Faculty Bibliography

Microbes are readily cultured from epithelial surfaces of the skin, mouth, and colon. In the last 10 years, culture-independent DNA-based techniques demonstrated that much more complex microbial communities reside on most epithelial surfaces; this includes the lower airways, where bacterial culture had failed to reliably demonstrate resident bacteria. Exposure to a diverse bacterial environment is important for adequate immunological development. The most common microbes found in the lower airways are also found in the upper airways. Increasing abundance of oral characteristic taxa is associated with increased inflammatory cells and exhaled nitric oxide, suggesting that the airway microbiome induces an immunological response in the lung. Furthermore, rhinovirus infection leads to outgrowth of Haemophilus in patients with chronic obstructive pulmonary disease, and human immunodeficiency virus-infected subjects have more Tropheryma whipplei in the lower airway, suggesting a bidirectional interaction in which the host immune defenses also influence the microbial niche. Quantitative and/or qualitative changes in the lung microbiome may be relevant for disease progression and exacerbations in a number of pulmonary diseases. Future investigations with longitudinal follow-up to understand the dynamics of the lung microbiome may lead to the development of new therapeutic targets.

INTRODUCTION: Abnormality in distal lung function may occur in obesity due to reduction in resting lung volume; however, airway inflammation, vascular congestion and/or concomitant intrinsic airway disease may also be present. The goal of this study is to 1) describe the phenotype of lung function in obese subjects utilizing spirometry, plethysmography and oscillometry; and 2) evaluate residual abnormality when the effect of mass loading is removed by voluntary elevation of end expiratory lung volume (EELV) to predicted FRC. METHODS: 100 non-smoking obese subjects without cardio-pulmonary disease and with normal airflow on spirometry underwent impulse oscillometry (IOS) at baseline and at the elevated EELV. RESULTS: FRC and ERV were reduced (44+/-22, 62+/-14% predicted) with normal RV/TLC (29+/-9%). IOS demonstrated elevated resistance at 20 Hz (R20, 4.65+/-1.07 cmH2O/L/s); however, specific conductance was normal (0.14+/-0.04). Resistance at 5-20 Hz (R5-20, 1.86+/-1.11 cmH2O/L/s) and reactance at 5 Hz (X5, -2.70+/-1.44 cmH2O/L/s) were abnormal. During elevation of EELV, IOS abnormalities reversed to or towards normal. Residual abnormality in R5-20 was observed in some subjects despite elevation of EELV (1.16+/-0.8 cmH2O/L/s). R5-20 responded to bronchodilator at baseline but not during elevation of EELV. CONCLUSIONS: This study describes the phenotype of lung dysfunction in obesity as reduction in FRC with airway narrowing, distal respiratory dysfunction and bronchodilator responsiveness. When R5-20 normalized during voluntary inflation, mass loading was considered the predominant mechanism. In contrast, when residual abnormality in R5-20 was demonstrable despite return of EELV to predicted FRC, mechanisms for airway dysfunction in addition to mass loading could be invoked.

Rationale: Early COPD is characterized by inflammation leading to lung destruction. Recent data supports that enrichment of the lung microbiome with supraglottic characteristic taxa (SCT) is associated with inflammation. We hypothesize that in subjects with early COPD, areas at higher risk for microaspiration (right) or with greater degree of parenchymal abnormalities will be enriched with SCT or potential pathogenic taxa (PPT) compared to their contralateral lung segment. Methods: Subjects with early emphysema were enrolled for research bronchoscopy from the NYU/EDRN cohort. An independent radiologist semiquantitatively assessed all Chest CT scans: six-point score based on the presence of parenchymal damage in three zones (upper, middle, and lower). Broncho-alveolar lavages (BAL) were obtained from the right middle lobe and lingula segments. Sequencing 16S rDNA performed with 454 pyrosequence. Results: A total of 15 subjects with early COPD were studied. CT scans demonstrated n=7 with normal lower zones and n=8 with symmetrical or asymmetrical emphysema in the lower zones (p=ns). We used Wilcoxon paired comparisons to analyze the microbiome in areas of greater degree of parenchymal abnormalities (if asymmetric) or right compared to the contralateral lung segment. Data showed that the areas of greater abnormalities or right were associated with increased relative abundance (RA) of Haemophilus (RA 0.00170+/-0.002 vs. 0.00084+/-0.001, p=0.04), Neisseria (RA 0.0048+/-0.005 vs. 0.0023+/-0.003, p=0.028), Parvimonas (RA 0.017+/-0.003 vs. 0.0002+/-0.0008, p=0.05), and Serratia (RA 0.0122+/-0.02 vs. 0.0033+/-0.003, p=0.03) compared with the contralateral segment. Streptococcus appeared not to have a predilection for at-risk segments at the genus level. However, at the OTU level, Streptococcus mitis and Streptococcus pneumoniae species were higher in lung segments with more emphysema or right lung segments. Conclusions: Our data shows that areas of greater parenchymal damage or at higher risk for microaspiration (right) are enriched with potentially pathogenic taxa, such as Parvimonas, Neisseria, Haemophilus, Serratia, and Streptococcus. These taxa are known to be in high relative abundance in the oral and supraglottic region. Some of these taxa have been found to be at higher RA after viral infections, suggesting that enrichment of these low relative abundance taxa may play a critical role in disease. However, other supraglottic characteristic taxa such as Prevotella and Veillonella were not increased in these regions. These observations suggest a distinct selection pressure between the upper and lower airway microbiome

Rationale: Macrolide antibiotics, specifically azithromycin, have antimicrobial and immunomodulatory effects and, despite not having proven effect on spirometry, have been shown to prevent exacerbations in patients with moderate to severe chronic obstructive disease (COPD). We have previously shown that in asymptomatic smokers with early emphysema identified by computed tomography, distal lung dysfunction is an early marker of subclinical lung inflammation. Thus, we hypothesized that in early emphysema, treatment with azithromycin will impact both distal lung function and biomarkers of airway inflammation. Methods: Emphysema subjects were identified from the NYU Lung Cancer Biomarker Center CT-Scan Screening Cohort. Ten subjects (7M/3F) with emphysema were enrolled for pulmonary function evaluation and research bronchoscopy pre and post eight weeks 250mg/day azithromycin therapy. Physiologic assessment included spirometry, plethysmography, and diffusing capacity. Distal lung function was assessed (pre and post bronchodilator) with impulse oscillometry (IOS). Pre and post bronchodilator exhaled nitric oxide (NO) was measured at variable flow rates to determine airway and alveolar NO concentration. Results: Subjects were 65+/-4 years age. All had history of smoking with emphysema identified on computed tomography. Subjects were asymptomatic with GOLD 0 spirometry in 9/10. Lung volumes (FRC, RV and TLC) and diffusing capacity were within normal limits in all subjects. In contrast, baseline IOS revealed abnormal resistance spectrum in 5/10 and abnormal reactance spectrum in 8/10, consistent with dysfunction in the distal lung. Post bronchodilator there was significant reduction in frequency dependence of resistance and in the reactance spectrum (R5-20 = 3.88 [3.39, 5.85] vs. 3.39 [3.26, 5.06] cmH2O/L/s, p = 0.022; X5 = -1.40 [-2.02, -1.01] vs. -1.03 [-1.47, -0.90] cmH2 O/L/s, p = 0.022; resonant frequency 16.2 [13.2, 20.1] vs. 13.6 [10.9, 16.2] Hz, p = 0.007). Following azithromycin therapy, IOS demonstrated no change in resistance; however, improved reactance was seen in 8 patients (p<0.04) and bronchodilator responsiveness was no longer present. Alveolar NO normalized in all subjects post azithromycin (baseline range 1.2-9.9 vs. 0-3.6 PPB post azithromycin, p=0.06 ) despite lack of change in airway NO. (Figure presented) Conclusions: In patients with early emphysema, azithromycin administration was associated with improved oscillometry reactance but not resistance parameters and improved alveolar rather than airway NO. These data support a beneficial effect of azithromycin on distal lung function and inflammation that may not be detected by routine tests

BACKGROUND: The lung microbiome of healthy individuals frequently harbors oral organisms. Despite evidence that microaspiration is commonly associated with smoking-related lung diseases, the effects of lung microbiome enrichment with upper airway taxa on inflammation has not been studied. We hypothesize that the presence of oral microorganisms in the lung microbiome is associated with enhanced pulmonary inflammation. To test this, we sampled bronchoalveolar lavage (BAL) from the lower airways of 29 asymptomatic subjects (nine never-smokers, 14 former-smokers, and six current-smokers). We quantified, amplified, and sequenced 16S rRNA genes from BAL samples by qPCR and 454 sequencing. Pulmonary inflammation was assessed by exhaled nitric oxide (eNO), BAL lymphocytes, and neutrophils. RESULTS: BAL had lower total 16S than supraglottic samples and higher than saline background. Bacterial communities in the lower airway clustered in two distinct groups that we designated as pneumotypes. The rRNA gene concentration and microbial community of the first pneumotype was similar to that of the saline background. The second pneumotype had higher rRNA gene concentration and higher relative abundance of supraglottic-characteristic taxa (SCT), such as Veillonella and Prevotella, and we called it pneumotypeSCT. Smoking had no effect on pneumotype allocation, alpha, or beta diversity. PneumotypeSCT was associated with higher BAL lymphocyte-count (P= 0.007), BAL neutrophil-count (P= 0.034), and eNO (P= 0.022). CONCLUSION: A pneumotype with high relative abundance of supraglottic-characteristic taxa is associated with enhanced subclinical lung inflammation.

RATIONALE: Analysis of local in vivo inflammation is relevant to the understanding of pathogenesis and disease progression in emphysema. Bronchial reactivity is an early marker of disease in asthma but the relevance of reactivity to the natural history of emphysema is not understood. We hypothesize that bronchial reactivity is a phenotype of early emphysema that might be related to the degree of inflammation in the lung. METHODS: Normal subjects were enrolled as part of a normal volunteer protocol. Emphysema subjects were identified from the NYU Lung Cancer Biomarker Center CT-scan screening cohort. All patients underwent spirometry, plethysmography, diffusion, and oscillometry, as well as bronchoscopy with bronchoalveolar lavage (BAL). Bronchial reactivity was assessed by changes in FEV1, V50 and R5 . From the BAL fluid, cell count differential was obtained, as well as measurement of 39 cytokines in concentrated BAL fluid with Luminex using Human Cytokine Panel I (Millipore). Results amongst the groups were compared with ANOVA and post-hoc LSD comparison. RESULTS: Twenty patients were available for analysis: Six subjects in the control group, 6 emphysema subjects without bronchial reactivity (BR-), and 8 emphysema subjects with bronchial reactivity (BR+). Baseline demographics and pertinent spirometry/oscillometry are listed in Table 1. Emphysema subjects were all GOLD stage 0 or 1. Post-bronchodilator spirometric and oscillometric parameters were not significantly different between BR- and BR+ emphysema groups. There were 28/39 cytokines with reliably measurable levels. Both emphysema groups had elevated neutrophils and higher degree of inflammation as compared to controls (significant data shown Table 1). However, the BR+ emphysema group evidenced higher degree of neutrophils, IL-6, IL-8, G-CSF, Eotaxin, GRO and Fractalkine as compared with the BR- emphysema group. CONCLUSION: These data suggest that in early emphysema a phenotype of proximal and/or distal bronchial reactivity is associated with an increased degree of inflammation as assessed by neutrophils and in vivo inflammatory cytokines. In contrast with early asthma, the phenotype of bronchial reactivity in early emphysema may be characterized by neutrophilic inflammation produced by increased IL-8 in the lung. The role of IL-6, G-CSF, Eotaxin, GRO and Fractalkine in producing emphysema related bronchial reactivity requires further investigation. (Table Presented)

Rationale: The use of culture-independent techniques to evaluate resident microbial communities in the lung has opened opportunities to evaluate host response phenotype in health and disease. Background environmental microbiome found in saline and bronchoscope prior to bronchoscopy is characterized by high relative abundance of Propionibacterium. Our preliminary data from the lung microbiome project suggest that substitution of background environmental microbiome by Prevotella or Streptococcus microbiome is associated with higher inflammation. We hypothesize that patients with emphysema who have asymmetric disease on CT will have disappearance of background environmental microbiome in the more affected lung segments. We will also evaluate whether background environmental microbiome is associated with lower inflammation (neutrophil counts, and chemo-attractant cytokines). Methods: Subjects with emphysema were enrolled for research bronchoscopy from NYU/EDRN cohort and CT scans were classified as symmetrical or asymmetrical lung disease. Broncho-alveolar lavages (BAL) were obtained from the right and left lung. Sequencing of 300 bp 16S rDNA included V1-V2 region, performed with 454 pyrosequence. Propionibacterium was used as a marker of background environmental microbiome. Cytokines in BAL fluid will be assayed using Human Cytokine Panel I (Millipore). Results: To date, 15 subjects had sequence data from two segments of different lungs (5 normal volunteers, 6 symmetrical lung disease patients, and 4 asymmetrical lung disease patients). Healthy volunteers were younger than subjects with emphysema (41 +/- 11, 61 +/- 6 respectively, p = 0.003). Although no significant difference in FEV1 was observed, emphysema groups trended to have lower FEV1/FVC (p=ns). There were no differences in high relative abundant taxa (greater than 0.05) between the right and left lung of normal volunteers and emphysema subjects with symmetrical lung disease. However, despite the small n, emphysema subjects with asymmetrical lung disease trended to have higher relative abundance of background environmental microbiome in lung segments with less disease ( Propionibacterium relative abundance = 0.13 +/- 0.04 for segments with less disease as compared with 0.03 +/- 0.04 in the more disease segments, p < 0.08). We will complete sequence in 5 more emphysema subjects and compare microbiota with in-vivo BAL cytokines. Conclusions: Patients with observable asymmetrical lung disease have lower background environmental microbiome in more diseased lung when compared to the less diseased side. This difference was not observed in normal volunteers and patients with symmetrical lung disease. Disappearance of background environmental microbiome in more diseased lung segments suggests higher airway colonization, which might be associated with subclinical inflammation

Rationale: While bacterial colonization leads to airway inflammation and accelerated airway obstruction in advanced COPD, its role in early disease is not well understood. Major limitations have been the ability to study airway colonization in early COPD and measurements of in vivo cytokines levels in the lung. Here, we used a pyrosequence approach for 16s rDNA to study the airway microbiome and a concentration technique to achieve measurable levels of cytokines in BAL fluid from early emphysema and normal volunteers. We hypothesize that the microbiome of early emphysema will be characterized by the presence of potential pathogens that are associated with subclinical inflammation. Methods: CT-scan defined emphysema. Supraglotic and broncho-alveolar lavage (BAL) samples were obtained with two different bronchoscopes. Bacteria speciation was performed with 454 sequencing of rDNA. BAL differential was performed on diff quick stained cytospine slides. BAL was concentrated 50 fold by lyophilization and cytokes were measured using Luminex. Results: 24 subjects were available for analysis (8 healthy normal volunteers and 16 with emphysema). All emphysema subjects were ex-smokers (normal 1+/-0.5 vs. 39+/-20 pack-yr., p=0.019). Lung function of emphysema subjects was characterized by lower FEV1/FVC (78.9+/-5.1 vs. 69.6+/-6.1, p=0.001) and hyperinflation (TLC=87.7+/-10.3 vs. 104.3+/-15.2% predicted, p=0.016). Background environmental microbiome, present in "sterile" saline, is enriched with Staphylococcus and Propionobacterium rDNA (Figure 1 right panel). Supraglotic microbiome is enriched with Prevotella and Streptococcus (left panel). Individuals' BAL microbiome varied from a microbiome more similar to supraglotic with higher relative abundance of Prevotella to a background microbiome (middle panel). In this small sample there was a non-significant trend to higher relative abundance of Prevotella in emphysema vs. normal (p=0.078). There was significant positive correlation between Prevotella and BAL inflammatory cytokines (r2=0.48,p<0.001 and r2=0.22,p<0.02 for IL-1alpha and IL-8 respectively, Figure 2 panel A and B). Furthermore, Prevotella directly correlates with Neutrophils in lung (r2=0.24,p=0.02, Panel C). Conclusions: This data shows that inflammatory cytokines are produced and neutrophils recruited to the alveolar space when the lung and supraglotic microibome are similar. In patients with Prevotella, the bacteria has been present long enough to produce subclinical inflammation. It is therefore unlikely that the Prevotella microbiome is due to carryover during bronchoscopy. In individuals with a BAL microbiome similar to saline, poor sinal-to-noise ratio prevents investigation of the lung microbiome. The Prevotella microbiome more common in emphysema is associated with increased bronco-alveolar cytokines and neutrophils, suggesting an immunological response to this lung microbiome. (Figure Presented)

Rationale: Cigarette smoke causes a field of injury and molecular changes in the airways even in histologically normal areas termed "field cancerization" which describes the site(s) of neoplasia and adjacent normal tissue with molecular abnormalities in common. MicroRNAs ( miRNAs) are small, non-coding RNAs that act as post-transcriptional regulators of gene expression by recognizing target sites in the 3' untranslated regions (3'UTRs) via incomplete base-pairing and induce mRNA degradation or translational repression. Deregulation of miRNAs has been linked to cancer initiation and progression, and miRNAs may act as tumor suppressor genes or oncogenes. We hypothesized that miRNA expression in the peripheral airways of smokers with lung cancer is distinct from that of smokers without lung cancer and therefore, miRNAs can be used as biomarkers for the early detection of lung cancer. Methods: We collected human peripheral airway epithelial cells by bronchoscopic brushing from the unaffected lung of thirteen smokers with lung adenocarcinoma and twelve control smokers. Total RNA was extracted from the peripheral airway epithelial cells by miRNAeasy and miRNA profiling was performed using the TaqMan Quantitative qRT-PCR miRNA Assay. Results: Comparison of miRNA levels in peripheral airway epithelial cells from smokers with or without lung cancer demonstrated 53 miRNAs that were significantly different (p<0.05) between the two groups. The majority of miRNAs were up-regulated (41 miRNAs) in lung cancer patients, including miR-21, miR-26a, miR-31, miR-34c, and miR-205. Down-regulated miRNAs included let-7b, let-7e, and miR-126. Several of the miRNAs with increased expression are of interest: miR-21 inhibits tumor suppressor protein PTEN, miR-26a suppresses PTEN and increases AKT phosphorylation and nuclear factor kappaB (NFkappaB) activation, miR-31 represses tumor suppressor genes LATS2 and PPP2R2A, miR-205 is associated with cancer relapses, and miR-34c, a p53 target induced by DNA damage, suggests the involvement of p53 pathway in field carcinogenesis. Down-regulated let-7b leads to higher expression of CYP2J2 and decreased miR-126 enhances adhesion, migration and invasion through increased Crk protein. Further gene expression and pathway analyses will corroborate the relationship between miRNAs and predicted pathways in real time. Conclusion: We discovered a profile of miRNAs in the contralateral lung of patients with lung cancer as biomarkers of field cancerization in smokers with lung adenocarcinoma. Further knowledge of field cancerization may lead to better understanding of tumorigenesis and development of biomarkers for early lung cancer detection

OBJECTIVES/SPECIFIC AIMS: The lung is classically thought to be sterile although molecular techniques for microbial identification are now suggesting the existence of a human airway microbiota. The study of the microbiome has now opened an opportunity to characterize resident microbial flora without the need for bacterial culture although the lung microbiome in smokers has not been characterized. We therefore tested the hypothesis that in smokers, the upper and lower airways contain a distinct microbiota. METHODS/STUDY POPULATION: We obtained supraglotic and broncho-alveolar lavage (BAL) samples in 8 subjects. Bacterial quantification of supraglotic aspirate and BAL was determined by qPCR using universal primers for 16S rDNA. Dilution was corrected by urea. We defined bacteria OTU by 454 sequencing. We performed cluster analysis, principal coordinate analysis and weighted UniFrac to determine microbiome. RESULTS/ANTICIPATED RESULTS: Subjects were 55 +/- 13 yo, 4/8 female and 7/8 significant smokers (>10 pack/year). FEV1 was 94 +/- 11%, FVC 108 +/- 10% and FEV1/FVC was 71 +/- 8. Bacteria rDNA was higher in the supraglotic area than BAL (1.5e9 +/- 3.2e9 vs. 1e7 +/- 8.2e6 copies/mL of adjusted fluid, p < 0.001). Clustering of the bacterial community at the family level showed distinct microbiome in the upper airway and the lung (BAL). While Prevotellaceae, Veillonellaceae and Fusobacteriaceae predominated in the supraglotic sample, Micrococcaceae, Propionibacteriaceae and Staphylococcaceae among others predominated in BAL. UniFrac calculated distances showed no overlapping circle of inertia between supraglotic and BAL (p < 0.0001 for first principal axis). DISCUSSION/SIGNIFICANCE OF IMPACT: In the absence of signs or symptoms of infection, subjects had significant airway resident bacteria. Th is supports the existence of a bacterial reservoir in the lung, which might be influenced by smoking and/or innate immunity