Bioinformatic analysis of next‑generation sequencing data to identify dysregulated genes in fibroblasts of idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a lethal fibrotic lung disease with an increasing global burden. It is hypothesized that fibroblasts have a number of functions that may affect the development and progression of IPF. However, the present understanding of cellular and molecular mechanisms associated with fibroblasts in IPF remains limited. The present study aimed to identify the dysregulated genes in IPF fibroblasts, elucidate their functions and explore potential microRNA (miRNA)-mRNA interactions. mRNA and miRNA expression profiles were obtained from IPF fibroblasts and normal lung fibroblasts using a next-generation sequencing platform, and bioinformatic analyses were performed in a step-wise manner. A total of 42 dysregulated genes (>2 fold-change of expression) were identified, of which 5 were verified in the Gene Expression Omnibus (GEO) database analysis, including the upregulation of neurotrimin (NTM), paired box 8 (PAX8) and mesoderm development LRP chaperone, and the downregulation of ITPR interacting domain containing 2 and Inka box actin regulator 2 (INKA2). Previous data indicated that PAX8 and INKA2 serve roles in cell growth, proliferation and survival. Gene Ontology analysis indicated that the most significant function of these 42 dysregulated genes was associated with the composition and function of the extracellular matrix (ECM). A total of 60 dysregulated miRNAs were also identified, and 1,908 targets were predicted by the miRmap database. The integrated analysis of mRNA and miRNA expression data, combined with GEO verification, finally identified Homo sapiens (hsa)-miR-1254-INKA2 and hsa-miR-766-3p-INKA2 as the potential miRNA-mRNA interactions in IPF fibroblasts. In summary, the results of the present study suggest that dysregulation of PAX8, hsa-miR-1254-INKA2 and hsa-miR-766-3p-INKA2 may promote the proliferation and survival of IPF fibroblasts. In the functional analysis of the dysregulated genes, a marked association between fibroblasts and the ECM was identified. These data improve the current understanding of fibroblasts as key cells in the pathogenesis of IPF. As a screening study using bioinformatics approaches, the results of the present study require additional validation.

Infections Caused by Carbapenem-Resistant Enterobacteriaceae: An Update on Therapeutic Options

Carbapenems are considered as last-resort antibiotics for the treatment of infections caused by multidrug-resistant Gram-negative bacteria. With the increasing use of carbapenems in clinical practice, the emergence of carbapenem-resistant pathogens now poses a great threat to human health. Currently, antibiotic options for the treatment of carbapenem-resistant Enterobacteriaceae (CRE) are very limited, with polymyxins, tigecycline, fosfomycin, and aminoglycosides as the mainstays of therapy. The need for new and effective anti-CRE therapies is urgent. Here, we describe the current understanding of issues related to CRE and review combination therapeutic strategies for CRE infections, including high-dose tigecycline, high-dose prolonged-infusion of carbapenem, and double carbapenem therapy. We also review the newly available antibiotics which have potential in the future treatment of CRE infections: ceftazidime/avibactam, which is active against KPC and OXA-48 producers; meropenem/vaborbactam, which is active against KPC producers; plazomicin, which is a next-generation aminoglycoside with in vitro activity against CRE; and eravacycline, which is a tetracycline class antibacterial with in vitro activity against CRE. Although direct evidence for CRE treatment is still lacking and the development of resistance is a concern, these new antibiotics provide additional therapeutic options for CRE infections. Finally, we review other potential anti-CRE antibiotics in development: imipenem/relebactam and cefiderocol. Currently, high-dose and combination strategies that may include the new β-lactam/β-lactamase inhibitors should be considered in severe CRE infections to maximize treatment success. In the future, when more treatment options are available, therapy for CRE infections should be individualized and based on molecular phenotypes of resistance, susceptibility profiles, disease severity, and patient characteristics. More high-quality studies are needed to guide effective treatment for infections caused by CRE.

Deducting MicroRNA-Mediated Changes Common in Bronchial Epithelial Cells of Asthma and Chronic Obstructive Pulmonary Disease-A Next-Generation Sequencing-Guided Bioinformatic Approach

Asthma and chronic obstructive pulmonary disease (COPD) are chronic airway inflammatory diseases that share some common features, although these diseases are somewhat different in etiologies, clinical features, and treatment policies. The aim of this study is to investigate the common microRNA-mediated changes in bronchial epithelial cells of asthma and COPD. The microRNA profiles in primary bronchial epithelial cells from asthma (AHBE) and COPD (CHBE) patients and healthy subjects (NHBE) were analyzed with next-generation sequencing (NGS) and the significant microRNA changes common in AHBE and CHBE were extracted. The upregulation of hsa-miR-10a-5p and hsa-miR-146a-5p in both AHBE and CHBE was confirmed with quantitative polymerase chain reaction (qPCR). Using bioinformatic methods, we further identified putative targets of these microRNAs, which were downregulated in both AHBE and CHBE: miR-10a-5p might suppress BCL2, FGFR3, FOXO3, PDE4A, PDE4C, and PDE7A; miR-146a-5p might suppress BCL2, INSR, PDE4D, PDE7A, PDE7B, and PDE11A. We further validated significantly decreased expression levels of FOXO3 and PDE7A in AHBE and CHBE than in NHBE with qPCR. Increased serum miR-146a-5p level was also noted in patients with asthma and COPD as compared with normal control subjects. In summary, our study revealed possible mechanisms mediated by miR-10a-5p and miR-146a-5p in the pathogenesis of both asthma and COPD. The findings might provide a scientific basis for developing novel diagnostic and therapeutic strategies.

Predictors of survival in patients with influenza pneumonia-related severe acute respiratory distress syndrome treated with prone positioning

Background

Patients with influenza complicated with pneumonia are at high risk of rapid progression to acute respiratory distress syndrome (ARDS). Prone positioning with longer duration and lung-protective strategies might reduce the mortality level in ARDS. The aim of this study is to investigate the survival predictors of prone positioning in patients with ARDS caused by influenza pneumonia.

Methods

This retrospective study was conducted by eight tertiary referral centers in Taiwan. From January 1 to March 31 in 2016, all of the patients in intensive care units with virology-proven influenza pneumonia were collected, while all of those patients with ARDS and receiving prone positioning were enrolled. Demographic data, laboratory examinations, management records, ventilator settings and clinical outcomes were collected for analysis.

Results

During the study period, 336 patients with severe influenza pneumonia were screened and 263 patients met the diagnosis of ARDS. Totally, 65 patients receiving prone positioning were included for analysis. The 60-day survivors had lower Acute Physiology and Chronic Health Evaluation (APACHE) II score, pneumonia severity index (PSI), creatinine level and lower rate of receiving renal replacement therapy than non-survivors (22.4 ± 8.5 vs. 29.2 ± 7.4, p = 0.003; 106.6 ± 40.9 vs. 135.3 ± 48.6, p = 0.019; 1.2 ± 0.9 mg/dL vs. 3.1 ± 3.6 mg/dL, p = 0.040; and 4% vs. 42%, p < 0.005). Multivariate Cox regression analysis identified PSI (hazard ratio 1.020, 95% confidence interval 1.009–1.032; p < 0.001), renal replacement therapy (hazard ratio 6.248, 95% confidence interval 2.245–17.389; p < 0.001), and increase in dynamic driving pressure (hazard ratio 1.372, 95% confidence interval 1.095–1.718; p = 0.006) which were independent predictors associated with 60-day mortality.

Conclusions

In the present study, in evaluating the effect of prone positioning in patients with influenza pneumonia-related ARDS, pneumonia severity index, renal replacement therapy and increase in dynamic driving pressure were associated with 60-day mortality in patients with influenza pneumonia-related ARDS receiving prone positioning.

Electronic supplementary material

The online version of this article (10.1186/s13613-018-0440-4) contains supplementary material, which is available to authorized users.

Identification of mutations in SLC4A1, GP1BA and HFE in a family with venous thrombosis of unknown cause by next-generation sequencing

Various risk factors, including high age, female gender, obesity and certain genetic defects have been linked to venous thrombosis. A Taiwanese family with venous thrombosis of unknown cause were enrolled in the present study. In this pedigree, two women without any specific underlying diseases suffered from venous thrombotic events at the same age. No specific risk factors or coagulation abnormalities were identified. The main proband's younger brother also had intestinal arterial thrombosis at 54 years of age. Therefore, it was hypothesized that familial genetic defects may be the cause of venous thrombosis within this family. Blood samples collected from certain members of this pedigree were subjected to whole-exome sequencing, and three genetic variants were identified, including a missense variant of solute carrier family 4 member 1 (SLC4A1) (c.388G>A), a deletion on glycoprotein Ib platelet α subunit (GP1BA) (c.1322_1344del23) and an insertion in the splice site of homeostatic iron regulator (HFE). To date, none of these three genetic variants have been reported to be associated with venous thrombosis, to the best of our knowledge. The present study suggests that these genetic variants of SLC4A1, GP1BA and HFE may be associated with venous thrombosis in an Asian pedigree.

Systematic analysis of transcriptomic profiles of COPD airway epithelium using next-generation sequencing and bioinformatics

Introduction

COPD is a chronic inflammatory disease of lung. The inflammatory response in COPD is associated with neutrophils, macrophages, T lymphocytes, and bronchial epithelial cells, and occurs mainly in the small airway, leading to irreversible airflow limitation.

Methods

In order to investigate the microRNA–mRNA interaction in the microenvironment of the COPD airway, we used next-generation sequencing and bioinformatics in this study.

Results

We identified four genes with microRNA–mRNA interactions involved in COPD small-airway bronchial epithelial cells: NT5E, SDK1, TNS1, and PCDH7. Furthermore, miR6511a-5p–NT5E interaction was found to be involved in small-airway bronchial epithelial cells, large-airway bronchial epithelial cells, and alveolar macrophages.

Conclusion

Our results showed that miR6511a-5p–NT5E interaction plays an important role in COPD, which might be associated with cell–cell contact, activation of leukocytes, activation of T lymphocytes, and cellular homeostasis. These findings provide new information for further investigations of the COPD microenvironment, and may help to develop new diagnostic or therapeutic strategies targeting the bronchial epithelium for COPD.

Possible mechanisms mediating apoptosis of bronchial epithelial cells in chronic obstructive pulmonary disease - A next-generation sequencing approach

PURPOSE

Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory airway disease characterized by persistent airflow limitation. Apoptosis of pulmonary structural cells contributes to pulmonary destruction and dysfunction. This study aimed to explore the possible mechanisms underlying decreased cell proliferation and increased apoptosis of bronchial epithelial cells of COPD.

MATERIALS AND METHODS

The expression profiles of mRNAs and microRNAs in bronchial epithelial cells from a COPD patient and a normal subject were identified using next-generation sequencing (NGS) and analyzed using bioinformatic tools.

RESULTS

We identified 233 significantly upregulated and 204 significantly downregulated genes in COPD bronchial epithelial cells. The PI3K-Akt pathway was one of the most important dysregulated pathways in bronchial epithelial cells. We further identified that 3 genes involved in the PI3K-Akt signaling pathway, including IL6, F2R, and FGFR3, might be associated with inhibition of cell proliferation in bronchial epithelial cells, while 5 genes involved in the PI3K-Akt signaling pathway, including TLR4, IL6, F2R, FGFR3, and FGFR1, might be associated with apoptosis of bronchial epithelial cells. FGFR1 was also a predicted target for some up-regulated miRNAs in COPD bronchial epithelial cells, including hsa-miR-195-5p, hsa-miR-424-5p, and hsa-miR-6724-5p.

CONCLUSION

Our findings suggest PI3K-Akt signaling pathway plays an important role in COPD. We observed altered expression of apoptosis and cell proliferation-related genes that might contribute to the pathogenesis of COPD.

First tidal volume greater than 8 mL/kg is associated with increased mortality in complicated influenza infection with acute respiratory distress syndrome

BACKGROUNDS

Severe influenza infection causes substantial morbidity and mortality worldwide and remains an important threat to global health. This study addressed factors related to treatment outcomes in subjects of complicated influenza infection with acute respiratory distress syndrome (ARDS) during the Taiwan epidemic in the Spring of 2016.

METHODS

This is a retrospective study conducted by Taiwan Severe Influenza Research Consortium (TSIRC), including eight tertiary referral medical centers. Patients with virology-proven influenza infection admitted to intensive care unit (ICU) between January and March 2016 were included for analysis.

RESULTS

We identified 263 patients with complicated influenza infection who fulfilled ARDS criteria; the mean age was 59.8 ± 14.6 (years), and 66.1% (166/263) were male. Type A influenza (77.9%, 205/263) virus was the main pathogen during this epidemic. The 30-day mortality rate was 23.2% (61/263). The mean tidal volume (V_T) in the first three days after intubation was greater than 8 mL/kg of predicted body weight (PBW). Patients whose first measured V_T was >8 mL/kg PBW had an increased 30-day mortality (p = 0.04, log-rank test). In a multivariate Cox proportional hazard regression model, an increase of 1 mL/kg PBW of first V_T was associated with 26.1% increase in 30-day mortality (adjusted hazard ratio 1.261, 95% confidence interval [CI] 1.072-1.484, p < 0.01).

CONCLUSION

First tidal volume, shortly after intubation, greater than 8 mL/kg PBW is an independent risk factor for mortality in complicated influenza infection with ARDS. Timely recognition of ARDS with strict adherence to protective ventilation strategy of lowering V_T may be important in reducing mortality.

2018 Expert Consensus on the Management of Adverse Effects of Antiplatelet Therapy for Acute Coronary Syndrome in Taiwan

Antiplatelet therapy is a key component in the treatment of acute coronary syndrome (ACS). The management of ACS has evolved considerably over recent years with the development of new and more potent antiplatelet agents. Clinical trials on ACS have demonstrated that potent antiplatelet agents can more effectively reduce cardiovascular events. However, there is a tipping point between safety and efficacy, beyond which the risk of bleeding and other adverse effects can outweigh the benefits of antiplatelet therapy. Striking a balance between safety and efficacy remains a major challenge. A consensus meeting of an expert panel composed of Taiwanese experts was held to provide recommendations for the management of adverse effects in patients with ACS receiving antiplatelet therapy. The common adverse effects of antiplatelet therapy include upper gastrointestinal bleeding, ecchymosis, hematuria, epistaxis and ticagrelor-related dyspnea. In this study, a literature review of these adverse events was performed and recommendations for the management were made.

A prominent air pollutant, Indeno[1,2,3-cd]pyrene, enhances allergic lung inflammation via aryl hydrocarbon receptor

Chronic exposure to ambient polycyclic aromatic hydrocarbons (PAHs) is associated with asthma, but its regulatory mechanisms remain incompletely defined. We report herein that elevated levels of urinary 1-hydroxypyrene, a biomarker of PAH exposure, were found in asthmatic subjects (n = 39) as compared to those in healthy subjects (n = 43) living in an industrial city of Taiwan, where indeno[1,2,3-cd]pyrene (IP) was found to be a prominent PAH associated with ambient PM2.5. In a mouse model, intranasal exposure of mice with varying doses of IP significantly enhanced antigen-induced allergic inflammation, including increased airway eosinophilia, Th2 cytokines, including IL-4 and IL-5, as well as antigen-specific IgE level, which was absent in dendritic cell (DC)-specific aryl hydrocarbon receptor (AhR)-null mice. Mechanistically, IP treatment significantly altered DC's function, including increased level of pro-inflammatory IL-6 and decreased generation of anti-inflammatory IL-10. The IP's effect was lost in DCs from mice carrying an AhR-mutant allele. Taken together, these results suggest that chronic exposure to environmental PAHs may pose a significant risk for asthma, in which IP, a prominent ambient PAH in Taiwan, was shown to enhance the severity of allergic lung inflammation in mice through, at least in part, its ability in modulating DC's function in an AhR-dependent manner.

Management of infections caused by extended-spectrum β-lactamase-producing Enterobacteriaceae: current evidence and future prospects

INTRODUCTION

The spread of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae has become a major public health threat worldwide. Area covered: A thorough systematic literature review describing the current evidence and future prospects of therapeutic options for infections caused by ESBL-producing Enterobacteriaceae. Expert commentary: The methods of detecting ESBLs have been evolving. The Clinical and Laboratory Standards Institute and the European Committee on Antimicrobial Susceptibility Testing lowered the MIC breakpoints of cephalosporins against ESBL-producing Enterobacteriaceae in 2010. Phenotypic testing for ESBLs is no longer recommended. Instead, the selection of appropriate antimicrobial agents largely depends on the report of minimum inhibitory concentrations (MICs). To date, therapeutic options for these multidrug-resistant organisms remain limited. The clinical efficacy of piperacillin/tazobactam and cefepime on in vitro-susceptible ESBL-producing Enterobacteriaceae remains a concern. Many studies found an in vitro-in vivo discordance based on current breakpoints. Carbapenems are the most reliable antibiotics for severe infections caused by ESBL-producing Enterobacteriaceae. However, their overuse has led to a serious problem of increasing drug resistance. Recently, ceftolozane/tazobactam and ceftazidime/avibactam have been approved for the treatment of complicated urinary tract infections and complicated intra-abdominal infections. The introduction of these new β-lactam/β-lactamase inhibitor combinations offers new carbapenem-sparing options for the treatment of ESBL infections.

Altered pattern of monocyte differentiation and monocyte-derived TGF-β1 in severe asthma

CD14⁺ monocytes contain precursors for macrophages and fibrocytes, known to be involved in regulating airway remodeling in human asthma and distinguishable by the PM-2K marker. We sought to identify circulating subsets of PM-2K⁺ macrophage-like cells and evaluate their relationships to lung function, severity and control status. Circulating PM-2K⁺ macrophage-like cells and fibrocytes could be identified and distinguished between normal individuals (N = 152) and asthmatic subjects (N = 133) using multi-parametric flow cytometry. PM-2K⁺ macrophage-like cells were found to be significantly lower in asthmatic subjects, particularly noted for the CD14⁻PM-2K⁺ subset and PM-2K⁺CCR7⁻CD86⁺ cells in subjects with poor lung function (FEV%/FVC% < 80%) as compared to those of normal subjects and asthmatics with normal lung function, whereas the frequency of fibrocytes was higher in asthmatics and the CCR7⁻CD86⁺ subset distribution was significantly different in subjects with varying severity. Moreover, exogenous transforming growth factor beta 1 (TGF-β1) was found to inhibit the generation of PM-2K⁺ macrophage^-like cells, but promote the growth of fibrocytes, from CD14⁺ monocytes^, and monocyte-derived TGF-β1 was found to correlate with the lung function, severity and control status in asthmatic patients. Collectively, aberrant differentiation of monocytes into PM-2K⁺ macrophage-like cell subsets and fibrocytes, together with increased monocyte-derived TGF-β1, characterized patients with severe asthma.

Identification of novel genetic regulations associated with airway epithelial homeostasis using next-generation sequencing data and bioinformatics approaches

Airway epithelial cells play important roles in airway remodeling. Understanding gene regulations in airway epithelial homeostasis may provide new insights into pathogenesis and treatment of asthma. This study aimed to combine gene expression (GE) microarray, next generation sequencing (NGS), and bioinformatics to explore genetic regulations associated with airway epithelial homeostasis. We analyzed expression profiles of mRNAs (GE microarray) and microRNAs (NGS) in normal and asthmatic bronchial epithelial cells, and identified 9 genes with potential microRNA-mRNA interactions. Of these 9 dysregulated genes, downregulation of MEF2C and MDGA1 were validated in a representative microarray (GSE43696) from the gene expression omnibus (GEO) database. Our findings suggested that upregulated mir-203a may repress MEF2C, a transcription factor, leading to decreased cellular proliferation. In addition, upregulated mir-3065-3p may repress MDGA1, a cell membrane anchor protein, resulting in suppression of cell-cell adhesion. We also found that KCNJ2, a potassium channel, was downregulated in severe asthma and may promote epithelial cell apoptosis. We proposed that aberrant regulations of mir-203a-MEF2C and mir-3065-3p-MDGA1, as well as downregulation of KCNJ2, play important roles in airway epithelial homeostasis in asthma. These findings provide new perspectives on diagnostic or therapeutic strategies targeting bronchial epithelium for asthma. The approach in this study also provides a new aspect of studying asthma.

Epigenetic synergism between interleukin-4 and aryl-hydrocarbon receptor in human macrophages

The aryl hydrocarbon receptor (AhR)-ligand axis is involved in immune regulation, but its molecular basis remains to be fully elucidated. Chemokine (C-C motif) ligand 1 (CCL1) is an important chemoattractant, but how CCL1 is regulated remains to be defined. The role of AhR in regulating CCL1 expression in two major subsets of macrophage was investigated. We used a human THP-1 cell line, monocytes, and mouse peritoneal macrophages to generate M(IFN-γ/LPS) and M(IL-4) subsets, and the AhR's ligand effect was determined by the use of a combination of chromatin immunoprecipitation, PCR, and ELISA. Upon exposure to a classical AhR ligand, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), selective induction of CCL1 was noted only in M(IL-4), not M(IFN-γ/LPS) cells in human but not murine macrophages. This selectivity was mediated by AhR's binding to the distal dioxin-responsive element (DRE) in the CCL1 promoter of the M(IL-4) subset, and a deletion mutant lacking the distal DRE sequence lost its activity. In contrast to the M(IFN-γ/LPS) cells, the distal DRE was devoid of tri-methylated histone 3 lysine 27 (H3K27) in M(IL-4) cells, and the addition of a H3K27 demethylase inhibitor blocked AhR-mediated CCL1 expression. Similar selectivity of CCL1 expression was also noted in monocyte-derived M(IL-4) subsets, and the level of AhR binding to distal DRE in monocytes was correlated with the levels of plasma interleukin-4 (IL-4) in 23 human subjects. These findings suggested the existence of a new regulatory epigenetic-based mechanism, wherein AhR in concert with IL-4 differentially regulated human, not murine, macrophage CCL1 response.

KEY MESSAGE

Human CCL1 gene is selectively targeted by AhR in M(IL-4) macrophage. IL-4-induced epigenetic modification potentiates AhR-mediated CCL1 expression. This epigenetic control of CCL1 expression is not operative in murine macrophages.

A new grid-scale model simulating the spatiotemporal distribution of PM2.5-PAHs for exposure assessment

Exposure to polycyclic aromatic hydrocarbons (PAHs) associated with ambient air particulate matter (PM) poses significant health concerns. Several modeling approaches have been developed for simulating ambient PAHs, but no hourly intra-urban spatial data are currently available. The aim of this study is to develop a new modeling strategy in simulating, on an hourly basis, grid-scale PM2.5-PAH levels. PM and PAHs were collected over a one-year time frame through an established air quality monitoring network within a metropolitan area of Taiwan. Multivariate linear regression models, in combination with correlation analysis and PAH source identification by principal component analysis (PCA), were performed to simulate hourly grid-scale PM2.5-PAH concentrations, taking criteria pollutants and meteorological variables selected as possible predictors. The simulated levels of 72-h personal exposure were found to be significantly (R=0.729**, p<0.01) correlated with those analyzed from portable personal monitors. A geographic information system (GIS) was used to visualize spatially distributed PM2.5-PAH concentrations of the modeling results. This new grid-scale modeling strategy, incorporating the output of simulated data by GIS, provides a useful and versatile tool in personal exposure analysis and in the health risk assessment of air pollution.

An antibiotic decision-making tool for patients with pneumonia admitted to a medical intensive care unit

Pneumonia is a leading cause of death in medical intensive care units (MICUs). Delayed or inappropriate antibiotic therapy largely increases morbidity and mortality. Multidrug-resistant (MDR) micro-organisms are major reasons for inappropriate antibiotic use. Currently there is no good antibiotic decision-making tool designed for critically ill patients. The objective of this study was to develop a convenient MDR prediction scoring system for patients admitted to MICUs with pneumonia. A retrospective cohort study was conducted using databases and chart reviews of pneumonia patients admitted to a 30-bed MICU from 2012 to 2013. Forward logistic regression was applied to identify independent MDR risk factors for prediction tool development. A total of 283 pneumonia episodes from 263 patients with positive cultures from blood or respiratory secretions were recruited, of which 154 (54.4%) were MDR episodes. Long-term ventilation (OR = 11.09; P = 0.026), residence in a long-term care facility (OR = 2.50; P = 0.005), MDR infection/colonisation during the preceding 90 days (OR = 2.08; P = 0.041), current hospitalisation ≥2 days (OR = 1.98; P = 0.019) and stroke (OR = 1.81; P = 0.035) were identified as independent predictors for MDR pneumonia. The area under the ROC curve of this prediction tool was much higher than that of ATS/IDSA classification (0.69 vs. 0.54; P <0.001). The prediction accuracy of this tool with risk score ≥1 for MDR infections was 63.7%. This simple five-item, one-step scoring tool for critically ill patients admitted to the MICU could help physicians provide timely appropriate empirical antibiotics.

Hepatitis C Virus Infection Is Associated With an Increased Risk of Active Tuberculosis Disease: A Nationwide Population-Based Study

Tuberculosis (TB) and hepatitis C virus (HCV) infection contribute to major disease mortality and morbidity worldwide. However, the causal link between HCV infection and TB risk remains unclear. We conducted a population-based cohort study to elucidate the association between HCV infection and TB disease by analyzing Taiwan National Health Insurance Database. We enrolled 5454 persons with HCV infection and 54,274 age- and sex-matched non-HCV-infected persons between January 1998 and December 2007. Time-dependent Cox proportional hazards regression analysis was used to measure the association between HCV infection and active TB disease. Incidence rate of active TB disease was higher among HCV infection than in control (134.1 vs 89.1 per 100,000 person-years; incidence rate ratio 1.51; P = 0.014). HCV infection was significantly associated with active TB disease in multivariate Cox regression (adjusted hazard ratio [HR] 3.20; 95% confidence interval [CI], 1.85-5.53; P < 0.001) and competing death risk event analysis (adjusted HR 2.11; 95% CI, 1.39-3.20; P < 0.001). Multivariate stratified analysis further revealed that HCV infection was a risk of active TB disease in most strata. This nationwide cohort study suggests that HCV infection is associated with a higher risk of developing active TB disease.

Metformin decreases lung cancer risk in diabetic patients in a dose-dependent manner

OBJECTIVES

Higher risk of lung cancer has been noted in patients with type 2 diabetes mellitus (DM). Some observational studies have shown a reduced risk of lung cancer in DM patients taking metformin, but a dose-response relationship has never been reported. The aim of this study is to exam the association between the dose of metformin and the incidence of lung cancer in a Chinese population.

MATERIALS AND METHODS

The dataset used for this nationwide population-based study is a cohort of 1 million subjects randomly sampled from individuals enrolled in the Taiwan National Health Insurance system. We enrolled all subjects with newly diagnosed type 2 DM between 1997 and 2007. Subjects with a diagnosis of neoplasm before DM diagnosis, those using metformin before DM diagnosis, those with polycystic ovary syndrome, and those with a DM diagnosis before their 15 years of age were excluded. The demographic data and duration, cumulative dose and intensity of metformin use were compared between patients developing lung cancer and those without lung cancer.

RESULTS

Totally, 47,356 subjects were identified. After adjusting for age, gender, and modified Charlson Comorbidity Index score, the utilization of metformin was an independent protecting factor, and the risk of developing lung cancer decreased progressively with either the higher cumulative dose or the higher intensity of metformin use.

CONCLUSIONS

This study revealed that the use of metformin decreased the risk of lung cancer in a dose-dependent manner in patients with type 2 DM. The chemo-preventive effect of metformin deserves further study.

Betel chewing and arecoline affects eotaxin-1, asthma and lung function

Background

Betel nut is commonly used in many countries. Despite evidence suggesting an association with asthma, few studies have investigated the connection between betel nut use and asthma; thus, the underlying mechanism for the association with asthma is also unclear. The aim of this study was to investigate the association between betel chewing and asthma as well as the associations of plasma arecoline (a biomarker for exposure) and eotaxin-1 (a potential mediator) with asthma and lung function.

Methods

We recruited 600 hospital-based asthmatic patients and 1200 age- and gender-matched community controls in southern Taiwan. To clarify the mechanism of action for eotaxin-1 in the association between betel chewing and asthma, we also designed an in vitro experiment to study the functional associations between arecoline exposure and eotaxin-1 levels.

Results

A significant association was found between asthma and current betel chewing (adjusted odds ratio 2.05, 95% CI = 1.12–3.76), which was independent of potential confounders but was attenuated following adjustment for eotaxin-1. Arecoline and eotaxin-1 levels were positively correlated (Spearman r = 0.303, p = 0.02), while arecoline and arecaidine were negatively correlated with lung function. Functionally, arecoline alone does not induce eotaxin-1 release in vitro from dermal and gingival fibroblasts. However, in the presence of IL-4 and TNF-alpha, arecoline at 100 μg/ml induced more eotaxin-1 release than arecoline at 0 μg/ml (2700±98 pg/ml vs 1850±142 pg/ml, p = 0.01 in dermal fibroblast cells, and 1489±78 pg/ml vs 1044±95 pg/ml, p = 0.03 in gingival fibroblast cells, respectively).

Conclusion

Betel chewing is associated with asthma in this population, with arecoline induction of eotaxin-1 supported as a plausible causal pathway.

Adiponectin gene polymorphisms and acute respiratory distress syndrome susceptibility and mortality

RATIONALE

Adiponectin is an anti-inflammatory adipokine that is the most abundant gene product of adipose tissue. Lower levels have been observed in obesity, insulin resistance, and in critical illness. However, elevated levels early in acute respiratory failure have been associated with mortality. Polymorphisms in adiponectin-related genes (ADIPOQ, ADIPOR1, ADIPOR2) have been examined for relationships with obesity, insulin resistance and diabetes, cardiovascular disease, and to circulating adipokine levels, but many gaps in knowledge remain. The current study aims to assess the association between potentially functional polymorphisms in adiponectin-related genes with acute respiratory distress syndrome (ARDS) risk and mortality.

METHODS

Consecutive patients with risk factors for ARDS admitted to the ICU were enrolled and followed prospectively for development of ARDS. ARDS cases were followed through day 60 for all-cause mortality. 2067 patients were successfully genotyped using the Illumina CVD BeadChip high-density platform. Of these, 567 patients developed ARDS. Forty-four single nucleotide polymorphisms (SNPs) on ADIPOQ, ADIPOR1 and ADIPOR2 were successfully genotyped. Of these, 9 SNPs were hypothesized to be functional based on their location (promoter, exon, or 3' untranslated region). These 9 SNPs were analyzed for association with ARDS case status and mortality among ARDS cases.

RESULTS

After multivariable analysis and adjustment for multiple comparisons, no SNPs were significantly associated with ARDS case status. Among ARDS cases, homozygotes for the minor allele of rs2082940 (ADIPOQ) had increased mortality (hazard ratio 2.61, 95% confidence interval 1.36-5.00, p = 0.0039) after adjustment for significant covariates. The significance of this association persisted after adjustment for multiple comparisons (FDR_q = 0.029).

CONCLUSIONS

A common and potentially functional polymorphism in ADIPOQ may impact survival in ARDS. Further studies are required to replicate these results and to correlate genotype with circulating adiponectin levels.

IL1RN coding variant is associated with lower risk of acute respiratory distress syndrome and increased plasma IL-1 receptor antagonist

RATIONALE

Acute respiratory distress syndrome (ARDS) behaves as a complex genetic trait, yet knowledge of genetic susceptibility factors remains incomplete.

OBJECTIVES

To identify genetic risk variants for ARDS using large scale genotyping.

METHODS

A multistage genetic association study was conducted of three critically ill populations phenotyped for ARDS. Stage I, a trauma cohort study (n = 224), was genotyped with a 50K gene-centric single-nucleotide polymorphism (SNP) array. We tested SNPs associated with ARDS at P < 5 × 10(-4) for replication in stage II, a trauma case-control population (n = 778). SNPs replicating their association in stage II (P < 0.005) were tested in a stage III nested case-control population of mixed subjects in the intensive care unit (n = 2,063). Logistic regression was used to adjust for potential clinical confounders. We performed ELISA to test for an association between ARDS-associated genotype and plasma protein levels.

MEASUREMENTS AND MAIN RESULTS

A total of 12 SNPs met the stage I threshold for an association with ARDS. rs315952 in the IL1RN gene encoding IL-1 receptor antagonist (IL1RA) replicated its association with reduced ARDS risk in stages II (P < 0.004) and III (P < 0.02), and was robust to clinical adjustment (combined odds ratio = 0.81; P = 4.2 × 10(-5)). Plasma IL1RA level was associated with rs315952C in a subset of critically ill subjects. The effect of rs315952 was independent from the tandem repeat variant in IL1RN.

CONCLUSIONS

The IL1RN SNP rs315952C is associated with decreased risk of ARDS in three populations with heterogeneous ARDS risk factors, and with increased plasma IL1RA response. IL1RA may attenuate ARDS risk.

Distinct and replicable genetic risk factors for acute respiratory distress syndrome of pulmonary or extrapulmonary origin

BACKGROUND

The role of genetics in the development of acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) from direct or indirect lung injury has not been specifically investigated. The aim of this study was to identify genetic variants contributing to ALI/ARDS from pulmonary or extrapulmonary causes.

METHODS

We conducted a multistage genetic association study. We first performed a large-scale genotyping (50K ITMAT-Broad_CARe Chip) in 1717 critically ill Caucasian patients with either pulmonary or extrapulmonary injury, to identify single nucleotide polymorphisms (SNPs) associated with the development of ARDS from direct or indirect insults to the lung. Identified SNPs (p≤0.0005) were validated in two separated populations (Stage II), with trauma (Population I; n=765) and pneumonia/pulmonary sepsis (Population II; n=838), as causes for ALI/ARDS. Genetic variants replicating their association with trauma related-ALI in Stage II were validated in a second trauma-associated ALI population (n=224, Stage III).

RESULTS

In Stage I, non-overlapping SNPs were significantly associated with ARDS from direct/indirect lung injury, respectively. The association between rs1190286 (POPDC3) and reduced risk of ARDS from pulmonary injury was validated in Stage II (p<0.003). SNP rs324420 (FAAH) was consistently associated with increased risk of ARDS from extrapulmonary causes in two independent ALI-trauma populations (p<0.006, Stage II; p<0.05, Stage III). Meta-analysis confirmed these associations.

CONCLUSIONS

Different genetic variants may influence ARDS susceptibility depending on direct versus indirect insults. Functional SNPs in POPDC3 and FAAH genes may be driving the association with direct and indirect ALI/ARDS, respectively.

Abstract 2760: Nicotinic acetylcholine receptor SNPs are associated with smoking cessation

Introduction: Several genes have been linked with smoking behavior, and recent findings from candidate gene and genome wide association studies (GWAS) point to an area on Chr15q24-25.1 as a plausible site. The association region contains several genes, including three that encode nicotinic acetylcholine receptor subunits (CHRNA5, CHRNA3 and CHRNB4). Consistent results have been reported for cigarettes smoked per day (CPD), but data for smoking initiation, duration and cessation remain mixed. In this study, we assessed the relationship between the two most significant and consistently reported single nucleotide polymorphisms (SNPs), rs1051730 and rs8034191 and various smoking phenotypes.

Methods: From a large ongoing case-control study of the molecular epidemiology of lung cancer, which began in 1992 at the Massachusetts General Hospital, we derived this study population of controls only (i.e., no diagnosis of lung cancer). The polymorphisms were genotyped by the 5’ nuclease assay (Taqman) using the ABI Prism 7900HT Sequence Detection System (Applied Biosystems, Foster City, CA). Interviewer-administered questionnaires collected information on demographics, and detailed smoking histories from each subject. We log transformed all the continuous smoking phenotype variables. Multiple linear regression models were used to assess the association between SNPs and continuous outcomes and estimates for the association with binary outcomes were obtained from logistic regression. We used the additive genetic model for individual SNPs, controlling for age, gender and college education.

Results: There were 1452 subjects. There were statistically significant differences in age, gender, and college education between never, former and current smokers. Never smokers were excluded in the comparison of smoking variables. Age of smoking initiation and smoking duration differed significantly between former and current smokers. There was no significant difference between genotypes of rs1051730 except by smoking status (never, former, current). The proportion of never smokers was much higher in the wildtype group compared to heterozygous and homozygous variant group.

The association of smoking cessation (current vs. former smokers) with rs1051730, adjusted for age, gender and college education was statistically significant (p=0.05). Results for the other smoking phenotype included smoking initiation (never vs. ever smokers) (P=0.62), age of smoking initiation (P=0.83), smoking duration (P=0.76), CPD (0.08), and number of year of smoking cessation (0.36). We obtained similar results for SNP rs8034191.

Conclusion In conclusion, we have shown an association between rs1051730 and smoking cessation. We also replicated previous findings for intensity (CPD). If confirmed in future studies, these findings may provide a role for genetic screening in smoking cessations programs.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2760. doi:10.1158/1538-7445.AM2011-2760