Faculty Bibliography

Background: Airway abnormalities, increased tissue citrullination and local inflammation are found in the lungs of early RA. Recent data suggest that the gut and oral microbiome might potentially contribute to the priming of aberrant systemic immune response in RA. Our objective was to study whether RA lung microbiome contains distinct taxonomic features associated with local and/or systemic autoimmunity. Materials: Bronchoalveolar lavage (BAL) from twenty RA, ten sarcoidosis and twenty-eight healthy individuals were obtained by research bronchoscopy. 16S rDNA sequencing was performed to define microbiota composition. Autoantibodies, including anti-CCP, RF and ACPAs were measured in sera of RA subjects. Results: The16S sequencing data showed similar alpha/beta diversity between RA and sarcoid groups, but significantly different from healthy. Taxonomic comparison between groups was performed using LEfSe, which revealed several significant differences. Multiple taxa, including Rhanella and Rhodanobacter were present only in the RA and sarcoid groups, but completely absent from healthy. While RA BAL samples were enriched with Sphingobacteria, sarcoidosis BAL was enriched with Bacteroidia, Rhizobiales, Nitrospirales, and Campylobacter. Raoultella and Barnesiella correlated with CCP2 levels in BAL. Serum levels of CCP-IgA had a negative correlation with Massilia and Tannerella, and a positive correlation with Vagococcus and Lactobacillus. Serum levels of anti-CCP2 antibodies had a positive correlation with Porphyromonas, Rahnella and Chryseobacterium. Conclusion: Despite the relatively small number of samples, several taxonomic differences were noted between groups. Further evaluation of functional aspects of this microbiome may provide insights into its possible contribution to RA

Background: Therapies targeting the inflammatory process revealed inconsistent results in Idiopathic Pulmonary Fibrosis (IPF). Aerosolized Interferon Gamma (IFN-y) has been proposed as a novel therapy. Additionally, changes in the host airway microbiome have been associated with inflammatory tone and, in IPF, may be associated with disease progression.We evaluate whether treatment with aerosolized IFN-y impacts the lower airway microbiome or host immune phenotype. Methods: Patients with IPF were enrolled in an aerosolized IFNy trial. Patients underwent a bronchoscopy at baseline and after 6 months. 16S rRNA sequencing of BAL samples were used to evaluate the lower airway microbiome. Cytokines were measured by Luminex on plasma, BAL fluid and BAL cell supernatant. Findings: IFN-y treatment did not change alpha or beta diversity of the lung microbiome and few taxonomic changes in low abundant taxa occurred (Figure 1). The measured cytokines were unchanged in plasma, however, there was an increase in IFN-y and a decrease in Fit 3 Ligand, IFN-A2 and IL- 5 in BAL cell supernatant, and TNF-B in BAL. Multiple correlations between taxa and inflammatory cytokines were found. Network analysis showed correlations were more abundant between lung microbial taxa and local inflammatory cytokines (either in BAL or by ex vivo BAL cell production) than between lung microbial taxa and systemic inflammatory cytokines. Importantly, analysis showed persistent of these association post IFN treatment. Interpretation: This data suggests that the lower airway microbiome has an independent effect on host immune tone and thus may provide a novel therapeutic target for treatment of IPF

Background: Airway abnormalities and increased lung tissue citrullination is found in both RA patients and individuals at at-risk for the development of disease. Recent data suggest that the gut (Prevotella copri) and oral (Porphyromonas gingivalis) microbiome might potentially contribute to the priming of an aberrant systemic immune response characteristic of RA. Objectives: Our objective was to study whether RA lung microbiome contains distinct taxonomic features associated with local and/or systemic autoimmunity. Methods: Bronchoalveolar lavage (BAL) samples from 20 subjects with RA, 10 with sarcoidosis and 28 healthy controls were obtained by research bronchoscopy. 16S rRNA sequencing was performed to define microbiota composition. Autoantibodies, including anti-CCP, RF and ACPAs were also measured in sera of RA subjects. Results: The 16s sequencing data showed similar alpha/beta diversity between RA and sarcoid groups, but significantly different from healthy (ANOSIM test; p=0.002 and 0.021 for healthy vs RA and healthy vs sarcoid, respectively). Taxonomic comparison between groups was performed using LEfSe, which revealed several significant differences. RA BALF samples had a decrease in the families Actinomycetaceae (P<0.0001) and Spirochaetaceae (P=0.0009) compared to healthy. Burkholderia was significantly decreased in both RA and sarcoidosis compared to controls. The genus Treponema (also highly associated with periodontitis) was exclusively found in healthy subjects' BALF (P<0.01 vs RA). RA disease activity was positively correlated with Micrococcus and Renibaterium at the genus level, and with various OTUs belonging to Pseudonocardia and Xanthomonadaceae whereas, the genus Veillonella and unclassified Oxalobacteraceae had a negative correlation. Levels of local autoantibodies i.e., anti-CCP2 correlated positively with the genus Corynebacterium, Megasphera and unclassified Comamonadaceae. Circulating anti-CCP (IgA isotype), had a positive significant correlation with relative abundance of BALF Enhydrobacter and unclassified Bradyrhizobiaceae (P=0.015 and 0.004, respectively). A modest association with erosive disease was observed with the presence and abundance of Pseudonocardia in the RA BALF (85% of erosive RA patients vs. 23% of non-erosive RA; P=0.019). Conclusions: Despite the relatively small number of samples analyzed, several taxonomic differences were noted between groups. Correlations between relative abundance of specific taxa in RA BAL with serum autoantibodies (i.e., anti-CCP) support an association between the lung microbiome and the host immune phenotype in RA. Further evaluation of the functional aspects of this microbiome may provide insights into its possible contribution to RA

Microaspiration is a common phenomenon in healthy subjects, but its frequency is increased in chronic inflammatory airway diseases, and its role in inflammatory and immune phenotypes is unclear. We have previously demonstrated that acellular bronchoalveolar lavage samples from half of the healthy people examined are enriched with oral taxa (here called pneumotypeSPT) and this finding is associated with increased numbers of lymphocytes and neutrophils in bronchoalveolar lavage. Here, we have characterized the inflammatory phenotype using a multi-omic approach. By evaluating both upper airway and acellular bronchoalveolar lavage samples from 49 subjects from three cohorts without known pulmonary disease, we observed that pneumotypeSPT was associated with a distinct metabolic profile, enhanced expression of inflammatory cytokines, a pro-inflammatory phenotype characterized by elevated Th-17 lymphocytes and, conversely, a blunted alveolar macrophage TLR4 response. The cellular immune responses observed in the lower airways of humans with pneumotypeSPT indicate a role for the aspiration-derived microbiota in regulating the basal inflammatory status at the pulmonary mucosal surface.

Background and objectives Airway abnormalities and increased lung tissue citrullination is found in both RA patients and individuals at at-risk for the development of disease. Recent data suggest that the gut (Prevotella copri) and oral (Porphyromonas gingivalis) microbiome might potentially contribute to the priming of an aberrant systemic immune response characteristic of RA. Our objective was to study whether the RA lung microbiome contains distinct taxonomic features associated with local and/or systemic autoimmunity. Materials and methods Bronchoalveolar lavage (BAL) samples from 20 subjects with RA, 10 with sarcoidosis (DC) and 24 healthy controls (HC) were obtained by research bronchoscopy. 16S rDNA sequencing was performed to define microbiota composition. Autoantibodies, including anti-CCP, RF and ACPAs were also measured in sera of RA subjects. Statistical analysis was performed using wilcoxon test and Spearman correlation. Results The16S sequencing data showed similar alpha/beta diversity between RA and DC groups, but significantly different from HC. Taxonomic comparison between groups was performed using LEfSe, which revealed several significant differences (LDA score>2). Multiple taxa, including Rhanella and Rhodanobacter were present only in the RA and DC groups, but completely absent from HC (p < 0.001). While RA BAL samples were enriched with Sphingobacteria, sarcoidosis BAL was enriched with Bacteroidia, Rhizobiales, Nitrospirales, and Campylobacter. Raoultella and Barnesiella correlated with CCP2 levels in BAL (rho = 0.49 and 0.47; p-value = 0.026 and 0.032). Serum levels of CCP-IgA had a negative correlation with Massilia and Tannerella (rho = -0.63 and 0.53; p-value 0.003 and 0.016), and a positive correlation with Vagococcus and Lactobacillus (rho= 0.59 and 0.54; p-value 0.006 and 0.014). Unclas-Lactobacillales also had a positive correlation with serum levels of RF-IgA (rho = 0.71; p-value <0.001). Serum levels of anti-CCP2 antibodies had a positive correlation with Porphyromonas, Rahnella and Chryseobacterium (rho =0.46, 0.46 and 0.45; p-value = 0.03, 0.03 and 0.04). Conclusions Despite the relatively small number of samples analysed, several taxonomic differences were noted between groups. Correlations between relative abundance of specific taxa in RA BAL with serum autoantibodies (ie, anti-CCP) support an association between the lung microbiome and the host immune phenotype in RA. Further evaluation of functional aspects of this microbiome may provide further insights into its possible contribution to RA