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Purpose: Identification of single-nucleotide polymorphisms (SNP) associated with development of advanced colorectal adenomas.Experimental Design: Discovery phase: 1,406 Caucasian patients (139 advanced adenoma cases and 1,267 controls) from the Adenoma Prevention with Celecoxib (APC) trial were included in a genome-wide association study (GWAS) to identify variants associated with postpolypectomy disease recurrence. Genome-wide significance was defined as false discovery rate less than 0.05, unadjusted P = 7.4 × 10−7. Validation phase: results were further evaluated using 4,175 familial colorectal adenoma cases and 5,036 controls from patients of European ancestry [COloRectal Gene Identification consortium (CORGI), Scotland, Australia, and VQ58].Results: Our study identified eight SNPs associated with advanced-adenoma risk in the APC trial (rs2837156, rs7278863, rs2837237, rs2837241, rs2837254, rs741864 at 21q22.2, and rs1381392 and rs17651822 at 3p24.1, at P < 10−7 level with OR > 2). Five variants in strong pairwise linkage disequilibrium (rs7278863, rs2837237, rs741864, rs741864, and rs2837241; r2 = 0.8–1) are in or near the coding region for the tight junction adhesion protein, IGSF5. An additional variant associated with advanced adenomas, rs1535989 [minor allele frequency, 0.11; OR, 2.09; 95% confidence interval (CI), 1.50–2.91], also predicted colorectal cancer development in a validation analysis (P = 0.019) using a series of adenoma cases or colorectal cancer (CORGI study) and 3 sets of colorectal cancer cases and controls (Scotland, VQ58, and Australia; N = 9,211).Conclusions: Our results suggest that common polymorphisms contribute to the risk of developing advanced adenomas and might also contribute to the risk of developing colorectal cancer. The variant at rs1535989 may identify patients whose risk for neoplasia warrants increased colonoscopic surveillance. Clin Cancer Res; 19(23); 6430–7. ©2013 AACR.

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Introduction Obstructive sleep apnea (OSA) is characterized by recurrent airway obstruction causing intermittent hypoxia, arousal from sleep, and autonomic instability, and is associated with a variety of long-term health sequala. The fragmented sleep resulting from these respiratory events leads to disruption in normal sleep architecture and progression to deeper stages of sleep, a potential mediator for some of the functional and neurocognitive impairments seen in this population. Similarly, psychoactive substance use (i.e., nicotine, alcohol, and caffeine) impacts sleep architecture in healthy individuals, but their effects in those with OSA have not been well described. We aimed to describe the association between psychoactive substance use and sleep characteristics and daytime symptoms in individuals with untreated OSA. Methods We performed a secondary, cross-sectional analysis of The Apnea Positive Pressure Long-term Efficacy Study (APPLES). Exposures included current smoking, alcohol, and caffeine use in individuals with untreated OSA. Outcome domains included subjective and objective sleep characteristics, daytime symptoms, and co-morbid conditions. Linear or logistic regression assessed the association between substance use and each domain (e.g., self-reported sleep duration, total polysomnographic sleep time, sleepiness, and anxiety). Results Of the 919 individuals with untreated OSA, 116 (12.6%) were current cigarette smokers, 585 (63.7%) were moderate or heavy alcohol users, and 769 (83.7%) were moderate or heavy caffeine users. Current smokers exhibited lower sleep duration (0.3 hours) and longer sleep latency (5 minutes) compared with non-smokers (all p-values< 0.05). REM sleep increased in those with moderate and heavy alcohol use (2.5 and 5% of total sleep time respectively), and moderate caffeine use (2%, all p-values < 0.05)). The combined smoker plus caffeine group exhibited shorter sleep duration (0.4 hours) and higher risk for chronic pain [Odds Ratio (95%CI) = 4.83 (1.57, 14.9). . Conclusion Both psychoactive substances and untreated OSA impact normal sleep architecture, their cumulative effect may have clinical implications in this subgroup. Stimulating or sedating substances may be used in OSA patients to mitigate daytime and nighttime symptoms respectively. Further investigation into the effects substances have on this population may present opportunities to better understand disease mechanisms and increase the effectiveness of treatment in OSA Support (if any)

BackgroundAlpha-1 antitrypsin deficiency (AATD) is a genetic condition that causes early onset pulmonary emphysema and airways obstruction. The complete mechanisms via which AATD causes lung disease are not fully understood. To improve our understanding of the pathogenesis of AATD, we investigated gene expression profiles of bronchoalveolar lavage (BAL) and peripheral blood mononuclear cells (PBMCs) in AATD individuals.MethodsWe performed RNA-Seq on RNA extracted from matched BAL and PBMC samples isolated from 89 subjects enrolled in the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) study. Subjects were stratified by genotype and augmentation therapy. Supervised and unsupervised differential gene expression analyses were performed using Weighted Gene Co-expression Network Analysis (WGCNA) to identify gene profiles associated with subjects’ clinical variables. The genes in the most significant WGCNA module were used to cluster AATD individuals. Gene validation was performed by NanoString nCounter Gene Expression Assay.ResultWe observed modest effects of AATD genotype and augmentation therapy on gene expression. When WGCNA was applied to BAL transcriptome, one gene module, ME31 (2312 genes), correlated with the highest number of clinical variables and was functionally enriched with numerous immune T-lymphocyte related pathways. This gene module identified two distinct clusters of AATD individuals with different disease severity and distinct PBMC gene expression patterns.ConclusionsWe successfully identified novel clusters of AATD individuals where severity correlated with increased immune response independent of individuals’ genotype and augmentation therapy. These findings may suggest the presence of previously unrecognised disease endotypes in AATD that associate with T-lymphocyte immunity and disease severity.

RationaleAsthma is a chronic airway disease driven by multiple immunologic pathways that determine the clinical response to therapy. Current diagnostic methods are incapable of discriminating subtypes of asthma and guiding targeted treatment. We hypothesized that sputum cytokine profiles could help to identify immunologically-defined disease subtypes and individualize therapy in patients with severe asthma.ObjectivesDefine asthma subtypes associated with sputum alarmin and cytokine levels.MethodsCross-sectional analysis of clinical features and sputum from 200 asthmatic patients was performed. 10 cytokines belonging to alarmin, T2, and non-T2 pathways were measured. Pearson correlation was used to identify cytokine modules. Latent class analysis was used to cluster patients by cytokine expression.Measurements and Main ResultsThree modules of highly correlated cytokines were identified including a non-T2 module, the IL-1βmod (IL-1β, IL-6, GCSF), and two distinct T2 modules: TSLPmod (TSLP, IL-4, IL-5, IL-9) and IL-33mod (IL-33, IL-13, IL-21). The TSLPmod was associated with asthma severity, airway obstruction, eosinophilia, and elevated FeNO. Patient clustering revealed three subgroups; two different subgroups showed expression of T2 modules.ConclusionsAnalysis of sputum cytokines revealed three discrete signaling modules in patients with asthma. Unexpectedly, the inclusion of alarmins led to separation of canonical T2 cytokines into two unique modules; IL-5 grouped with TSLP, while IL-13 grouped with IL-33. In addition, patient clustering revealed two distinct endotypes associated with T2 immune signaling. These findings indicate a new layer of immunologic heterogeneity within the T2 paradigm, and suggest that sputum cytokine profiling may hold diagnostic utility for patients with asthma.

Exposure to traffic-related pollutants, including diesel exhaust, is associated with increased risk of cardiopulmonary disease and mortality; however, the precise biochemical pathways underlying these effects are not known. To investigate biological response mechanisms underlying exposure to traffic related pollutants, we used an integrated molecular response approach that included high-resolution metabolomic profiling and peripheral blood gene expression to identify biological responses to diesel exhaust exposure. Plasma samples were collected from 73 non-smoking males employed in the US trucking industry between February 2009 and October 2010, and analyzed using untargeted high-resolution metabolomics to characterize metabolite associations with shift- and week-averaged levels of elemental carbon (EC), organic carbon (OC) and particulate matter with diameter ≤ 2.5 μm (PM2.5). Metabolic associations with EC, OC and PM2.5 were evaluated for biochemical processes known to be associated with disease risk. Annotated metabolites associated with exposure were then tested for relationships with the peripheral blood transcriptome using multivariate selection and network correlation. Week-averaged EC and OC levels, which were averaged across multiple shifts during the workweek, resulted in the greatest exposure-associated metabolic alterations compared to shift-averaged exposure levels. Metabolic changes associated with EC exposure suggest increased lipid peroxidation products, biomarkers of oxidative stress, thrombotic signaling lipids, and metabolites associated with endothelial dysfunction from altered nitric oxide metabolism, while OC exposures were associated with antioxidants, oxidative stress biomarkers and critical intermediates in nitric oxide production. Correlation with whole blood RNA gene expression provided additional evidence of changes in processes related to endothelial function, immune response, inflammation, and oxidative stress. We did not detect metabolic associations with PM2.5. This study provides an integrated molecular assessment of human exposure to traffic-related air pollutants that includes diesel exhaust. Metabolite and transcriptomic changes associated with exposure to EC and OC are consistent with increased risk of cardiovascular diseases and the adverse health effects of traffic-related air pollution.

Rationale: Untreated obstructive sleep apnea (OSA) is associated with adverse outcomes in patients with coronary artery disease (CAD). Continuous positive airway pressure (CPAP) is the most common treatment, but despite interventions addressing established adherence determinants, CPAP use remains poor. Objectives: To determine whether physiological traits that cause OSA are associated with long-term CPAP adherence in patients with CAD. Methods: Participants in the RICCADSA (Randomized Intervention with CPAP in CAD and OSA) trial with objective CPAP adherence (h/night) over 2 years and analyzable raw polysomnography data were included (N = 249). The physiological traits—loop gain, arousal threshold (ArTH), pharyngeal collapsibility (Vpassive), and pharyngeal muscle compensation (Vcomp)—were measured by using polysomnography. Linear mixed models were used to assess the relationship between the traits and adherence. We also compared actual CPAP adherence between those with physiologically predicted “poor” adherence (lowest quartile of predicted adherence) and those with physiologically predicted “good” adherence (all others). Measurements and Main Results: The median (interquartile range) CPAP use declined from 3.2 (1.0–5.8) h/night to 3.0 (0.0–5.6) h/night over 24 months (P

Introduction Continuous positive airway pressure (CPAP) is the first-line therapy for OSA. CPAP improves OSA severity, sleep architecture, and daytime symptoms. The effectiveness of CPAP, however, is limited to poor adherence. Individual's risk perception, outcome expectancy, and treatment self-efficacy predict CPAP adherence. CPAP adherence also differs by sex. However, it is unknown if predictors of CPAP use are different for women and men. We thus assessed sex differences in risk perception, outcome expectancy, and treatment self-efficacy among those with OSA. Methods Individuals enrolled to date (target n=267) in the NICEPAP study (NCT05067088), a prospective, observational cohort examining predictors of CPAP adherence, were included. Adults newly diagnosed with OSA prescribed CPAP therapy were included, while those with a need for non-CPAP therapy or unstable medical conditions (e.g., cancer receiving chemotherapy, severe lung, heart, or mental health disorders) were excluded. The exposure was sex. Co-primary outcomes were sub-scale scores from the Self-Efficacy Measure for Sleep Apnea (SEMSA) tool: Perceived Risk, Outcome Expectancies, and Treatment Self-Efficacy before starting CPAP. In addition, we assessed a comprehensive set of established psycho-social and biomedical CPAP adherence predictors using validated measures. SEMSA sub-scale scores for males and females were compared using Kruskal-Wallis statistics. Results We analyzed data for 33 females and 19 males. Females and males were 52 (41.0, 60.5) and 52 (35.0, 58) years old respectively (median [Q1, Q3]). Ten of 33 females and 4 of 19 males were Black with majority of others being White. The apnea-hypopnea index was 17.0 (9.1, 27.0) and 19.0 (13.3, 38.4), Epworth sleepiness scale and insomnia severity index scores were 9.0 (5.0, 12.0) & 15.0 (11.0, 18.0) and 6.0 (4.0, 9.0) & 17.0 (8.0, 19.5) for females and males respectively. There were no statistical differences in scores of Perceived Risk 2.4 (1.6, 2.9) vs 2.1 (1.8, 2.5) (p=0.717), Outcome Expectancies 2.8 (2.3, 3.4) vs 3.3 (2.4, 3.5) (p=0.371) or Treatment Self-Efficacy 3.1 (2.3, 3.7) vs 3.1 (2.0, 3.5) (p=0.977) for females vs. males. Conclusion We found no statistically significant differences in determinants of self-efficacy between women and men. Our findings may reflect a small sample size recruited to date or that self-efficacy of CPAP therapy is independent of sex. Support (If Any) This work was supported by Parker B. Francis Foundation and National Heart, Lung, and Blood Institute/NIH (1K23HL159259-01).

Introduction Continuous positive airway pressure (CPAP) therapy is the first-line treatment for OSA, yet its effectiveness is limited by poor adherence. Self-efficacy is an individual’s belief that they can successfully execute a behavior to achieve a desired outcome. Evidence shows that self-efficacy predicts adherence to and outcomes of CPAP therapy, as do race and ethnicity. Little, however, is known about how self-efficacy may differ between racial and ethnic groups. Accordingly, we aimed to determine whether self-efficacy for CPAP differs by race and ethnicity among individuals newly diagnosed with OSA. Methods Adults newly diagnosed with OSA and prescribed CPAP who were enrolled in the NICEPAP Study (n=267, NCT05067088), a prospective, observational cohort study investigating predictors of CPAP adherence were assessed. Those with need for non-CPAP therapy or with unstable medical conditions (e.g., cancer receiving chemotherapy, severe lung, heart or mental health disorders) were excluded. Exposures were race and ethnicity. Outcomes were subscale scores of the Self-Efficacy Measure for Sleep Apnea (SEMSA) completed prior to CPAP initiation: perceived risk, outcome expectancy, and self-efficacy. SEMSA sub-scale scores for race/ethnicity were compared using Kruskal-Wallis test. Medians (Q1, Q3) are reported. Results We analyzed data for 52 participants (33 women) enrolled to date who identified as White (n=29), Black (n=14), More than one race (n=5) and Other (N=5). Participants were 51.0 (36.8, 58.8) years old with an apnea-hypopnea index of 17.0/hour (11.1, 26.0) and body-mass-index of 35.0 (31.6, 43.5) kg/m2. Baseline characteristics did not differ by race, except higher poverty (p=0.005) and less completed years of education (p=0.010) for Black participants. The SEMSA scores were not statistically different between each race. However, self-efficacy was significantly lower for Black participants vs. rest of the cohort combined (2.4 (1.9, 3.1) vs. 3.3 (2.7, 3.8) p=0.020). Poverty, but not education, may be a potential mediator of this relationship (mediation analysis p=0.052). There were no differences in SEMSA scores between Hispanic and Non-Hispanic participants. Conclusion In our cohort, self-efficacy for OSA therapy was lower for Black participants compared to those of other races. Targeting early interventions to improve CPAP self-efficacy in Black patients may improve OSA therapy outcomes. Support (If Any)

BACKGROUND: Fine particulate matter (PM(2.5)) has been associated with breast cancer specific mortality, particularly for women with Stage I cancer. We examined the biological pathways that are perturbed by PM(2.5) exposures by analyzing gene expression measurements from breast tissue specimens. METHODS: The Nurses’ Health Studies (NHS and NHSII) are prospective cohorts with archival breast tissue specimens from breast cancer cases. Global gene expression data were ascertained with the Affymetrix Glue Human Transcriptome Array 3.0. PM(2.5) was estimated using spatio-temporal models linked to participants’ home addresses. All analyses were performed separately in tumor (n=591) and adjacent-normal (n=497) samples, and stratified by estrogen receptor (ER) status and stage. We used multivariable linear regression, gene-set enrichment analyses (GSEA), and the least square kernel machine (LSKM) to assess whether 3-year cumulative average pre-diagnosis PM(2.5) exposure was associated with breast-tissue gene expression pathways among predominately Stage I and II women (90.7%) and postmenopausal (81.2%) women. Replication samples (tumor, n=245; adjacent-normal, n=165) were measured on Affymetrix Human Transcriptome Array (HTA 2.0). RESULTS: Overall, no pathways in the tumor area were significantly associated with PM(2.5) exposure. Among 272 adjacent-normal samples from Stage I ER-positive women, PM(2.5) was associated with perturbations in the oxidative phosphorylation, protein secretion, and mTORC1 signaling pathways (GSEA and LSKM p-values

BACKGROUND AND OBJECTIVE Molecular biomarkers are needed to refine prognostication and phenotyping of pulmonary hypertension (PH) patients. S100A12 is an emerging biomarker of various inflammatory diseases. This study aims to determine the prognostic value of S100A12 in PH. METHODS Exploratory microarray analysis performed on peripheral blood mononuclear cells (PBMC) collected from idiopathic pulmonary fibrosis (IPF) patients suggested an association between S100A12 and both PH and mortality. So the current study was designed to evaluate for an association between S100A12 in peripheral blood collected from two well-phenotyped PH cohorts in two other centres to derive and validate an association between S100A12 protein serum concentrations and mortality. RESULTS The majority of the patients in the discovery and validation cohorts were either World Health Organization (WHO) group 1 (pulmonary arterial hypertension (PAH)) or 3 (lung disease-associated) PH. In the discovery PH cohort, S100A12 was significantly increased in patients with PH (n = 51) compared to controls (n = 22) (29.8 vs 15.7 ng/mL, P < 0.001) and negatively correlated with cardiac output (r = -0.58, P < 0.001) in PH patients. When S100A12 data were pooled from both cohorts, PAH and non-PAH PH patients had higher S100A12 compared to healthy external controls (32.6, 30.9, 15.7 ng/mL; P < 0.001). S100A12 was associated with an increased risk in overall mortality in PH patients in both the discovery (n = 51; P = 0.008) and validation (n = 40; P < 0.001) cohorts. CONCLUSION S100A12 levels are increased in PH patients and are associated with increased mortality.

Introduction Continuous positive airway pressure therapy (CPAP) is an efficacious treatment for obstructive sleep apnea (OSA). However, despite interventions targeting established determinants of CPAP use, adherence to CPAP remains poor. An Individual’s chronotype can influence behavior including adherence to dietary changes and alcohol abstinence. We hypothesized that chronotype will be associated with CPAP adherence and aimed to identify the mechanisms of this association. Methods Secondary data analysis of the active CPAP arm (n=469) from the Apnea Positive Pressure Long-term Efficacy Study, a multicenter randomized controlled trial of CPAP therapy in a sleep clinic population was performed. The Morningness-Eveningness Questionnaire (MEQ) was used to identify three chronotype categories: Evening (MEQ score: 16–41), Neither (42–58) and Morning (59–86) types. CPAP adherence over 6-months (hours/night) was objectively measured using smart-card downloads. Linear mixed modelling evaluated the association between the chronotype and CPAP adherence, adjusting for confounders (e.g., age). Mechanisms of this association were examined by change in beta estimates for the chronotype with addition of a potential mediator (e.g., sleep duration). Results There were 206(44%), 38(8%) and 219(47%) Morning, Evening and Neither chronotype patients respectively. Evening types were youngest (48.0±13.4 vs. 50.3±11.3 and 56.3±11.4 years, p Conclusion In this cohort of sleep clinic patients, the Morning chronotype was associated with better CPAP adherence. Only a small proportion of this association was mediated by observed clinical differences between the chronotypes. Understanding the influence of chronotype on CPAP use may provide novel insight for improving OSA therapy effectiveness. Support (if any)

The PD-L1/PD-1 pathway is a critical component of the immunosuppressive tumor microenvironment in acute myeloid leukemia (AML), but little is known about its regulation. We investigated the role of the MUC1 oncoprotein in modulating PD-L1 expression in AML. Silencing of MUC1 in AML cell lines suppressed PD-L1 expression without a decrease in PD-L1 mRNA levels, suggesting a post-transcriptional mechanism of regulation. We identified the microRNAs miR-200c and miR-34a as key regulators of PD-L1 expression in AML. Silencing of MUC1 in AML cells led to a marked increase in miR-200c and miR-34a levels, without changes in precursor microRNA, suggesting that MUC1 might regulate microRNA-processing. MUC1 signaling decreased the expression of the microRNA-processing protein DICER, via the suppression of c-Jun activity. NanoString (Seattle, WA, USA) array of MUC1-silenced AML cells demonstrated an increase in the majority of probed microRNAs. In an immunocompetent murine AML model, targeting of MUC1 led to a significant increase in leukemia-specific T cells. In concert, targeting MUC1 signaling in human AML cells resulted in enhanced sensitivity to T-cell-mediated lysis. These findings suggest MUC1 is a critical regulator of PD-L1 expression via its effects on microRNA levels and represents a potential therapeutic target to enhance anti-tumor immunity.

Background and objective Idiopathic pulmonary fibrosis (IPF) is a progressive disease with poor prognosis and variable clinical course. Although matrix metalloproteinase-7 (MMP-7) is emerging as an important IPF biomarker, reproducibility across studies is unclear. We aimed to determine whether a previously reported prognostic threshold for MMP-7 was predictive of mortality in an independent cohort of IPF patients. Methods MMP-7 concentrations obtained from heparinized plasma samples were determined by ELISA in 97 patients with IPF and 41 healthy controls. The association of the previously published heparin plasma MMP-7 threshold of 12.1 ng/mL with all-cause mortality or transplant-free survival (TFS) was determined, either as an independent biomarker or as part of the modified personal clinical and molecular mortality index (m-PCMI). Results MMP-7 plasma concentrations were significantly higher in IPF patients compared to healthy controls (14.40 ± 6.55 ng/mL vs 6.03 ± 2.51 ng/mL, P Conclusion This study confirms that MMP-7 concentrations could be used to accurately predict outcomes across cohorts and centres, when similar collection protocols are applied.

Introduction Obstructive sleep apnea (OSA) is common in patients with coronary artery disease (CAD), but adherence to continuous positive airway pressure (CPAP) in this population is poor. Low arousal threshold (ArTH), a pathophysiologic OSA trait, is associated with low rates of regular CPAP use in sleep clinic populations. We aimed to determine whether ArTH or other physiologic OSA traits (i.e. pharyngeal collapsibility, muscle compensation, loop gain) are associated with CPAP adherence in patients with CAD and OSA. Methods A secondary analysis of a randomized controlled trial of OSA treatment in patients with CAD (RICCADSA) was performed. OSA (apnea hypopnea index, AHI≥5/hour) was assessed by polysomnography. Arousal threshold (% eupneic ventilation, %Ve), loop gain (LG), pharyngeal collapsibility (%Ve) and compensation (%Ve) were estimated from polysomnography using a validated method. Adherence to auto-titrated CPAP (hours/night) was obtained from machine downloads at 1, 3, 6, 12 and 24 months. Mixed modelling was used to assess the association between OSA traits and CPAP adherence. Results Participants (n=262) were 64.1±7.9 years old, with BMI of 29.2±4.2 and 86% were men. The mean AHI was 40.8±23.6 events/hour with oxygen nadir of 81.3±7.1%. The median (IQR) CPAP adherence (hrs/night) was 3.0 (0.9, 5.8) at 1-mo and 3.0 (0.0, 5.6) at 24-mo. Compared to reference studies, the CAD patients exhibited an elevated LG 0.63 (0.53, 0.79), similar ArTH (%Ve) of 117.5% (106.5%, 136.4%), higher collapsibility (%Ve) at 90.1% (82.3%, 94.8%) and lower compensation (%Ve) at 3.7% (-0.7%, 8.7%).Only increasing pharyngeal muscle compensation was associated with lower CPAP adherence (β -0.04, p-value 0.048), effect modified by pharyngeal collapsibility (Compensation x Collapsibility, β Conclusion In this group of patients with CAD, increasing muscle compensation was associated with lower CPAP adherence. Physiologic OSA traits may provide insight into prediction of CPAP adherence among patients with OSA and CAD. Support Zinchuk: Parker B. Francis Fellowship Program in Clinical Research. Sands: American Heart Association. Peker: Swedish Research Council, Swedish Heart-Lung Foundation.

Molecular biomarkers are needed to refine prognostication and phenotyping of pulmonary hypertension (PH) patients. S100A12 is an emerging biomarker of various inflammatory diseases. This study aims to determine the prognostic value of S100A12 in PH.Exploratory microarray analysis performed on peripheral blood mononuclear cells (PBMC) collected from idiopathic pulmonary fibrosis (IPF) patients suggested an association between S100A12 and both PH and mortality. So the current study was designed to evaluate for an association between S100A12 in peripheral blood collected from two well-phenotyped PH cohorts in two other centres to derive and validate an association between S100A12 protein serum concentrations and mortality.The majority of the patients in the discovery and validation cohorts were either World Health Organization (WHO) group 1 (pulmonary arterial hypertension (PAH)) or 3 (lung disease-associated) PH. In the discovery PH cohort, S100A12 was significantly increased in patients with PH (n = 51) compared to controls (n = 22) (29.8 vs 15.7 ng/mL, P0.001) and negatively correlated with cardiac output (r = -0.58, P0.001) in PH patients. When S100A12 data were pooled from both cohorts, PAH and non-PAH PH patients had higher S100A12 compared to healthy external controls (32.6, 30.9, 15.7 ng/mL; P0.001). S100A12 was associated with an increased risk in overall mortality in PH patients in both the discovery (n = 51; P = 0.008) and validation (n = 40; P0.001) cohorts.S100A12 levels are increased in PH patients and are associated with increased mortality.

SummaryBackground Genetic studies have identified numerous genes reproducibly associated with asthma, yet these studies have focussed almost entirely on single nucleotide polymorphisms (SNPs), and virtually ignored another highly prevalent form of genetic variation: Copy Number Variants (CNVs). Objective To survey the prevalence of CNVs in genes previously associated with asthma, and to assess whether CNVs represent the functional asthma-susceptibility variants at these loci. Methods We genotyped 383 asthmatic trios participating in the Childhood Asthma Management Program (CAMP) using a competitive genomic hybridization (CGH) array designed to interrogate 20 092 CNVs. To ensure comprehensive assessment of all potential asthma candidate genes, we purposely used liberal asthma gene inclusion criteria, resulting in consideration of 270 candidate genes previously implicated in asthma. We performed statistical testing using FBAT-CNV. Results Copy number variation in asthma candidate genes was prevalent, with 21% of tested genes residing near or within one of 69 CNVs. In six instances, the complete candidate gene sequence resides within the CNV boundaries. On average, asthmatic probands carried six asthma-candidate CNVs (range 1–29). However, the vast majority of identified CNVs were of rare frequency (

Background Exposure to air pollution, including traffic-related pollutants, has been associated with a variety of adverse health outcomes, including increased cardiopulmonary morbidity and mortality, and increased lung cancer risk. Methods To better understand the cellular responses induced by air pollution exposures, we performed genome-wide gene expression microarray analysis using whole blood RNA sampled at three time-points across the work weeks of 63 non-smoking employees at 10 trucking terminals in the northeastern US. We defined genes and gene networks that were differentially activated in response to PM2.5 (particulate matter ≤ 2.5 microns in diameter) and elemental carbon (EC) and organic carbon (OC). Results Multiple transcripts were strongly associated (padj

Background Acute respiratory distress syndrome (ARDS) is an inflammatory condition comprising diffuse lung edema and alveolar damage. ARDS frequently results from regional injury mechanisms. However, it is unknown whether detectable inflammation precedes lung edema and opacification and whether topographically differential gene expression consistent with heterogeneous injury occurs in early ARDS. The authors aimed to determine the temporal relationship between pulmonary metabolic activation and density in a large animal model of early ARDS and to assess gene expression in differentially activated regions. Methods The authors produced ARDS in sheep with intravenous lipopolysaccharide (10 ng ⋅ kg−1 ⋅ h−1) and mechanical ventilation for 20 h. Using positron emission tomography, the authors assessed regional cellular metabolic activation with 2-deoxy-2-[(18)F]fluoro-d-glucose, perfusion and ventilation with 13NN-saline, and aeration using transmission scans. Species-specific microarray technology was used to assess regional gene expression. Results Metabolic activation preceded detectable increases in lung density (as required for clinical diagnosis) and correlated with subsequent histologic injury, suggesting its predictive value for severity of disease progression. Local time courses of metabolic activation varied, with highly perfused and less aerated dependent lung regions activated earlier than nondependent regions. These regions of distinct metabolic trajectories demonstrated differential gene expression for known and potential novel candidates for ARDS pathogenesis. Conclusions Heterogeneous lung metabolic activation precedes increases in lung density in the development of ARDS due to endotoxemia and mechanical ventilation. Local differential gene expression occurs in these early stages and reveals molecular pathways relevant to ARDS biology and of potential use as treatment targets.

Idiopathic pulmonary fibrosis (IPF) is a progressive disease with poor prognosis and variable clinical course. Although matrix metalloproteinase-7 (MMP-7) is emerging as an important IPF biomarker, reproducibility across studies is unclear. We aimed to determine whether a previously reported prognostic threshold for MMP-7 was predictive of mortality in an independent cohort of IPF patients.MMP-7 concentrations obtained from heparinized plasma samples were determined by ELISA in 97 patients with IPF and 41 healthy controls. The association of the previously published heparin plasma MMP-7 threshold of 12.1 ng/mL with all-cause mortality or transplant-free survival (TFS) was determined, either as an independent biomarker or as part of the modified personal clinical and molecular mortality index (m-PCMI).MMP-7 plasma concentrations were significantly higher in IPF patients compared to healthy controls (14.40 ± 6.55 ng/mL vs 6.03 ± 2.51 ng/mL, P 0.001). The plasma MMP-7 threshold of 12.1 ng/mL was significantly associated with both all-cause mortality and TFS (unadjusted Cox proportional hazard ratio (HR) = 25.85 and 15.49, 95% CI: 10.91-61.23 and 5.41-44.34, respectively, P 0.001). MMP-7 concentrations, split by 12.1 ng/mL, were significantly (P 0.05) predictive of mortality and TFS after adjusting for age, gender, smoking and baseline pulmonary function parameters, in a multivariate Cox proportional hazards model. MMP-7 concentrations were negatively correlated with diffusing lung capacity of carbon monoxide (DLThis study confirms that MMP-7 concentrations could be used to accurately predict outcomes across cohorts and centres, when similar collection protocols are applied.

Table S2. List of enriched diseases in the Comparative Toxicogenomic Database using the core set of 248 genes from differential expression analysis and GSEA. (DOCX 14Â kb)

QQ plots after permutation for gene-level analysis. (PDF 4315Â kb)

Table S1. List of the core set of 262 genes from differential expression analysis and GSEA. (DOCX 15Â kb)

Genome-wide association studies of human gene expression promise to identify functional regulatory genetic variation that contributes to phenotypic diversity. However, it is unclear how useful this approach will be for the identification of disease-susceptibility variants. We generated gene expression profiles for 22 184 mRNA transcripts using RNA derived from peripheral blood CD4+ lymphocytes, and genome-wide genotype data for 516 512 autosomal markers in 200 subjects. We screened for cis-acting variants by testing variants mapping within 50 kb of expressed transcripts for association with transcript abundance using generalized linear models. Significant associations were identified for 1585 genes at a false discovery rate of 0.05 (corresponding to P-values ranging from 1 × 10(-91) to 7 × 10(-4)). Importantly, we identified evidence of regulatory variation for 119 previously mapped disease genes, including 24 examples where the variant with the strongest evidence of disease-association demonstrates strong association with specific transcript abundance. The prevalence of cis-acting variants among disease-associated genes was 63% higher than the genome-wide rate in our data set (P = 6.41 × 10(-6)), and although many of the implicated loci were associated with immune-related diseases (including asthma, connective tissue disorders and inflammatory bowel disease), associations with genes implicated in non-immune-related diseases including lipid profiles, anthropomorphic measurements, cancer and neurologic disease were also observed. Genetic variants that confer inter-individual differences in gene expression represent an important subset of variants that contribute to disease susceptibility. Population-based integrative genetic approaches can help identify such variation and enhance our understanding of the genetic basis of complex traits.

It is increasingly recognized that asthma is a heterogeneous disease. Therefore, it is possible that analysis of gene expression in the airway will reveal clinically meaningful transcriptional endotypes of asthma (TEA clusters).We measured whole transcriptome gene expression profiles in the sputum and whole blood of 100 individuals with asthma and 12 control subjects using the Affymetrix HuGene ST 1.0 gene arrays. Unsupervised clustering was conducted using pathways from Kyoto Encyclopedia of Genes and Genomes (KEGG). This identified three TEA clusters that were correlated with clinical, physiologic, and inflammatory characteristics of the disease. TEA cluster 1 is a cluster of patients with asthma with a significantly higher rate of intubation (P = 0.05), a lower prebronchodilator FEV1 (P = 0.006), a higher bronchodilator response (P = 0.03), and higher exhaled nitric oxide levels (P = 0.04) than the other two TEA clusters. TEA cluster 2 has a higher rate of hospitalization for asthma (P = 0.04) and is heterogeneous. TEA cluster 3 is the largest cluster and has normal lung function, low exhaled nitric oxide levels, and lower inhaled steroid requirements. TEA cluster 1 had the highest sputum Th2 gene signature (IL-4, -5, and -13) compared with the other clusters. A classifier was developed that predicts TEA cluster assignment using 53 predictive genes in the circulation. The classifier was applied to gene expression data of children from the Asthma Biorepository for Integrative Genomic Exploration (Asthma BRIDGE) consortium cohort and confirmed that TEA clusters 1 and 2 are associated with history of intubation (P = 5.58 × 10(-06)) and hospitalization (P = 0.01), respectively.Analysis of the sputum transcriptome reveals three TEA clusters with different clinical and physiologic characteristics of disease in children and adults with asthma. This suggests that there are common transcriptomic signatures in the blood in children and adults with asthma that are associated with features of severe asthma.

Circadian rhythms are known to regulate immune responses in healthy animals, but it is unclear whether they persist during acute illnesses where clock gene expression is disrupted by systemic inflammation. Here we use a genome-wide approach to investigate circadian gene and metabolite expression in the lungs of endotoxemic mice and find that novel cellular and molecular circadian rhythms are elicited in this setting. The endotoxin-specific circadian programme exhibits unique features, including a divergent group of rhythmic genes and metabolites compared with the basal state and a distinct periodicity and phase distribution. At the cellular level, endotoxin treatment also alters circadian rhythms of leukocyte counts within the lung in a bmal1-dependent manner, such that granulocytes rather than lymphocytes become the dominant oscillating cell type. Our results show that inflammation produces a complex re-organization of cellular and molecular circadian rhythms that are relevant to early events in lung injury.

Background The investigation of complex disease heterogeneity has been challenging. Here, we introduce a network-based approach, using partial correlations, that analyzes the relationships among multiple disease-related phenotypes. Results We applied this method to two large, well-characterized studies of chronic obstructive pulmonary disease (COPD). We also examined the associations between these COPD phenotypic networks and other factors, including case-control status, disease severity, and genetic variants. Using these phenotypic networks, we have detected novel relationships between phenotypes that would not have been observed using traditional epidemiological approaches. Conclusion Phenotypic network analysis of complex diseases could provide novel insights into disease susceptibility, disease severity, and genetic mechanisms.

Purpose: Identification of single-nucleotide polymorphisms (SNP) associated with development of advanced colorectal adenomas. Experimental Design: Discovery phase: 1,406 Caucasian patients (139 advanced adenoma cases and 1,267 controls) from the Adenoma Prevention with Celecoxib (APC) trial were included in a genome-wide association study (GWAS) to identify variants associated with postpolypectomy disease recurrence. Genome-wide significance was defined as false discovery rate less than 0.05, unadjusted P = 7.4 × 10−7. Validation phase: results were further evaluated using 4,175 familial colorectal adenoma cases and 5,036 controls from patients of European ancestry [COloRectal Gene Identification consortium (CORGI), Scotland, Australia, and VQ58]. Results: Our study identified eight SNPs associated with advanced-adenoma risk in the APC trial (rs2837156, rs7278863, rs2837237, rs2837241, rs2837254, rs741864 at 21q22.2, and rs1381392 and rs17651822 at 3p24.1, at P < 10−7 level with OR > 2). Five variants in strong pairwise linkage disequilibrium (rs7278863, rs2837237, rs741864, rs741864, and rs2837241; r2 = 0.8–1) are in or near the coding region for the tight junction adhesion protein, IGSF5. An additional variant associated with advanced adenomas, rs1535989 [minor allele frequency, 0.11; OR, 2.09; 95% confidence interval (CI), 1.50–2.91], also predicted colorectal cancer development in a validation analysis (P = 0.019) using a series of adenoma cases or colorectal cancer (CORGI study) and 3 sets of colorectal cancer cases and controls (Scotland, VQ58, and Australia; N = 9,211). Conclusions: Our results suggest that common polymorphisms contribute to the risk of developing advanced adenomas and might also contribute to the risk of developing colorectal cancer. The variant at rs1535989 may identify patients whose risk for neoplasia warrants increased colonoscopic surveillance. Clin Cancer Res; 19(23); 6430–7. ©2013 AACR.

Background The relationships between total serum IgE levels and gene expression patterns in peripheral blood CD4+ T cells (in all subjects and within each sex specifically) are not known. Methods Peripheral blood CD4+ T cells from 223 participants from the Childhood Asthma Management Program (CAMP) with simultaneous measurement of IgE. Total RNA was isolated, and expression profiles were generated with Illumina HumanRef8 v2 BeadChip arrays. Modeling of the relationship between genome-wide gene transcript levels and IgE levels was performed in all subjects, and stratified by sex. Results Among all subjects, significant evidence for association between gene transcript abundance and IgE was identified for a single gene, the interleukin 17 receptor B (IL17RB), explaining 12% of the variance (r2) in IgE measurement (p value = 7 × 10-7, 9 × 10-3 after adjustment for multiple testing). Sex stratified analyses revealed that the correlation between IL17RB and IgE was restricted to males only (r2 = 0.19, p value = 8 × 10-8; test for sex-interaction p < 0.05). Significant correlation between gene transcript abundance and IgE level was not found in females. Additionally we demonstrated substantial sex-specific differences in IgE when considering multi-gene models, and in canonical pathway analyses of IgE level. Conclusions Our results indicate that IL17RB may be the only gene expressed in CD4+ T cells whose transcript measurement is correlated with the variation in IgE level in asthmatics. These results provide further evidence sex may play a role in the genomic regulation of IgE.

Although population differences in gene expression have been established, the impact on differential gene expression studies in large populations is not well understood. We describe the effect of self-reported race on a gene expression study of lung function in asthma. We generated gene expression profiles for 254 young adults (205 non-Hispanic whites and 49 African Americans) with asthma on whom concurrent total RNA derived from peripheral blood CD4(+) lymphocytes and lung function measurements were obtained. We identified four principal components that explained 62% of the variance in gene expression. The dominant principal component, which explained 29% of the total variance in gene expression, was strongly associated with self-identified race (P