Faculty Bibliography

In lung cancer, enrichment of the lower airway microbiota with oral commensals commonly occurs and ex vivo models support that some of these bacteria can trigger host transcriptomic signatures associated with carcinogenesis. Here, we show that this lower airway dysbiotic signature was more prevalent in group IIIB-IV TNM stage lung cancer and is associated with poor prognosis, as shown by decreased survival among subjects with early stage disease (I-IIIA) and worse tumor progression as measured by RECIST scores among subjects with IIIB-IV stage disease. In addition, this lower airway microbiota signature was associated with upregulation of IL-17, PI3K, MAPK and ERK pathways in airway transcriptome, and we identified Veillonella parvula as the most abundant taxon driving this association. In a KP lung cancer model, lower airway dysbiosis with V. parvula led to decreased survival, increased tumor burden, IL-17 inflammatory phenotype and activation of checkpoint inhibitor markers.

INTRODUCTION/BACKGROUND:Workers' exposure to metalworking fluid (MWF) has been associated with respiratory disease. As part of a public health investigation of a manufacturing facility, we performed paired environmental and human sampling to evaluate cross-pollination of microbes between environment and host and possible effects on lung pathology present among workers. METHODS:Workplace environmental microbiota was evaluated in air and MWF samples. Human microbiota was evaluated in lung tissue samples from workers with respiratory symptoms found to have lymphocytic bronchiolitis and alveolar ductitis with B-cell follicles and emphysema, lung tissue controls, and in skin, nasal and oral samples from 302 workers from different areas of the facility. In vitro effects of MWF exposure on murine B-cells were assessed. RESULTS:Increased similarity of microbial composition was found between MWF samples and lung tissue samples of case workers compared to controls. Among workers in different locations within the facility, those that worked in machine shop area had skin, nasal and oral microbiota more closely related to the microbiota present in MWF samples. Lung samples from four index cases, and skin and nasal samples from workers in machine shop area were enriched with Pseudomonas, the dominant taxa in MWF. Exposure to used MWF stimulated murine B-cell proliferation in vitro, a hallmark cell subtype found in pathology of index cases. CONCLUSIONS:Evaluation of a manufacturing facility with a cluster of workers with respiratory disease supports cross-pollination of microbes from MWF to humans and suggests the potential for exposure to these microbes to be a health hazard.

INTRODUCTION/BACKGROUND:Neutrophilic inflammation is a major driver of bronchiectasis pathophysiology, and neutrophil elastase activity is the most promising biomarker evaluated in sputum to date. How active neutrophil elastase correlates with lung microbiome in bronchiectasis is still unexplored. We aimed at understanding if active neutrophil elastase is associated with low microbial diversity and distinct microbiome characteristics. METHODS:An observational, cross-sectional study was conducted at the Bronchiectasis Program of the Policlinico Hospital in Milan, Italy, where adults with bronchiectasis were enrolled between March 2017 and March 2019. Active neutrophil elastase was measured on sputum collected during stable state, microbiota analysed through 16S rRNA gene sequencing, molecular assessment of respiratory pathogens through real time PCR and clinical data collected. MEASUREMENTS AND MAIN RESULTS/RESULTS:with elevated active neutrophil elastase was found based on standard culture and targeted real-time PCR. CONCLUSIONS:infection.

BACKGROUND:Platelets are effector cells of the innate and adaptive immune system, however understanding their role during inflammation-driven pathologies can be challenging due to several drawbacks associated with current platelet depletion methods. The generation of antisense oligonucleotides (ASO)s directed to thrombopoietin (Tpo) mRNA represents a novel method to reduce circulating platelet count. OBJECTIVE:To understand if Tpo-targeted ASO treatment represents a viable strategy to specifically reduce platelet count in mice. METHODS:Female and male mice were treated with TPO-targeted ASOs and platelet count and function assessed, in addition to circulating blood cell counts and hematopoietic stem and progenitor cells. The utility of the platelet-depletion strategy was assessed in a murine model of lower airway dysbiosis. RESULTS AND CONCLUSIONS/CONCLUSIONS:Herein, we describe how in mice, ASO-mediated silencing of hepatic TPO expression reduces platelet, megakaryocyte, and megakaryocyte progenitor count, without altering platelet activity. TPO ASO-mediated platelet depletion can be achieved acutely and sustained chronically in the absence of adverse bleeding. TPO ASO-mediated platelet depletion allows for the reintroduction of new platelets, an advantage over commonly used antibody-mediated depletion strategies. Using a murine model of lung inflammation, we demonstrate that platelet depletion, induced by either TPO ASO or anti-CD42b treatment, reduces the accumulation of inflammatory immune cells, including monocytes and macrophages, in the lung. Altogether, we characterize a new platelet depletion method that can be sustained chronically and allows for the reintroduction of new platelets highlighting the utility of the TPO ASO method to understand the role of platelets during chronic immune-driven pathologies.

The diverse microbial communities within our bodies produce metabolites that modulate host immune responses. Even the microbiome at distal sites has an important function in respiratory health. However, the clinical importance of the microbiome in tuberculosis, the biggest infectious cause of death worldwide, is only starting to be understood. Here, we critically review research on the microbiome's association with pulmonary tuberculosis. The research indicates five main points: (1) susceptibility to infection and progression to active tuberculosis is altered by gut Helicobacter co-infection, (2) aerosol Mycobacterium tuberculosis infection changes the gut microbiota, (3) oral anaerobes in the lung make metabolites that decrease pulmonary immunity and predict progression, (4) the increased susceptibility to reinfection of patients who have previously been treated for tuberculosis is likely due to the depletion of T-cell epitopes on commensal gut non-tuberculosis mycobacteria, and (5) the prolonged antibiotic treatment required for cure of tuberculosis has long-term detrimental effects on the microbiome. We highlight knowledge gaps, considerations for addressing these knowledge gaps, and describe potential targets for modifying the microbiome to control tuberculosis.

RATIONALE/BACKGROUND:Obstructive Sleep Apnea (OSA) is associated with recurrent obstruction, sub-epithelial edema, and airway inflammation. The resultant inflammation may influence or be influenced by the nasal microbiome. OBJECTIVES/OBJECTIVE:To evaluate whether the composition of the nasal microbiota is associated with obstructive sleep apnea and inflammatory biomarkers. METHODS:Two large cohorts were utilized: 1) a discovery cohort of 472 subjects from the WTCSNORE cohort; and 2) a validation cohort of 93 subjects from the Zaragoza Sleep cohort. Sleep apnea was diagnosed using home sleep tests. Nasal lavages were obtained from cohort subjects to measure: 1) microbiome composition (based on 16S rRNA gene sequencing); 2) biomarkers for inflammation (inflammatory cells, IL-8, and IL-6). Longitudinal 3 months samples were obtained in the validation cohort including post-CPAP treatment when indicated. RESULTS:In both cohorts, we identified that: 1) severity of OSA correlated with differences in microbiome diversity and composition; 2) the nasal microbiome of subjects with severe OSA were enriched with Streptococcus, Prevotella, and Veillonella; 3) the nasal microbiome differences were associated with inflammatory biomarkers. Network analysis identified clusters of co-occurring microbes that defined communities. Several common oral commensals (e.g., Streptococcus, Rothia, Veillonella, and Fusobacterium) correlated with apnea-hypopnea index. Three months of treatment with CPAP did not change the composition of the nasal microbiota. CONCLUSIONS:We demonstrate that the presence of an altered microbiome in severe OSA is associated with inflammatory markers. Further experimental approaches to explore causal links are needed.

Lung cancer remains the leading cause of cancer death worldwide1. With new treatment modalities, there has been a shift in focus to how we can predict who may respond to targeted treatments. Current data suggest that the human microbiome can affect lung cancer treatment through its effects on the systemic immune tone. Our group has shown that the lower airway microbiota of lung cancer patients is characterized by enrichment with oral commensals2 which triggers transcriptomic signatures (PI3K, MAPK) previously described in NSCLC 2,3. The impact of local lung dysbiosis on lung cancer progression and survival is unknown. Patients with suspicious nodules on imaging who underwent bronchoscopy were recruited. High-throughput sequencing of bacterial 16S rRNA-encoding gene amplicons was performed. Clustering was based on Dirichlet-Multinomial mixtures (DMM) modeling. RNAseq was performed on bronchial epithelial cells obtained by airway brushing. We focused our analysis on 83 NSCLC samples. Overall alpha-diversity showed that advanced stage (IIIb-VI) lower airway samples were more similar to buccal samples than local stage (I-IIIa), p<0.0001. In addition, worse 6-month and 1-year survival was associated with more similar alpha-diversity between lower airway and buccal samples (Figure 1A-D). Utilizing DMM two clusters were identified, Supraglottic-Predominant-Taxa (SPT) and Background-Predominant-Taxa (BPT). There was a significant increase in percentage of SPT in advance stage compared to local stage (p<0.008) Kaplan-Meir survival analysis shows worse survival in those with NSCLC who were clustered into the SPT group compared to BPT (p=0.0003, Figure 1E). With RNAseq, differentially expressed genes between advanced stage vs. local stage and 6-month vs. 1-year survival were not as pronounced as SPT vs. BPT (Figure 1F) suggesting that globally, transcriptomic changes between different stage and NSCLC survival were difficult to detect as compared to when airway microbiome were differentiated. In lung cancer, dysbiosis within the lower airway microenvironment, possibly by micro-aspiration, is associated with a worse 6-month and 1-year survival. This change is also associated with transcriptome changes in the local environment