Faculty Bibliography

Mycobacterium tuberculosis develops spontaneous resistance mutants to virtually every drug in use. Courses of therapy select for these mutants and drug-resistant organisms emerge. The development of drug-resistant organisms has reached the point that drug resistance now threatens to undermine global success against tuberculosis (TB). New drugs are needed. The last new class of drugs specifically developed for treatment of TB was the rifamycins over 40 years ago. New funding sources and the development of product development partnerships have energized the TB drug development effort. There are now more TB drugs in development than at any time in the past. The first of these drugs to be developed and marketed was bedaquiline. Bedaquiline has an entirely novel mechanism of action and so should be active against otherwise highly resistant organisms. It acts on the transmembrane component of adenosine triphosphate synthase and acts by preventing electron transport. This raises the exciting possibility that bedaquiline may be active against less metabolically active organisms. Drug-drug interactions between rifamycins and the cytochrome P450-3A system will limit bedaquiline's utility and create complexity in treatment regimens. In clinical trials, treatment with bedaquiline added to a background multidrug-resistant TB regimen was associated with earlier culture conversion and higher cure rates, but there were unexplained excess deaths in the bedaquiline arms of these trials. Food and Drug Administration approved bedaquiline for the treatment of multidrug-resistant TB when an effective treatment regimen cannot otherwise be provided. They required a black box warning about excess deaths and require that a phase III trial be completed. A planned Phase III trial is being reorganized. While bedaquiline is an exciting drug and marks a dramatic moment in the history of TB treatment, its ultimate place in the anti-TB drug armamentarium is unclear pending the Phase III trial and the development of other new drugs that are in the pipeline.

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

While exploring the effects of aerosol IFN-gamma treatment in HIV-1/tuberculosis co-infected patients, we observed A to G mutations in HIV-1 envelope sequences derived from bronchoalveolar lavage (BAL) of aerosol IFN-gamma-treated patients and induction of adenosine deaminase acting on RNA 1 (ADAR1) in the BAL cells. IFN-gamma induced ADAR1 expression in monocyte-derived macrophages (MDM) but not T cells. ADAR1 siRNA knockdown induced HIV-1 expression in BAL cells of four HIV-1 infected patients on antiretroviral therapy. Similar results were obtained in MDM that were HIV-1 infected in vitro. Over-expression of ADAR1 in transformed macrophages inhibited HIV-1 viral replication but not viral transcription measured by nuclear run-on, suggesting that ADAR1 acts post-transcriptionally. The A to G hyper-mutation pattern observed in ADAR1 over-expressing cells in vitro was similar to that found in the lungs of HIV-1 infected patients treated with aerosol IFN-gamma suggesting the model accurately represented alveolar macrophages. Together, these results indicate that ADAR1 restricts HIV-1 replication post-transcriptionally in macrophages harboring HIV-1 provirus. ADAR1 may therefore contribute to viral latency in macrophages.

BACKGROUND: CT screening for lung cancer is effective in reducing mortality, but there are areas of concern, including a positive predictive value of 4% and development of interval cancers. A blood test that could manage these limitations would be useful, but development of such tests has been impaired by variations in blood collection that may lead to poor reproducibility across populations. RESULTS: Blood-based proteomic profiles were generated with SOMAscan technology, which measured 1033 proteins. First, preanalytic variability was evaluated with Sample Mapping Vectors (SMV), which are panels of proteins that detect confounders in protein levels related to sample collection. A subset of well collected serum samples not influenced by preanalytic variability was selected for discovery of lung cancer biomarkers. The impact of sample collection variation on these candidate markers was tested in the subset of samples with higher SMV scores so that the most robust markers could be used to create disease classifiers. The discovery sample set (n = 363) was from a multi-center study of 94 non-small cell lung cancer (NSCLC) cases and 269 long-term smokers and benign pulmonary nodule controls. The analysis resulted in a 7-marker panel with an AUC of 0.85 for all cases (68% adenocarcinoma, 32% squamous) and an AUC of 0.93 for squamous cell carcinoma in particular. This panel was validated by making blinded predictions in two independent cohorts (n = 138 in the first validation and n = 135 in the second). The model was recalibrated for a panel format prior to unblinding the second cohort. The AUCs overall were 0.81 and 0.77, and for squamous cell tumors alone were 0.89 and 0.87. The estimated negative predictive value for a 15% disease prevalence was 93% overall and 99% for squamous lung tumors. The proteins in the classifier function in destruction of the extracellular matrix, metabolic homeostasis and inflammation. CONCLUSIONS: Selecting biomarkers resistant to sample processing variation led to robust lung cancer biomarkers that performed consistently in independent validations. They form a sensitive signature for detection of lung cancer, especially squamous cell histology. This non-invasive test could be used to improve the positive predictive value of CT screening, with the potential to avoid invasive evaluation of nonmalignant pulmonary nodules.

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

INTRODUCTION: Prior studies comparing abnormalities in pulmonary function between HIV-infected and HIV-uninfected persons in the current era are limited. OBJECTIVES: To determine the pattern and severity of impairment in pulmonary function in HIV-infected compared with HIV-uninfected individuals. METHODS: Cross-sectional analysis of 300 HIV-infected men and 289 HIV-uninfected men enrolled from 2009 to 2011 in 2 clinical centers of the Lung HIV Study. Participants completed pre- and postbronchodilator spirometry, diffusing capacity of the lung for carbon monoxide (DLCO) measurement, and standardized questionnaires. RESULTS: Most participants had normal airflow; 18% of HIV-infected and 16% of HIV-uninfected men had airflow obstruction. The mean percent predicted DLCO was 69% in HIV-infected vs. 76% in HIV-uninfected men (P < 0.001). A moderately to severely reduced DLCO of /=200 cells per microliter and to HIV-uninfected men. Respiratory symptoms of cough, phlegm and dyspnea were more prevalent in HIV-infected patients particularly those with abnormal pulmonary function compared with HIV-uninfected patients. CONCLUSIONS: HIV infection is an independent risk factor for reduced DLCO, particularly in individuals with a CD4 cell count below 200 cells per microliter. Abnormalities in pulmonary function among HIV-infected patients manifest clinically with increased respiratory symptoms. Mechanisms accounting for the reduced DLCO require further evaluation.