Exposure to extracellular vesicles from Pseudomonas aeruginosa result in loss of DNA methylation at enhancer and DNase hypersensitive site regions in lung macrophages

Abstract

Various pathogens use differing strategies to evade host immune response including modulating the host’s epigenome. Here, we investigate if EVs secreted from P. aeruginosa alter DNA methylation in human lung macrophages, thereby potentially contributing to a dysfunctional innate immune response. Using a genome-wide DNA methylation approach, we demonstrate that P. aeruginosa EVs alter certain host cell DNA methylation patterns. We identified 1,185 differentially methylated CpGs (FDR < 0.05), which were significantly enriched for distal DNA regulatory elements including enhancer regions and DNase hypersensitive sites. Notably, all but one of the 1,185 differentially methylated CpGs were hypomethylated in association with EV exposure. Significantly hypomethylated CpGs tracked to genes including AXL, CFB and CCL23 . Gene expression analysis identified 310 genes exhibiting significantly altered expression 48 hours post P. aeruginosa EV treatment, with 75 different genes upregulated and 235 genes downregulated. Some CpGs associated with cytokines such as CSF3 displayed strong negative correlations between DNA methylation and gene expression. Our infection model illustrates how secreted products (EVs) from bacteria can alter DNA methylation of the host epigenome. Changes in DNA methylation in distal DNA regulatory regions in turn can modulate cellular gene expression and potential downstream cellular processes.

Bacterial Outer Membrane Vesicles and Immune Modulation of the Host

“…involved in the proinflammatory response to infection [83]. More research has shown that trained immunity can be induced by non-specific stimuli, such as exposure to microbial components like OMVs [22,23]. OMVs also play a significant role in suppressing the host immune response in CF, where chronic bacterial infections are established in a thick mucus layer in the lungs overlying epithelial cells, limiting direct contact of the invading pathogens with host lung epithelia [85].…”

Extracellular Vesicles of Pseudomonas: Friends and Foes

“…This seems to be the first description of trans-kingdom regulatory activity of an sRNA contained in EVs. Likewise, in a genome-wide DNA methylation study, Kyung Lee and colleagues reported that EVs from P. aeruginosa can alter human lung macrophage methylation patterns by producing differential CpG methylation [ 74 ] and that some of the CpG affected was associated with cytokines, such as CSF3 [ 74 ]. These results indicate that the role of bacterial EVs and their cargo is more complex than previously thought.…”

Outer membrane vesicles from bacteria: Role and potential value in the pathogenesis of chronic respiratory diseases

“…P. aeruginosa OMVs causes dysregulation of the appropriate immune response to infection in macrophages by altering DNA methylation in human lung macrophages ( Kyung Lee et al., 2021 ). Epigenetic modifications alter the pattern of gene expression and have been reported to be important during the innate immune response, regulating B-cell fate and function and controlling T-cell differentiation and memory responses ( Lau et al., 2018 ; Zhang and Cao, 2019 ; Zhang and Good-Jacobson, 2019 ).…”