Health 2022; 4:e862-e872. [PMID: 36333179 DOI: 10.1016/s2589-7500(22)00173-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 08/11/2022] [Accepted: 08/25/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND Idiopathic pulmonary fibrosis is a progressive fibrotic lung disease with a variable clinical trajectory. Decline in forced vital capacity (FVC) is the main indicator of progression; however, missingness prevents long-term analysis of patterns in lung function. We aimed to identify distinct clusters of lung function trajectory among patients with idiopathic pulmonary fibrosis using machine learning techniques. METHODS We did a secondary analysis of longitudinal data on FVC collected from a cohort of patients with idiopathic pulmonary fibrosis from the PROFILE study; a multicentre, prospective, observational cohort study. We evaluated the imputation performance of conventional and machine learning techniques to impute missing data and then analysed the fully imputed dataset by unsupervised clustering using self-organising maps. We compared anthropometric features, genomic associations, serum biomarkers, and clinical outcomes between clusters. We also performed a replication of the analysis on data from a cohort of patients with idiopathic pulmonary fibrosis from an independent dataset, obtained from the Chicago Consortium. FINDINGS 415 (71%) of 581 participants recruited into the PROFILE study were eligible for further analysis. An unsupervised machine learning algorithm had the lowest imputation error among tested methods, and self-organising maps identified four distinct clusters (1-4), which was confirmed by sensitivity analysis. Cluster 1 comprised 140 (34%) participants and was associated with a disease trajectory showing a linear decline in FVC over 3 years. Cluster 2 comprised 100 (24%) participants and was associated with a trajectory showing an initial improvement in FVC before subsequently decreasing. Cluster 3 comprised 113 (27%) participants and was associated with a trajectory showing an initial decline in FVC before subsequent stabilisation. Cluster 4 comprised 62 (15%) participants and was associated with a trajectory showing stable lung function. Median survival was shortest in cluster 1 (2·87 years [IQR 2·29-3·40]) and cluster 3 (2·23 years [1·75-3·84]), followed by cluster 2 (4·74 years [3·96-5·73]), and was longest in cluster 4 (5·56 years [5·18-6·62]). Baseline FEV1 to FVC ratio and concentrations of the biomarker SP-D were significantly higher in clusters 1 and 3. Similar lung function clusters with some shared anthropometric features were identified in the replication cohort. INTERPRETATION Using a data-driven unsupervised approach, we identified four clusters of lung function trajectory with distinct clinical and biochemical features. Enriching or stratifying longitudinal spirometric data into clusters might optimise evaluation of intervention efficacy during clinical trials and patient management. FUNDING National Institute for Health and Care Research, Medical Research Council, and GlaxoSmithKline.
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Affiliation(s)
- Hernan P Fainberg
- National Heart and Lung Institute, Imperial College London, London, UK.
| | - Justin M Oldham
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Philip L Molyneau
- National Heart and Lung Institute, Imperial College London, London, UK; Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Richard J Allen
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Luke M Kraven
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - William A Fahy
- Discovery Medicine, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Joanne Porte
- Nottingham Respiratory Research Unit, NIHR Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Rebecca Braybrooke
- Nottingham Respiratory Research Unit, NIHR Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Gauri Saini
- Nottingham Respiratory Research Unit, NIHR Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | | | | | | | - Isaac Triguero
- Computational Optimisation and Learning Lab, School of Computer Science, University of Nottingham, Nottingham, UK; DaSCI Andalusian Institute in Data Science and Computational Intelligence, University of Granada, Granada, Spain
| | - Eunice Oballa
- Discovery Medicine, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Athol U Wells
- National Heart and Lung Institute, Imperial College London, London, UK; Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Elisabetta Renzoni
- National Heart and Lung Institute, Imperial College London, London, UK; Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK; National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Imre Noth
- Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, VA, USA
| | - Toby M Maher
- National Heart and Lung Institute, Imperial College London, London, UK; Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK; Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Iain D Stewart
- National Heart and Lung Institute, Imperial College London, London, UK
| | - R Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, UK; Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
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Ghodrati S, Pugashetti JV, Kadoch MA, Ghasemiesfe A, Oldham JM. Diagnostic Accuracy of Chest Radiography for Detecting Fibrotic Interstitial Lung Disease. Ann Am Thorac Soc 2022; 19:1934-1937. [PMID: 35608402 PMCID: PMC9667806 DOI: 10.1513/annalsats.202112-1377rl] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
| | | | - Michael A. Kadoch
- University of California at DavisSacramento, California
- Sutter Medical Center,Sacramento, California
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39
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Partanen JJ, Häppölä P, Zhou W, Lehisto AA, Ainola M, Sutinen E, Allen RJ, Stockwell AD, Leavy OC, Oldham JM, Guillen-Guio B, Cox NJ, Hirbo JB, Schwartz DA, Fingerlin TE, Flores C, Noth I, Yaspan BL, Jenkins RG, Wain LV, Ripatti S, Pirinen M, Laitinen T, Kaarteenaho R, Myllärniemi M, Daly MJ, Koskela JT. Leveraging global multi-ancestry meta-analysis in the study of idiopathic pulmonary fibrosis genetics. Cell Genom 2022; 2:100181. [PMID: 36777997 PMCID: PMC9903787 DOI: 10.1016/j.xgen.2022.100181] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/24/2022] [Accepted: 09/07/2022] [Indexed: 04/12/2023]
Abstract
The research of rare and devastating orphan diseases, such as idiopathic pulmonary fibrosis (IPF) has been limited by the rarity of the disease itself. The prognosis is poor-the prevalence of IPF is only approximately four times the incidence, limiting the recruitment of patients to trials and studies of the underlying biology. Global biobanking efforts can dramatically alter the future of IPF research. We describe a large-scale meta-analysis of IPF, with 8,492 patients and 1,355,819 population controls from 13 biobanks around the globe. Finally, we combine this meta-analysis with the largest available meta-analysis of IPF, reaching 11,160 patients and 1,364,410 population controls. We identify seven novel genome-wide significant loci, only one of which would have been identified if the analysis had been limited to European ancestry individuals. We observe notable pleiotropy across IPF susceptibility and severe COVID-19 infection and note an unexplained sex-heterogeneity effect at the strongest IPF locus MUC5B.
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Affiliation(s)
- Juulia J. Partanen
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Paavo Häppölä
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Wei Zhou
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Arto A. Lehisto
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Mari Ainola
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pulmonary Medicine, Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
| | - Eva Sutinen
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pulmonary Medicine, Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
| | - Richard J. Allen
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Olivia C. Leavy
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Justin M. Oldham
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of California, Davis, Sacramento, CA, USA
| | | | - Nancy J. Cox
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetic Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jibril B. Hirbo
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetic Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Tasha E. Fingerlin
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Carlos Flores
- Research Unit, Hospital Universitario Ntra. Sra. de Candelaria, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Imre Noth
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | | | - R. Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Louise V. Wain
- Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Samuli Ripatti
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matti Pirinen
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - International IPF Genetics Consortium
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pulmonary Medicine, Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
- Department of Health Sciences, University of Leicester, Leicester, UK
- Human Genetics, Genentech, South San Francisco, CA, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of California, Davis, Sacramento, CA, USA
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetic Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, University of Colorado, Aurora, CO, USA
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
- Research Unit, Hospital Universitario Ntra. Sra. de Candelaria, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
- Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Administration Center, Tampere University Hospital and University of Tampere, Tampere, Finland
- Research Unit of Internal Medicine, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | - Global Biobank Meta-Analysis Initiative (GBMI)
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pulmonary Medicine, Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
- Department of Health Sciences, University of Leicester, Leicester, UK
- Human Genetics, Genentech, South San Francisco, CA, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of California, Davis, Sacramento, CA, USA
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetic Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, University of Colorado, Aurora, CO, USA
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
- Research Unit, Hospital Universitario Ntra. Sra. de Candelaria, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
- Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Administration Center, Tampere University Hospital and University of Tampere, Tampere, Finland
- Research Unit of Internal Medicine, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | - Tarja Laitinen
- Administration Center, Tampere University Hospital and University of Tampere, Tampere, Finland
| | - Riitta Kaarteenaho
- Research Unit of Internal Medicine, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | - Marjukka Myllärniemi
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pulmonary Medicine, Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
| | - Mark J. Daly
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jukka T. Koskela
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
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40
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Newton CA, Oldham JM, Applegate C, Carmichael N, Powell K, Dilling D, Schmidt SL, Scholand MB, Armanios M, Garcia CK, Kropski JA, Talbert J. The Role of Genetic Testing in Pulmonary Fibrosis. Chest 2022; 162:394-405. [PMID: 35337808 PMCID: PMC9424324 DOI: 10.1016/j.chest.2022.03.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/08/2022] [Accepted: 03/15/2022] [Indexed: 11/25/2022] Open
Abstract
Patients with familial pulmonary fibrosis represent a subset of patients with pulmonary fibrosis in whom inherited gene variation predisposes them to disease development. In the appropriate setting, genetic testing allows for personalized assessment of disease, recognition of clinically relevant extrapulmonary manifestations, and assessing susceptibility in unaffected relatives. However currently, the use of genetic testing is inconsistent, partly because of the lack of guidance regarding high-yield scenarios in which the results of genetic testing can inform clinical decision-making. To address this, the Pulmonary Fibrosis Foundation commissioned a genetic testing work group comprising pulmonologists, geneticists, and genetic counselors from the United States to provide guidance on genetic testing in patients with pulmonary fibrosis. This CHEST special feature presents a concise review of these proceedings and reviews pulmonary fibrosis susceptibility, clinically available genetic testing methods, and clinical scenarios in which genetic testing should be considered.
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41
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Allen RJ, Stockwell A, Oldham JM, Guillen-Guio B, Schwartz DA, Maher TM, Flores C, Noth I, Yaspan BL, Jenkins RG, Wain LV. Genome-wide association study across five cohorts identifies five novel loci associated with idiopathic pulmonary fibrosis. Thorax 2022; 77:829-833. [PMID: 35688625 PMCID: PMC9329250 DOI: 10.1136/thoraxjnl-2021-218577] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/24/2022] [Indexed: 11/03/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic lung condition with poor survival times. We previously published a genome-wide meta-analysis of IPF risk across three studies with independent replication of associated variants in two additional studies. To maximise power and to generate more accurate effect size estimates, we performed a genome-wide meta-analysis across all five studies included in the previous IPF risk genome-wide association studies. We used the distribution of effect sizes across the five studies to assess the replicability of the results and identified five robust novel genetic association signals implicating mTOR (mammalian target of rapamycin) signalling, telomere maintenance and spindle assembly genes in IPF risk.
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Affiliation(s)
- Richard J Allen
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Justin M Oldham
- Department of Internal Medicine, University of California Davis, Davis, USA
| | | | - David A Schwartz
- Center for Genes, Environment and Health, National Jewish Health, Denver, USA,Department of Medicine, University of Colorado Denver, Denver, USA,Department of Immunology, University of Colorado Denver, Denver, USA
| | - Toby M Maher
- National Heart and Lung Institute, Imperial College London, London, UK,Royal Brompton and Harefield Hospitals, London, UK,Division of Pulmonary and Critical Care Medicine, University of Southern California, Los Angeles, USA
| | - Carlos Flores
- Research Unit, Hospital Universitario Ntra. Sra. de Candelaria, Santa Cruz de Tenerife, Spain,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain,Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Imre Noth
- Division of Pulmonary & Critical Care Medicine, University of Virginia, Charlottesville, USA
| | | | - R Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK,National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
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42
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Spagnolo P, Oldham JM. On Target: CYFRA 21-1 as an Idiopathic Pulmonary Fibrosis Biomarker. Am J Respir Crit Care Med 2022; 205:1376-1377. [PMID: 35446243 PMCID: PMC9875889 DOI: 10.1164/rccm.202203-0474ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Paolo Spagnolo
- Department of Cardiac, Thoracic, Vascular Sciences, and Public Health University of Padova Padova, Italy
| | - Justin M Oldham
- Division of Pulmonary, Critical Care, and Sleep Medicine University of California Davis Sacramento, California
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43
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Oldham JM, Lee CT, Wu Z, Bowman WS, Pugashetti JV, Dao N, Tonkin J, Seede H, Echt G, Adegunsoye A, Chua F, Maher TM, Garcia CK, Strek ME, Newton CA, Molyneaux PL. Lung function trajectory in progressive fibrosing interstitial lung disease. Eur Respir J 2022; 59:13993003.01396-2021. [PMID: 34737223 PMCID: PMC10039317 DOI: 10.1183/13993003.01396-2021] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 10/20/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Proposed criteria for progressive fibrosing interstitial lung disease (PF-ILD) have been linked to increased mortality risk, but lung function trajectory after satisfying individual criteria remains unknown. Because survival is rarely employed as the primary end-point in therapeutic trials, identifying PF-ILD criteria that best predict subsequent change in forced vital capacity (FVC) could improve clinical trial design. METHODS A retrospective, multicentre longitudinal cohort analysis was performed in consecutive patients with fibrotic connective tissue disease-associated ILD (CTD-ILD), chronic hypersensitivity pneumonitis and idiopathic interstitial pneumonia at three US centres (test cohort) and one UK centre (validation cohort). 1-year change in FVC after satisfying proposed PF-ILD criteria was estimated using joint modelling. Subgroup analyses were performed to determine whether results varied across key subgroups. RESULTS 1227 patients were included, with CTD-ILD predominating. Six out of nine PF-ILD criteria were associated with differential 1-year change in FVC, with radiological progression of fibrosis, alone and in combination with other features, associated with the largest subsequent decline in FVC. Findings varied significantly by ILD subtype, with CTD-ILD demonstrating little change in FVC after satisfying most PF-ILD criteria, while other ILDs showed significantly larger changes. Findings did not vary after stratification by radiological pattern or exposure to immunosuppressant therapy. Near-term change in FVC after satisfying proposed PF-ILD criteria was heterogeneous depending on the criterion assessed and was strongly influenced by ILD subtype. CONCLUSIONS These findings may inform future clinical trial design and suggest ILD subtype should be taken into consideration when applying PF-ILD criteria.
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Affiliation(s)
- Justin M Oldham
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California at Davis, Sacramento, CA, USA
- These authors contributed equally
| | - Cathryn T Lee
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, IL, USA
- These authors contributed equally
| | - Zhe Wu
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton Hospital, London, UK
| | - Willis S Bowman
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California at Davis, Sacramento, CA, USA
| | - Janelle Vu Pugashetti
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California at Davis, Sacramento, CA, USA
| | - Nam Dao
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California at Davis, Sacramento, CA, USA
| | - James Tonkin
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton Hospital, London, UK
| | - Hasan Seede
- Division of Pulmonary and Critical Care Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Gabrielle Echt
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California at Davis, Sacramento, CA, USA
| | - Ayodeji Adegunsoye
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, IL, USA
| | - Felix Chua
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton Hospital, London, UK
| | - Toby M Maher
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Southern California, Los Angeles, CA, USA
| | - Christine K Garcia
- Dept of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Columbia University, New York, NY, USA
| | - Mary E Strek
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, IL, USA
| | - Chad A Newton
- Division of Pulmonary and Critical Care Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
- These authors contributed equally
| | - Philip L Molyneaux
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton Hospital, London, UK
- These authors contributed equally
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Bowman WS, Newton CA, Linderholm AL, Neely ML, Pugashetti JV, Kaul B, Vo V, Echt GA, Leon W, Shah RJ, Huang Y, Garcia CK, Wolters PJ, Oldham JM. Proteomic biomarkers of progressive fibrosing interstitial lung disease: a multicentre cohort analysis. The Lancet Respiratory Medicine 2022; 10:593-602. [DOI: 10.1016/s2213-2600(21)00503-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 10/25/2022]
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Pugashetti JV, Oldham JM. Weighing on Our Minds: Baseline BMI and Weight Loss as Predictors of Interstitial Lung Disease Outcome. Chest 2022; 161:1134-1135. [PMID: 35526883 DOI: 10.1016/j.chest.2021.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 10/18/2022] Open
Affiliation(s)
- Janelle Vu Pugashetti
- Division of Pulmonary, Critical Care and Sleep Medicine; University of California at Davis, Sacramento, CA.
| | - Justin M Oldham
- Division of Pulmonary, Critical Care and Sleep Medicine; University of California at Davis, Sacramento, CA
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Hunninghake GM, Goldin JG, Kadoch MA, Kropski JA, Rosas IO, Wells AU, Yadav R, Lazarus HM, Abtin FG, Corte TJ, de Andrade JA, Johannson KA, Kolb MR, Lynch DA, Oldham JM, Spagnolo P, Strek ME, Tomassetti S, Washko GR, White ES. Detection and Early Referral of Patients With Interstitial Lung Abnormalities: An Expert Survey Initiative. Chest 2022; 161:470-482. [PMID: 34197782 PMCID: PMC10624930 DOI: 10.1016/j.chest.2021.06.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 06/04/2021] [Accepted: 06/14/2021] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Interstitial lung abnormalities (ILA) may represent undiagnosed early-stage or subclinical interstitial lung disease (ILD). ILA are often observed incidentally in patients who subsequently develop clinically overt ILD. There is limited information on consensus definitions for, and the appropriate evaluation of, ILA. Early recognition of patients with ILD remains challenging, yet critically important. Expert consensus could inform early recognition and referral. RESEARCH QUESTION Can consensus-based expert recommendations be identified to guide clinicians in the recognition, referral, and follow-up of patients with or at risk of developing early ILDs? STUDY DESIGN AND METHODS Pulmonologists and radiologists with expertise in ILD participated in two iterative rounds of surveys. The surveys aimed to establish consensus regarding ILA reporting, identification of patients with ILA, and identification of populations that might benefit from screening for ILD. Recommended referral criteria and follow-up processes were also addressed. Threshold for consensus was defined a priori as ≥ 75% agreement or disagreement. RESULTS Fifty-five experts were invited and 44 participated; consensus was reached on 39 of 85 questions. The following clinically important statements achieved consensus: honeycombing and traction bronchiectasis or bronchiolectasis indicate potentially progressive ILD; honeycombing detected during lung cancer screening should be reported as potentially significant (eg, with the Lung CT Screening Reporting and Data System "S-modifier" [Lung-RADS; which indicates clinically significant or potentially significant noncancer findings]), recommending referral to a pulmonologist in the radiology report; high-resolution CT imaging and full pulmonary function tests should be ordered if nondependent subpleural reticulation, traction bronchiectasis, honeycombing, centrilobular ground-glass nodules, or patchy ground-glass opacity are observed on CT imaging; patients with honeycombing or traction bronchiectasis should be referred to a pulmonologist irrespective of diffusion capacity values; and patients with systemic sclerosis should be screened with pulmonary function tests for early-stage ILD. INTERPRETATION Guidance was established for identifying clinically relevant ILA, subsequent referral, and follow-up. These results lay the foundation for developing practical guidance on managing patients with ILA.
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Affiliation(s)
- Gary M Hunninghake
- Pulmonary and Critical Care Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Center for Pulmonary Functional Imaging, Brigham and Women's Hospital, Boston, MA.
| | - Jonathan G Goldin
- Department of Radiological Sciences, University of California at Los Angeles, Los Angeles, CA
| | - Michael A Kadoch
- Department of Radiology, University of California at Davis, Davis, CA
| | | | - Ivan O Rosas
- Pulmonary and Critical Care Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX
| | - Athol U Wells
- Interstitial Lung Disease Unit, Royal Brompton Hospital, London, England
| | - Ruchi Yadav
- Imaging Institute, Cleveland Clinic, Cleveland, OH
| | | | - Fereidoun G Abtin
- Department of Radiological Sciences, University of California at Los Angeles, Los Angeles, CA; Division of Interventional Radiology, University of California at Los Angeles, Los Angeles, CA
| | - Tamera J Corte
- Department of Respiratory Medicine, Royal Prince Alfred Hospital, and University of Sydney, Sydney NSW, Australia
| | | | | | - Martin R Kolb
- Firestone Institute for Respiratory Health, Research Institute at St. Joseph's Healthcare, McMaster University, Hamilton, ON, Canada
| | - David A Lynch
- Department of Radiology, National Jewish Health, Denver, CO
| | - Justin M Oldham
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California at Davis, Davis, CA; Department of Veterans Affairs Northern California, Sacramento, CA
| | - Paolo Spagnolo
- Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova and Padova City Hospital, Padova, Italy
| | - Mary E Strek
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, IL
| | - Sara Tomassetti
- Department of Experimental and Clinical Medicine, Careggi University Hospital, Florence, Italy
| | - George R Washko
- Pulmonary and Critical Care Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Center for Pulmonary Functional Imaging, Brigham and Women's Hospital, Boston, MA
| | - Eric S White
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI
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Affiliation(s)
- Justin M Oldham
- Division of Pulmonary Critical Care and Sleep Medicine University of California at Davis Sacramento, California
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Oldham JM, Vancheri C. Rethinking Idiopathic Pulmonary Fibrosis. Clin Chest Med 2021; 42:263-273. [PMID: 34024402 DOI: 10.1016/j.ccm.2021.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a devastating disease for patients and their loved ones. Since initial efforts to characterize this disease in the 1960s, understanding of IPF has evolved considerably. Such evolution has continually challenged prior diagnostic and treatment paradigms, ushering in an era of higher confidence diagnoses with less invasive procedures and more effective treatments. This review details how research and clinical experience over the past half century have led to a rethinking of IPF. Here, the evolution in understanding of IPF pathogenesis, diagnostic evaluation and treatment approach is discussed.
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Affiliation(s)
- Justin M Oldham
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of California, Davis, 4150 V Street Suite 3400, Sacramento, CA 95817, USA.
| | - Carlo Vancheri
- Department of Clinical and Experimental Medicine, University of Catania, Regional Referral Center for Rare Lung Diseases, University-Hospital "Policlinico -Vittorio Emanuele", Catania, Italy
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49
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Affiliation(s)
- Paolo Spagnolo
- Respiratory Disease Unit, Department of Cardiac Thoracic, Vascular Sciences and Public Health, University of Padova, Padova, Italy.
| | - Justin M Oldham
- Division of Pulmonary, Critical Care & Sleep Medicine, Department of Medicine, University of California at Davis, Davis, USA
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Kreuter M, Lee JS, Tzouvelekis A, Oldham JM, Molyneaux PL, Weycker D, Atwood M, Kirchgaessler KU, Maher TM. Monocyte Count as a Prognostic Biomarker in Patients with Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med 2021; 204:74-81. [PMID: 33434107 PMCID: PMC8437112 DOI: 10.1164/rccm.202003-0669oc] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 01/12/2021] [Indexed: 11/16/2022] Open
Abstract
Rationale: There is an urgent need for simple, cost-effective prognostic biomarkers for idiopathic pulmonary fibrosis (IPF); biomarkers that show potential include monocyte count. Objectives: We used pooled data from pirfenidone and IFNγ-1b trials to explore the association between monocyte count and prognosis in patients with IPF. Methods: This retrospective pooled analysis included patients (active and placebo arms) from the following four phase III, randomized, placebo-controlled trials: ASCEND (NCT01366209), CAPACITY (NCT00287729 and NCT00287716), and INSPIRE (NCT00075998). Outcomes included IPF progression (≥10% absolute decline in FVC% predicted, ≥50 m decline in 6-minute-walk distance, or death), all-cause hospitalization, and all-cause mortality over 1 year. The relationship between monocyte count (defined as time-dependent) and outcomes was assessed using bivariate and multivariable models. Measurements and Main Results: This analysis included 2,067 patients stratified by monocyte count (at baseline: <0.60 × 109 cells/L [n = 1,609], 0.60 to <0.95 × 109 cells/L [n = 408], and ≥0.95 × 109 cells/L [n = 50]). In adjusted analyses, a higher proportion of patients with monocyte counts of 0.60 to <0.95 × 109 cells/L or ≥0.95 × 109 cells/L versus <0.60 × 109 cells/L experienced IPF progression (P = 0.016 and P = 0.002, respectively), all-cause hospitalization (P = 0.030 and P = 0.003, respectively), and all-cause mortality (P = 0.005 and P < 0.001, respectively) over 1 year. Change in monocyte count from baseline was not associated with any of the outcomes over 1 year and did not appear to be affected by study treatment. Conclusions: In patients with IPF, elevated monocyte count was associated with increased risks of IPF progression, hospitalization, and mortality. Monocyte count may provide a simple and inexpensive prognostic biomarker in IPF.
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Affiliation(s)
- Michael Kreuter
- Center for Interstitial and Rare Lung Diseases, Pneumology, Thoraxklinik, University of Heidelberg, Heidelberg, Germany
- German Center for Lung Research, Heidelberg, Germany
| | - Joyce S Lee
- Department of Medicine, University of Colorado, Denver, Colorado
| | | | - Justin M Oldham
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of California Davis, Sacramento, California
| | - Philip L Molyneaux
- Interstitial Lung Disease Unit, Royal Brompton Hospital, London, United Kingdom
- Fibrosis Research Group, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | | | - Mark Atwood
- Policy Analysis, Inc., Brookline, Massachusetts
| | | | - Toby M Maher
- Interstitial Lung Disease Unit, Royal Brompton Hospital, London, United Kingdom
- Fibrosis Research Group, National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care, and Sleep Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
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