Microbes associate with host innate immune response in idiopathic pulmonary fibrosis

The goal of this study is to explore molecular mechanisms underpinning the progression-associated host-microbial interactions in IPF. Multi-omics analysis revealed that the majority (8/11) of the progression-associated pathways were involved in inflammatory response and pattern recognition receptors (PRRs), including NOD-, TOLL- and RIG-I-like receptor pathways. Microbial community richness was correlated with all of the three PRRs (Pearson's p<0.007). The known IPF-progression marker Streptococcus (OTU1345) was correlated with NOD like receptor signaling pathway (p=0.047). Up-regulated genes in PBMCs of CpG-ODN responsive patients were over-represented in 22 canonical pathways (FDR<0.01). Network modeling revealed that 14/22 pathways were significantly correlated with community diversity (Shannon's index) and three genera (Otu1341 Prevotella, OTU1348 Staphylococcus, and OTU1302 Pseuodomonadacea), as well as 10/11 host gene co-expression modules. Toll-like receptor signaling pathway was mutually linked by CpG-response, Otu1341 and microbial Shannon's index. Notably, OTU1341 and IPF-progression marker OTU1348 were also correlated with TLR9 (r=0.48, p=3x10-5; r=0.38, p=0.002, respectively). These findings suggest that PRR and immune response signaling pathways play a central role in PFS-associated host-microbial interactions and the probifbrotic differentiation induced by CpG-ODN upon TLR9 stimulation. Sixty-eight COMET-IPF participants with matched PBMC microarray data and 16s rRNA sequencing data are included in this study. In addition, 32/68 patients have matched leukocyte phenotypes by flow cytometry. Lung fibroblasts derived from transbronchial biopsy of COMET-IPF patients (n=27) were cultured in vitro with growth media. Fibroblasts were treated for 24 hours with or without CpG-ODN (hypomethylated DNA; 10 M). A > 2 fold change in alpha smooth muscle actin expression (i.e. treated vs. untreated) was deemed CpG-ODN “responsive”. Therefore, 27/68 patients have CpG-ODN reponsive data. This series contains the gene expression data for the 68 PBMC samples from COMET-IPF participants.