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Bamodu OA, Wu SM, Feng PH, Sun WL, Lin CW, Chuang HC, Ho SC, Chen KY, Chen TT, Tseng CH, Liu WT, Lee KY. lnc-IL7R Expression Reflects Physiological Pulmonary Function and Its Aberration Is a Putative Indicator of COPD. Biomedicines 2022; 10:biomedicines10040786. [PMID: 35453536 PMCID: PMC9031132 DOI: 10.3390/biomedicines10040786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/25/2022] [Accepted: 03/25/2022] [Indexed: 02/04/2023] Open
Abstract
Despite rapidly evolving pathobiological mechanistic demystification, coupled with advances in diagnostic and therapeutic modalities, chronic obstructive pulmonary disease (COPD) remains a major healthcare and clinical challenge, globally. Further compounded by the dearth of available curative anti-COPD therapy, it is posited that this challenge may not be dissociated from the current lack of actionable COPD pathognomonic molecular biomarkers. There is accruing evidence of the involvement of protracted ‘smoldering’ inflammation, repeated lung injury, and accelerated lung aging in enhanced predisposition to or progression of COPD. The relatively novel uncharacterized human long noncoding RNA lnc-IL7R (otherwise called LOC100506406) is increasingly designated a negative modulator of inflammation and regulator of cellular stress responses; however, its role in pulmonary physiology and COPD pathogenesis remains largely unclear and underexplored. Our previous work suggested that upregulated lnc-IL7R expression attenuates inflammation following the activation of the toll-like receptor (TLR)-dependent innate immune system, and that the upregulated lnc-IL7R is anti-correlated with concomitant high PM2.5, PM10, and SO2 levels, which is pathognomonic for exacerbated/aggravated COPD in Taiwan. In the present study, our quantitative analysis of lnc-IL7R expression in our COPD cohort (n = 125) showed that the lnc-IL7R level was significantly correlated with physiological pulmonary function and exhibited COPD-based stratification implications (area under the curve, AUC = 0.86, p < 0.001). We found that the lnc-IL7R level correctly identified patients with COPD (sensitivity = 0.83, specificity = 0.83), precisely discriminated those without emphysematous phenotype (sensitivity = 0.48, specificity = 0.89), and its differential expression reflected disease course based on its correlation with the COPD GOLD stage (r = −0.59, p < 0.001), %LAA-950insp (r = −0.30, p = 0.002), total LAA (r = −0.35, p < 0.001), FEV1(%) (r = 0.52, p < 0.001), FVC (%) (r = 0.45, p < 0.001), and post-bronchodilator FEV1/FVC (r = 0.41, p < 0.001). Consistent with other data, our bioinformatics-aided dose−response plot showed that the probability of COPD decreased as lnc-IL7R expression increased, thus, corroborating our posited anti-COPD therapeutic potential of lnc-IL7R. In conclusion, reduced lnc-IL7R expression not only is associated with inflammation in the airway epithelial cells but is indicative of impaired pulmonary function, pathognomonic of COPD, and predictive of an exacerbated/ aggravated COPD phenotype. These data provide new mechanistic insights into the ailing lung and COPD progression, as well as suggest a novel actionable molecular factor that may be exploited as an efficacious therapeutic strategy in patients with COPD.
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Affiliation(s)
- Oluwaseun Adebayo Bamodu
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235, Taiwan; (O.A.B.); (S.-M.W.); (P.-H.F.); (W.-L.S.); (H.-C.C.); (S.-C.H.); (K.-Y.C.); (T.-T.C.); (C.-H.T.)
- Department of Medical Research, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235, Taiwan
- Department of Urology, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235, Taiwan
- Division of Hematology and Oncology, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235, Taiwan
| | - Sheng-Ming Wu
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235, Taiwan; (O.A.B.); (S.-M.W.); (P.-H.F.); (W.-L.S.); (H.-C.C.); (S.-C.H.); (K.-Y.C.); (T.-T.C.); (C.-H.T.)
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- Division of Clinical Care Medicine, Department of Emergency and Critical Care Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235, Taiwan
- TMU Research Center of Thoracic Medicine, Taipei Medical University, Taipei 110, Taiwan;
| | - Po-Hao Feng
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235, Taiwan; (O.A.B.); (S.-M.W.); (P.-H.F.); (W.-L.S.); (H.-C.C.); (S.-C.H.); (K.-Y.C.); (T.-T.C.); (C.-H.T.)
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- TMU Research Center of Thoracic Medicine, Taipei Medical University, Taipei 110, Taiwan;
| | - Wei-Lun Sun
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235, Taiwan; (O.A.B.); (S.-M.W.); (P.-H.F.); (W.-L.S.); (H.-C.C.); (S.-C.H.); (K.-Y.C.); (T.-T.C.); (C.-H.T.)
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- TMU Research Center of Thoracic Medicine, Taipei Medical University, Taipei 110, Taiwan;
| | - Cheng-Wei Lin
- TMU Research Center of Thoracic Medicine, Taipei Medical University, Taipei 110, Taiwan;
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- International PhD Program for Cell Therapy and Regeneration Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Hsiao-Chi Chuang
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235, Taiwan; (O.A.B.); (S.-M.W.); (P.-H.F.); (W.-L.S.); (H.-C.C.); (S.-C.H.); (K.-Y.C.); (T.-T.C.); (C.-H.T.)
- TMU Research Center of Thoracic Medicine, Taipei Medical University, Taipei 110, Taiwan;
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Shu-Chuan Ho
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235, Taiwan; (O.A.B.); (S.-M.W.); (P.-H.F.); (W.-L.S.); (H.-C.C.); (S.-C.H.); (K.-Y.C.); (T.-T.C.); (C.-H.T.)
- TMU Research Center of Thoracic Medicine, Taipei Medical University, Taipei 110, Taiwan;
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Kuan-Yuan Chen
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235, Taiwan; (O.A.B.); (S.-M.W.); (P.-H.F.); (W.-L.S.); (H.-C.C.); (S.-C.H.); (K.-Y.C.); (T.-T.C.); (C.-H.T.)
- TMU Research Center of Thoracic Medicine, Taipei Medical University, Taipei 110, Taiwan;
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Tzu-Tao Chen
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235, Taiwan; (O.A.B.); (S.-M.W.); (P.-H.F.); (W.-L.S.); (H.-C.C.); (S.-C.H.); (K.-Y.C.); (T.-T.C.); (C.-H.T.)
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- TMU Research Center of Thoracic Medicine, Taipei Medical University, Taipei 110, Taiwan;
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Chien-Hua Tseng
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235, Taiwan; (O.A.B.); (S.-M.W.); (P.-H.F.); (W.-L.S.); (H.-C.C.); (S.-C.H.); (K.-Y.C.); (T.-T.C.); (C.-H.T.)
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- Division of Clinical Care Medicine, Department of Emergency and Critical Care Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235, Taiwan
- TMU Research Center of Thoracic Medicine, Taipei Medical University, Taipei 110, Taiwan;
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei 106, Taiwan
| | - Wen-Te Liu
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235, Taiwan; (O.A.B.); (S.-M.W.); (P.-H.F.); (W.-L.S.); (H.-C.C.); (S.-C.H.); (K.-Y.C.); (T.-T.C.); (C.-H.T.)
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- TMU Research Center of Thoracic Medicine, Taipei Medical University, Taipei 110, Taiwan;
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- Correspondence: (W.-T.L.); (K.-Y.L.); Tel.: +886-02-2249-0088 (ext. 2714) (W.-T.L. & K.-Y.L.)
| | - Kang-Yun Lee
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235, Taiwan; (O.A.B.); (S.-M.W.); (P.-H.F.); (W.-L.S.); (H.-C.C.); (S.-C.H.); (K.-Y.C.); (T.-T.C.); (C.-H.T.)
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- TMU Research Center of Thoracic Medicine, Taipei Medical University, Taipei 110, Taiwan;
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- Correspondence: (W.-T.L.); (K.-Y.L.); Tel.: +886-02-2249-0088 (ext. 2714) (W.-T.L. & K.-Y.L.)
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Wang C, Chen X, Du L, Zhan Q, Yang T, Fang Z. Comparison of machine learning algorithms for the identification of acute exacerbations in chronic obstructive pulmonary disease. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2020; 188:105267. [PMID: 31841787 DOI: 10.1016/j.cmpb.2019.105267] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 11/19/2019] [Accepted: 12/08/2019] [Indexed: 05/05/2023]
Abstract
OBJECTIVES Identifying acute exacerbations in chronic obstructive pulmonary disease (AECOPDs) is of utmost importance for reducing the associated mortality and financial burden. In this research, the authors aimed to develop identification models for AECOPDs and to compare the relative performance of different modeling paradigms to find the best model for this task. METHODS Data were extracted from electronic medical records (EMRs) of patients with chronic obstructive pulmonary disease who admitted to the China-Japan Friendship Hospital between February 2011 and March 2017. Five machine learning algorithms (random forest, support vector machine, logistic regression, K-nearest neighbor and naïve Bayes) were used to develop the AECOPDs identification models. Feature selection was performed to find an optimal feature subset. 10-folds cross-validation was used to find the best hyperparameters for each model. The following metrics: area under the receiver operating characteristic curve, sensitivity, specificity, positive predictive value, and negative predictive value were used to evaluate the performance of these models. RESULTS A total of 303 EMRs (AECOPDs patients:135; None AECOPDs patients: 168) were included in the study. The SVM model obtained the best performance (sensitivity: 0.80, specificity: 0.83, positive predictive value:0.81, negative predictive value:0.85 and area under the receiver operating characteristic curve: 0.90) after performing feature selection. CONCLUSIONS Our research confirms that the proposed model based on the support vector machine is a powerful tool to identify AECOPDs patients, and it is promising to provide decision support for clinicians when they are struggling to give a confirmed clinical diagnosis.
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Affiliation(s)
- Chenshuo Wang
- Institute of Electronics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xianxiang Chen
- Institute of Electronics, Chinese Academy of Sciences, Beijing, China; Personalized Management of Chronic Respiratory Disease, Chinese Academy of Medical Sciences, China
| | - Lidong Du
- Institute of Electronics, Chinese Academy of Sciences, Beijing, China; Personalized Management of Chronic Respiratory Disease, Chinese Academy of Medical Sciences, China
| | | | - Ting Yang
- China-Japan Friendship Hospital, Beijing, China.
| | - Zhen Fang
- Institute of Electronics, Chinese Academy of Sciences, Beijing, China; Personalized Management of Chronic Respiratory Disease, Chinese Academy of Medical Sciences, China; University of Chinese Academy of Sciences, Beijing, China.
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Hoesterey D, Das N, Janssens W, Buhr RG, Martinez FJ, Cooper CB, Tashkin DP, Barjaktarevic I. Spirometric indices of early airflow impairment in individuals at risk of developing COPD: Spirometry beyond FEV 1/FVC. Respir Med 2019; 156:58-68. [PMID: 31437649 PMCID: PMC6768077 DOI: 10.1016/j.rmed.2019.08.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/08/2019] [Accepted: 08/07/2019] [Indexed: 01/24/2023]
Abstract
Spirometry is the current gold standard for diagnosing and monitoring the progression of Chronic Obstructive Pulmonary Disease (COPD). However, many current and former smokers who do not meet established spirometric criteria for the diagnosis of this disease have symptoms and clinical courses similar to those with diagnosed COPD. Large longitudinal observational studies following individuals at risk of developing COPD offer us additional insight into spirometric patterns of disease development and progression. Analysis of forced expiratory maneuver changes over time may allow us to better understand early changes predictive of progressive disease. This review discusses the theoretical ability of spirometry to capture fine pathophysiologic changes in early airway disease, highlights the shortcomings of current diagnostic criteria, and reviews existing evidence for spirometric measures which may be used to better detect early airflow impairment.
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Affiliation(s)
- Daniel Hoesterey
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Nilakash Das
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism and Ageing, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Wim Janssens
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism and Ageing, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Russell G Buhr
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, USA; Department of Health Policy and Management, Fielding School of Public Health, University of California, Los Angeles, USA; Medical Service, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, USA
| | | | - Christopher B Cooper
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, USA; Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Donald P Tashkin
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Igor Barjaktarevic
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, USA.
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Dubé CE, Liu SH, Driban JB, McAlindon TE, Eaton CB, Lapane KL. The relationship between smoking and knee osteoarthritis in the Osteoarthritis Initiative. Osteoarthritis Cartilage 2016; 24:465-72. [PMID: 26432984 PMCID: PMC4761327 DOI: 10.1016/j.joca.2015.09.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 09/15/2015] [Accepted: 09/22/2015] [Indexed: 02/02/2023]
Abstract
OBJECTIVE To estimate the extent that smoking history is associated with symptoms and disease progression among individuals with radiographically confirmed knee Osteoarthritis (OA). METHOD Both cross-sectional (baseline) and longitudinal studies employed data from the Osteoarthritis Initiative (OAI) (n = 2250 participants). Smoking history was assessed at baseline with 44% current or former smokers. The Western Ontario and McMaster Universities Arthritis Index (WOMAC) was used to measure knee pain, stiffness, and physical function. Disease progression was measured using joint space width (JSW). We used adjusted multivariable linear models to examine the relationship between smoking status and exposure in pack years (PY) with symptoms and JSW at baseline. Changes in symptoms and JSW over time were further assessed. RESULTS In cross-sectional analyses, compared to never-smokers high PY (≥15 PY) was associated with slightly greater pain (beta 0.36, 95% CI: 0.01-0.71) and stiffness (beta 0.20, 95% CI: 0.03-0.37); and low PY (<15 PY) was associated with better JSW (beta 0.15, 95% CI: 0.02-0.28). Current smoking was associated with greater pain (beta 0.59, 95% CI: 0.04-1.15) compared to never-smokers. These associations were not confirmed in the longitudinal study. Longitudinally, no associations were found between high or low PY or baseline smoking status with changes in symptoms (at 72 months) or JSW (at 48 months). CONCLUSION Cross-sectional findings are likely due residual confounding. The more robust longitudinal analysis found no associations between smoking status and symptoms or JSW. Long-term smoking provides no benefits to knee OA patients while exposing them to other well-documented serious health risks.
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Affiliation(s)
- C E Dubé
- Department of Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, MA 01655, USA.
| | - S-H Liu
- Department of Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, MA 01655, USA.
| | - J B Driban
- Division of Rheumatology, Tufts Medical Center, Boston, MA 02111, USA.
| | - T E McAlindon
- Division of Rheumatology, Tufts Medical Center, Boston, MA 02111, USA.
| | - C B Eaton
- Center for Primary Care and Prevention, Memorial Hospital of Rhode Island, Pawtucket, RI 02860, USA; Department of Family Medicine, Warren Alpert Medical School, School of Public Health, Brown University, Providence, RI 02912, USA; Department of Epidemiology, Warren Alpert Medical School, School of Public Health, Brown University, Providence, RI 02912, USA.
| | - K L Lapane
- Department of Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, MA 01655, USA.
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