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Jain H, Chejara RS, Agarwal M, Mahavar S, Sharma R. Estimation of Predictors of Mortality in Patients with Acute Respiratory Failure Secondary to Chronic Obstructive Pulmonary Disease Admitted in Tertiary Care Center. THE JOURNAL OF THE ASSOCIATION OF PHYSICIANS OF INDIA 2025; 73:35-38. [PMID: 39927996 DOI: 10.59556/japi.73.0841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2025]
Abstract
INTRODUCTION Chronic obstructive pulmonary disease (COPD) is characterized by persistent airflow limitation and an increased chronic inflammatory response in the airways to noxious particles and gases. More than 10 million individuals in the United States (US) are affected with COPD, the fourth largest cause of mortality. Globally 250 million individuals are affected by COPD. D-dimer, C-reactive protein (CRP), acute physiology and chronic health evaluation (APACHE) II score, and hypoalbuminemia have significant correlation with morbidity, mortality, and risk stratification of hospitalized COPD patients with acute respiratory failure (ARF). The purpose of this study is to assess how well D-dimer, CRP, APACHE II score, and hypoalbuminemia predict death in COPD with ARF. MATERIALS AND METHODS A hospital-based prospective research (observational study) was conducted in a tertiary care center. The research was carried out from 1st February 2021, until 1st November 2022. The patients (sample size = 60; 35 survived and 25 died) were taken for detailed personal history, occupational history, chest X-ray, arterial blood gas (ABG) analysis, and thorough clinical examination to identify evidence of COPD. Our study included D-dimer, CRP, APACHE II score, and hypoalbuminemia in hospitalized COPD patients. RESULTS In our study, the median D-dimer levels for patients who lived and died were 1,012.34 and 7,222.64, respectively, with a p-value < 0.001. Patients who survived had a mean CRP of 3.56, whereas those who were dead had a value of 12.62. The mean serum albumin levels among survived and dead patients were 3.23 and 2.22, respectively. The mean APACHE II score in survived and dead patients were 9.91 and 28.48, respectively. The APACHE II score has sensitivity and specificity of 96 and 91.4%, respectively, with a critical cutoff of >19. Hypoalbuminemia has sensitivity and specificity of 96 and 65.7%, with a critical cutoff of <3. CONCLUSION High levels of CRP, an elevated APACHE II score, elevated levels of D-dimer, and lower levels of serum albumin are all independently related to an increased risk of in-hospital mortality.
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Affiliation(s)
- Hardik Jain
- Junior Resident, Sawai Man Singh Medical College, Jaipur, Rajasthan, India
| | - Radhey S Chejara
- Associate Professor, Sawai Man Singh Medical College, Jaipur, Rajasthan, India, Corresponding Author
| | - Madhulata Agarwal
- Assistant Professor, Sawai Man Singh Medical College, Jaipur, Rajasthan, India
| | - Sunil Mahavar
- Professor, Sawai Man Singh Medical College, Jaipur, Rajasthan, India
| | - Raman Sharma
- Senior Professor, Sawai Man Singh Medical College, Jaipur, Rajasthan, India
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Wei J, Tian Y, Wei J, Guan M, Yu X, Xie J, Fan G. Bilirubin regulates cell death type by alleviating macrophage mitochondrial dysfunction caused by cigarette smoke extract. Redox Rep 2024; 29:2382946. [PMID: 39074442 PMCID: PMC11288206 DOI: 10.1080/13510002.2024.2382946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024] Open
Abstract
OBJECTIVES To explore the effects and mechanisms of bilirubin on mitochondrial function and type of macrophage cell death after exposure to cigarette smoke extract (CSE). METHODS RAW264.7 macrophages were treated with different concentrations of CSE and bilirubin solutions and divided into four groups: control, CSE, bilirubin, and bilirubin + CSE groups. The necrotic and apoptotic states of the macrophages were determined using an Annexin V-fluorescein 5-isothiocyanate/propidium iodide (FITC/PI) staining kit. Cytoplasmic NOD-like receptor family, pyrin domain containing 3 (NLRP3) expression in macrophages was detected by immunofluorescence and the levels of IL-1β and IL-18 in the supernatants of culture medium were detected by enzyme linked immunosorbent assay (ELISA) test. A JC-1 mitochondrial membrane potential detection kit was used to assess mitochondrial membrane damage and the adenosine triphosphate (ATP) assay kit was used to determine intracellular ATP levels. After the macrophages were stained with reactive oxygen species (ROS) specific dye, 2',7'-Dichlorodihydrofluorescein diacetate (DCFH-DA), the fluorescence intensity and proportion of ROS-positive macrophages were measured using flow cytometry. RESULTS We observed that compared with those of 0 μM (control group), concentrations of 5, 10, or 20 μΜ bilirubin significantly decreased cell viability, which was increased by bilirubin exposure below 1 μM. The effect of CSE on macrophage viability was concentration- and time-dependent. Bilirubin of 0.2 μM could alleviate the inhibition of macrophage viability caused by 5% CSE. In addition, bilirubin intervention could reduce the occurrence of necrosis and pyroptosis to a certain extent. CONCLUSIONS CSE could cause mitochondrial dysfunction in macrophages, as demonstrated by a decrease in mitochondrial membrane potential and intracellular ATP levels and an increase in ROS production, while bilirubin could relieve mitochondrial dysfunction caused by CSE.
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Affiliation(s)
- Jingjing Wei
- Department of Pediatrics, Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
| | - Yuan Tian
- Department of Pediatrics, Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
| | - Jinshu Wei
- Department of Pediatrics, Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
| | - Meiqi Guan
- Department of Pediatrics, Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
| | - Xiaoya Yu
- Department of Pediatrics, Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
| | - Jianing Xie
- Department of Pediatrics, Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
| | - Guoquan Fan
- School of Basic Medical Science, Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
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Baldomero AK, MacDonald DM, Kaplan A, Lock E, Cho MH, Bowler R, Gillenwater L, Kunisaki KM, Wendt CH. Bilirubin-associated single nucleotide polymorphism (SNP) and respiratory health outcomes: a mendelian randomization study. Respir Res 2023; 24:190. [PMID: 37474940 PMCID: PMC10357606 DOI: 10.1186/s12931-023-02471-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 06/07/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND Observational studies have shown an association between higher bilirubin levels and improved respiratory health outcomes. Targeting higher bilirubin levels has been proposed as a novel therapeutic strategy in COPD. However, bilirubin levels are influenced by multiple intrinsic and extrinsic factors, and these observational studies are prone to confounding. Genetic analyses are one approach to overcoming residual confounding in observational studies. OBJECTIVES To test associations between a genetic determinant of bilirubin levels and respiratory health outcomes. METHODS COPDGene participants underwent genotyping at the baseline visit. We confirmed established associations between homozygosity for rs6742078 and higher bilirubin, and between higher bilirubin and decreased risk of acute respiratory events within this cohort. For our primary analysis, we used negative binomial regression to test associations between homozygosity for rs6742078 and rate of acute respiratory events. RESULTS 8,727 participants (n = 6,228 non-Hispanic white and 2,499 African American) were included. Higher bilirubin was associated with decreased rate of acute respiratory events [incidence rate ratio (IRR) 0.85, 95% CI 0.75 to 0.96 per SD increase in bilirubin intensity]. We did not find significant associations between homozygosity for rs6742078 and acute respiratory events (IRR 0.94, 95% CI 0.70 to 1.25 for non-Hispanic white and 1.09, 95% CI 0.91 to 1.31 for African American participants). CONCLUSIONS A genetic determinant of higher bilirubin levels was not associated with better respiratory health outcomes. These results do not support targeting higher bilirubin levels as a therapeutic strategy in COPD.
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Affiliation(s)
- Arianne K Baldomero
- Pulmonary, Allergy, Critical Care, and Sleep Medicine, Minneapolis Veterans Affairs Health Care System, One Veterans Drive, Minneapolis, MN, 55417, USA
- Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Minnesota, Minneapolis, MN, USA
| | - David M MacDonald
- Pulmonary, Allergy, Critical Care, and Sleep Medicine, Minneapolis Veterans Affairs Health Care System, One Veterans Drive, Minneapolis, MN, 55417, USA.
- Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Minnesota, Minneapolis, MN, USA.
| | - Adam Kaplan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Eric Lock
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Michael H Cho
- Division of Pulmonary and Critical Care, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Russell Bowler
- Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Lucas Gillenwater
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ken M Kunisaki
- Pulmonary, Allergy, Critical Care, and Sleep Medicine, Minneapolis Veterans Affairs Health Care System, One Veterans Drive, Minneapolis, MN, 55417, USA
- Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Chris H Wendt
- Pulmonary, Allergy, Critical Care, and Sleep Medicine, Minneapolis Veterans Affairs Health Care System, One Veterans Drive, Minneapolis, MN, 55417, USA
- Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Minnesota, Minneapolis, MN, USA
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Hamilton FW, Abeysekera KWM, Hamilton W, Timpson NJ. Effect of bilirubin and Gilbert syndrome on health: cohort analysis of observational, genetic, and Mendelian randomisation associations. BMJ MEDICINE 2023; 2:e000467. [PMID: 37456363 PMCID: PMC10347488 DOI: 10.1136/bmjmed-2022-000467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/06/2023] [Indexed: 07/18/2023]
Abstract
Objectives To compare associations between the Gilbert syndrome genotype in European populations, measured bilirubin concentrations, genetically predicted bilirubin using this genotype, and a wide range of health outcomes in a large cohort. Design Cohort study including observational, genetic, and Mendelian randomisation analyses. Setting 22 centres across England, Scotland, and Wales in UK Biobank (2006-10), with replication in a national Finnish cohort (FinnGen). Participants 463 060 participants in the UK Biobank were successfully genotyped for a genetic variant (rs887829) that is strongly associated with Gilbert syndrome and 438 056 participants had measured bilirubin concentrations with linked electronic health record data coded using the tenth edition of the International Classification of Diseases. Replication analyses were performed in FinnGen (n=429 209) with linked electronic health record data. Main outcome measures Odds ratios for the association between serum bilirubin concentrations, rs887829-T homozygosity (the risk genotype for Gilbert syndrome), genetically predicted bilirubin using rs887829-T allele carriage alone, and a wide range of health outcomes recorded in primary and secondary care. Results 46 189 participants in UK Biobank (about 10%) were homozygous for rs887829-T defining them as having the genotype characterising Gilbert syndrome. However, only 1701 (3%) of this group had a coded diagnosis of Gilbert syndrome. Variation at this locus explained 37.1% of all variation in measured serum bilirubin. In the observational analyses, higher bilirubin concentrations had strong inverse associations with a wide range of outcomes including overall health status, chronic obstructive pulmonary disease, myocardial infarction, and cholesterol measures. These associations were not identified in people with the Gilbert genotype. We identified associations with genetically predicted bilirubin concentrations and biliary and liver pathology (eg, odds ratio for cholelithiasis 1.16 (95% confidence interval 1.12 to 1.20); P=5.7×10-16) and a novel association with pityriasis rosea (1.47 (1.27 to 1.69), P=1.28×10-7). Conclusions Only 3% of participants who are homozygous for rs887829-T have a recorded diagnosis of Gilbert syndrome. Carriers of this genotype have modest increases in the odds of developing biliary pathology and pityriasis rosea. Evidence from the analyses of genetic data suggests that bilirubin has no likely causal role in protection from cardiovascular disease, chronic obstructive pulmonary disease, or other key healthcare outcomes and therefore represents a poor target for therapeutic intervention for these outcomes.
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Affiliation(s)
- Fergus W Hamilton
- MRC Integrative Epidemiology Unit, Bristol, UK
- Infection Science, North Bristol NHS Trust, Bristol, UK
| | - KWM Abeysekera
- MRC Integrative Epidemiology Unit, Bristol, UK
- Department of Liver Medicine, Bristol Royal Infirmary, Bristol, UK
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Xu J, Fan Y, Yu Y, Han Y, Kang Q, Tan N, Yang Y, Chen H, Pan J, Xu X. A Multicenter Real-World Study Evaluating the Hepatoprotective Effect of Polyene Phosphatidylcholine Against Chronic Hepatitis B. Front Med (Lausanne) 2022; 9:842098. [PMID: 35814776 PMCID: PMC9256938 DOI: 10.3389/fmed.2022.842098] [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: 12/23/2021] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
Background Polyene phosphatidylcholine (PPC) has been widely used to treat liver diseases in China. However, there is a lack of post-marketing evidence demonstrating its liver-protective efficiency among patients infected with hepatitis B virus (HBV). This study analyzed the multicenter real-world data to compare the effectiveness of PPC with those of magnesium isoglycyrrhizinate (IsoMag) and glutathione (GSH) in patients with liver injury. Methods This study comprised the real-world data analysis of a multicenter, retrospective observational cohort. The data were retrieved from the Cooperative Registry of the Hospital Prescription in China between 1 October 2018, and 30 September 2019. A growth curve analysis was performed to compare the effects of different treatments on liver function longitudinally for up to 30 days after treatment commencement. In addition, the dose effect of the PPC treatment was investigated. Results The final cohort included 6,052 patients with approximately 8% infected with HBV (N = 471). There were 1,649, 1,750, and 2,653 patients in the PPC, GSH, and IsoMag groups, respectively, with an average age of 53.9 years. In patients with HBV infection, the PPC treatment was associated with a significant decline in alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels (slopes: -3.7, 95% CI, -6.0 to -1.5 U/L/day; -2.4, 95% CI, -4.5 to -0.3 U/L/day, respectively). However, there were no significant differences in the effects among the three groups. In patients without HBV infection, the PPC treatment decreased ALT, AST, γ-glutamyl transferase (GGT), and albumin levels (-5.2, 95% CI, -5.8 to -4.5 U/L/day; -3.5, 95% CI, -4.2 to -2.7 U/L/day; -4.9, 95% CI, -6.2 to -3.7 U/L/day, -0.07, 95% CI, -0.09 to -0.04 g/L/day, respectively) and showed a stronger effect on lowering ALT levels than GSH (-2.6, 95% CI, -3.3 to -1.8 U/L/day, p < 0.05), as well as a stronger effect on lowering GGT levels than IsoMag (-1.4, 95% CI, -2.4 to -0.4 U/L/day, p < 0.05). PPC had no impact on prothrombin activity levels in patients with or without HBV infection. High-dose PPC exhibited a stronger effect on lowering ALT and AST levels than low-dose PPC. Conclusion This was the first real-world multicenter study to demonstrate that PPC efficiently lowers ALT and AST levels in patients with liver diseases regardless of the status of HBV infection. PPC treatment showed a comparable or better effect compared with GSH and IsoMag treatments. High-dose PPC resulted in a stronger effect than low-dose PPC.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Xiaoyuan Xu
- Department of Infectious Diseases, Peking University First Hospital, Beijing, China
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Wang JM, Han MK, Labaki WW. Chronic obstructive pulmonary disease risk assessment tools: is one better than the others? Curr Opin Pulm Med 2022; 28:99-108. [PMID: 34652295 PMCID: PMC8799486 DOI: 10.1097/mcp.0000000000000833] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Risk assessment tools are essential in COPD care to help clinicians identify patients at higher risk of accelerated lung function decline, respiratory exacerbations, hospitalizations, and death. RECENT FINDINGS Conventional methods of assessing risk have focused on spirometry, patient-reported symptoms, functional status, and a combination of these tools in composite indices. More recently, qualitatively and quantitatively assessed chest imaging findings, such as emphysema, large and small airways disease, and pulmonary vascular abnormalities have been associated with poor long-term outcomes in COPD patients. Although several blood and sputum biomarkers have been investigated for risk assessment in COPD, most still warrant further validation. Finally, novel remote digital monitoring technologies may be valuable to predict exacerbations but their large-scale performance, ease of implementation, and cost effectiveness remain to be determined. SUMMARY Given the complex heterogeneity of COPD, any single metric is unlikely to fully capture the risk of poor long-term outcomes. Therefore, clinicians should review all available clinical data, including spirometry, symptom severity, functional status, chest imaging, and bloodwork, to guide personalized preventive care of COPD patients. The potential of machine learning tools and remote monitoring technologies to refine COPD risk assessment is promising but remains largely untapped pending further investigation.
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Affiliation(s)
- Jennifer M Wang
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan, USA
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Dai C, Wang Z, Yang H, Xiao S, Xu J, Deng Z, Wu F, Wen X, Zheng Y, Lu L, Zhao N, Huang P, Zhou Y, Ran P. Association Between Serum Total Bilirubin and COPD: Results from a Cross-Sectional Study and a Bidirectional Mendelian Randomization Analysis. Clin Epidemiol 2022; 14:289-298. [PMID: 35299727 PMCID: PMC8922320 DOI: 10.2147/clep.s353389] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/25/2022] [Indexed: 11/23/2022] Open
Abstract
Background The potential protective role of serum total bilirubin (TB) for chronic obstructive pulmonary disease (COPD) is controversial. We aimed to investigate whether serum TB could prevent airflow limitation (reduce the risk of COPD) and whether these associations were causal or reversely causal. Methods We conducted a multi-center and cross-sectional study including 3069 participants. Logistic regression model (LRM) with restricted cubic spline (RCS) and priori defined quintile categories were used to assess the associations of TB with COPD. Besides, ordinary least squares (OLS) regression model with RCS curves were applied to assess the dose-response relationship between serum TB and airflow limitation (FEV1/FVC). To verify the causal direction between TB and COPD, a bidirectional Mendelian randomization analysis was carried out with GWAS data from European ancestry. Results In the cross-sectional study, the relationship between levels of TB and COPD risk was U shaped (P=0.001), and the low and high concentrations of TB apparently increasing the risk of COPD (OR 1.40, 95% CI 1.07 to 1.82 for less than 9 μmol/L; OR 1.36, 95% CI 1.06 to 1.76 for 9.01-1 0.88 μmol/L; OR 1.50, 95% CI 1.16 to 1.95 for more than 13 μmol/L). There was a significant non-linear relationship between TB and FEV1/FVC (non-linear p=0.004). Furthermore, results of bidirectional Mendelian randomization analysis (OR 1.000; 95% CI 0.983 to 1.017 for MR and OR 0.998; 95% CI 0.976 to 1.020 for reversal MR) did not support the causal effects between serum TB and FEV1/FVC after controlling the effect of potential confounders and revised causality. Conclusion Our study reveals that there was non-linear does-response pattern between serum TB and COPD. However, there was little evidence for the linear causal associations of serum TB with airflow limitation. The relationship of TB with COPD needs further study and careful interpretation.
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Affiliation(s)
- Cuiqiong Dai
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Zihui Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Huajing Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Shan Xiao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Jianwu Xu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Zhishan Deng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Fan Wu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
- Guangzhou Laboratory, Bio-Island, Guangzhou, People’s Republic of China
| | - Xiang Wen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Youlan Zheng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Lifei Lu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Ningning Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Peiyu Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Yumin Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
- Guangzhou Laboratory, Bio-Island, Guangzhou, People’s Republic of China
| | - Pixin Ran
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
- Guangzhou Laboratory, Bio-Island, Guangzhou, People’s Republic of China
- Correspondence: Pixin Ran; Yumin Zhou, Tel +86-20 3710 3616, Fax +86-20 81340482, Email ;
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Li W, Zhang Y, Wang Y, Rong Z, Liu C, Miao H, Chen H, He Y, He W, Chen L. Candidate gene prioritization for chronic obstructive pulmonary disease using expression information in protein-protein interaction networks. BMC Pulm Med 2021; 21:280. [PMID: 34481483 PMCID: PMC8418003 DOI: 10.1186/s12890-021-01646-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 08/23/2021] [Indexed: 11/30/2022] Open
Abstract
Background Identifying or prioritizing genes for chronic obstructive pulmonary disease (COPD), one type of complex disease, is particularly important for its prevention and treatment. Methods In this paper, a novel method was proposed to Prioritize genes using Expression information in Protein–protein interaction networks with disease risks transferred between genes (abbreviated as PEP). A weighted COPD PPI network was constructed using expression information and then COPD candidate genes were prioritized based on their corresponding disease risk scores in descending order. Results Further analysis demonstrated that the PEP method was robust in prioritizing disease candidate genes, and superior to other existing prioritization methods exploiting either topological or functional information. Top-ranked COPD candidate genes and their significantly enriched functions were verified to be related to COPD. The top 200 candidate genes might be potential disease genes in the diagnosis and treatment of COPD. Conclusions The proposed method could provide new insights to the research of prioritizing candidate genes of COPD or other complex diseases with expression information from sequencing or microarray data. Supplementary Information The online version contains supplementary material available at 10.1186/s12890-021-01646-9.
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Affiliation(s)
- Wan Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150000, Heilongjiang, China
| | - Yihua Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150000, Heilongjiang, China
| | - Yahui Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150000, Heilongjiang, China
| | - Zherou Rong
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150000, Heilongjiang, China
| | - Chenyu Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150000, Heilongjiang, China
| | - Hui Miao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150000, Heilongjiang, China
| | - Hongwei Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150000, Heilongjiang, China
| | - Yuehan He
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150000, Heilongjiang, China
| | - Weiming He
- Institute of Opto-Electronics, Harbin Institute of Technology, Harbin, 150000, Heilongjiang, China.
| | - Lina Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150000, Heilongjiang, China.
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