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

References

• Kim JH, Lee J, Park J, et al. Gram-negative and gram-positive bacterial extracellular vesicles. In: Seminars in cell and developmental biology. Vol. 40. Elsevier; Amsterdam, Netherlands: 2015. p. 97–104.
   Google Scholar
• Ellis TN, Kuehn MJ. Virulence and immunomodulatory roles of bacterial outer membrane vesicles. Microbiol Mol Biol Rev. 2010 Mar 1; 74(1):81–94.
   Google Scholar
• Choi D-S, Kim D-K, Choi SJ, et al. Proteomic analysis of outer membrane vesicles derived from Pseudomonas aeruginosa. Proteomics. 2011;11(16):3424–3429. Aug.
   Google Scholar
• Ellis TN, Leiman SA, Kuehn MJ. Naturally produced outer membrane vesicles from Pseudomonas aeruginosa elicit a potent innate immune response via combined sensing of both lipopolysaccharide and protein components. Infect Immun. 2010;78(9):3822–3831. Sep.
   Google Scholar
• Park K-S, Lee J, Jang SC, et al. Pulmonary inflammation induced by bacteria-free outer membrane vesicles from pseudomonas aeruginosa. Am J Respir Cell Mol Biol. 2013;49(4):637–645. Oct.
   Google Scholar
• Lee JC, Lee EJ, Lee JH, et al. Klebsiella pneumoniae secretes outer membrane vesicles that induce the innate immune response. FEMS Microbiol Lett. 2012;331(1):17–24. Jun.
   Google Scholar
• McGuigan L, Callaghan M. The evolving dynamics of the microbial community in the cystic fibrosis lung. Environ Microbiol. 2015;17(1):16–28. Jan.
   Google Scholar
• Malhotra S, Hayes D, Wozniak DJ. Cystic fibrosis and pseudomonas aeruginosa: the host-microbe interface. In: Clinical microbiology reviews. Vol. 32. American Society for Microbiology;. Washington DC: Jo-Anne H. Young. 2019. e00138-18.
   Google Scholar
• Bomberger JM, MacEachran DP, Coutermarsh BA, et al. Long-distance delivery of bacterial virulence factors by pseudomonas aeruginosa outer membrane vesicles. Ausubel FM, editor. PLoS Pathog. 2009 Apr 10;5(4):e1000382.
   Google Scholar
• Koeppen K, Hampton TH, Jarek M, et al. A novel mechanism of host-pathogen interaction through srna in bacterial outer membrane vesicles. Whiteley M, editor. PLOS Pathog. 2016 Jun 13;12(6):e1005672.
   Google Scholar
• Renelli M, Matias V, Lo RY, et al. DNA-containing membrane vesicles of pseudomonas aeruginosa PAO1 and their genetic transformation potential. Microbiology. 2004;150(7):2161–2169.
   Google Scholar
• Wu CT, Morris JR. Genes, genetics, and epigenetics: A correspondence. Science. 2001;293:1103–1105.
   Google Scholar
• Marsit CJ, Brummel SS, Kacanek D, et al. Infant peripheral blood repetitive element hypomethylation associated with antiretroviral therapy in utero. Epigenetics. 2015 Jan 1 10;(8)708–716.
   Google Scholar
• Nishiyama R, Ito M, Yamaguchi Y, et al. A chloroplast-resident DNA methyltransferase is responsible for hypermethylation of chloroplast genes in chlamydomonas maternal gametes. Proc Natl Acad Sci U S A. 2002 Apr 30; 99(9):5925–5930.
   Google Scholar
• Feng S, Cokus SJ, Zhang X, et al. Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci U S A. 2010 May 11 107;(19)8689–8694.
   Google Scholar
• Moore LD, Le T, Fan G. DNA methylation and its basic function. Neuropsychopharmacol. 2013;38:23–38.
   Google Scholar
• Sharifi-Zarchi A, Gerovska D, Adachi K, et al. DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism. BMC Genomics. 2017 Dec 12;18(1). DOI:https://doi.org/10.1186/s12864-017-4353-7
   Google Scholar
• Charlet J, Duymich CE, Lay FD, et al. Bivalent regions of cytosine methylation and H3K27 acetylation suggest an active role for DNA methylation at enhancers. Mol Cell. 2016 May 5 62;(3)422–431.
   Google Scholar
• He Y, Carrillo JA, Luo J, et al. Genome-wide mapping of DNase I hypersensitive sites and association analysis with gene expression in MSB1 cells. Front Genet. 2014 Oct 13;5. DOI:https://doi.org/10.3389/fgene.2014.00308
   Google Scholar
• Sinclair SHG, Yegnasubramanian S, Dumler JS. Global DNA methylation changes and differential gene expression in Anaplasma phagocytophilum-infected human neutrophils. Clin Epigenetics. 2015 Dec 29; 7(1):77.
   Google Scholar
• Cizmeci D, Dempster EL, Champion OL, et al. Mapping epigenetic changes to the host cell genome induced by burkholderia pseudomallei reveals pathogen-specific and pathogen-generic signatures of infection. Sci Rep. 2016 Aug 3;6: DOI:https://doi.org/10.1038/srep30861
   Google Scholar
• Pacis A, Tailleux L, Morin AM, et al. Bacterial infection remodels the DNA methylation landscape of human dendritic cells. Genome Res. 2015 Dec 1 25;(12)1801–1811.
   Google Scholar
• Bessich JL, Nymon AB, Moulton LA, et al. Low levels of insulin-like growth Factor-1 contribute to alveolar macrophage dysfunction in cystic fibrosis. J Immunol. 2013 Jul 1; 191(1):378–385.
   Google Scholar
• Armstrong DA, Chen Y, Dessaint JA, et al. DNA methylation changes in regional lung macrophages are associated with metabolic differences. ImmunoHorizons. 2019 Jul 1 3;(7)274–281.
   Google Scholar
• Pritt B, O’brien L, Winn W. Mucoid Pseudomonas in cystic fibrosis. Am J Clin Pathol [Internet]. 2007 [cited 2020 Feb 7];128:32–34. Available from: https://academic.oup.com/ajcp/article-abstract/128/1/32/1759840
   Google Scholar
• McLean CY, Bristor D, Hiller M, et al. GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol. 2010;28(5):495–501. May.
   Google Scholar
• Brown GR, Hem V, Katz KS, et al. Gene: A gene-centered information resource at NCBI. Nucleic Acids Res. 2015 Jan 28 43;(D1)D36–42.
   Google Scholar
• Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012;13:484–492.
   Google Scholar
• Jjingo D, Conley AB, Yi SV, et al. On the presence and role of human gene-body DNA methylation. Oncotarget. 2012;3(4):462–474.
   Google Scholar
• Maunakea AK, Nagarajan RP, Bilenky M, et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8 466;(7303)253–257.
   Google Scholar
• Pacis A, Mailhot-Léonard F, Tailleux L, et al. Gene activation precedes DNA demethylation in response to infection in human dendritic cells. Proc Natl Acad Sci U S A. [2019 Apr 2];116(14):6938–6943.
   Google Scholar
• Liu T, Zhang L, Joo D, et al. NF-κB signaling in inflammation. Nat Publ Gr. 2017;2.
   Google Scholar
• Wen AY, Sakamoto KM, Miller LS. The role of the transcription factor CREB in immune function hhs public access. J Immunol. 2010;185(11):6413–6419.
   Google Scholar
• Marr AK, MacIsaac JL, Jiang R, et al. Leishmania donovani infection causes distinct epigenetic dna methylation changes in host macrophages. PLoS Pathog. 2014 Oct 1;10(10). https://doi.org/10.1371/journal.ppat.1004419
   Google Scholar
• Katakura F, Nishiya K, Wentzel AS, et al. Paralogs of common carp granulocyte colony-stimulating factor (G-CSF) have different functions regarding development, trafficking and activation of neutrophils. Front Immunol. 2019 Feb 19;10: DOI:https://doi.org/10.3389/fimmu.2019.00255
   Google Scholar
• Lemke G. How macrophages deal with death. Nat Rev Immunol. 2019 Sep 24; 19(9):539–549.
   Google Scholar
• Wong SS, Sun NN, Fastje CD, et al. Role of neprilysin in airway inflammation induced by diesel exhaust emissions. Res Rep Health Eff Inst. 2011 Jun;(159):3–40.
   Google Scholar
• Barilla-LaBarca ML, Liszewski MK, Lambris JD, et al. Role of membrane cofactor protein (CD46) in regulation of C4b and C3b deposited on cells. J Immunol. 2002 Jun 15; 168(12):6298–6304.
   Google Scholar
• Wang X, Zhang D, Sjölinder M, et al. CD46 accelerates macrophage-mediated host susceptibility to meningococcal sepsis in a murine model. Eur J Immunol. 2017 Jan;47(1):119–130.
   Google Scholar
• Chen Y, Armstrong DA, Salas LA, et al. Genome-wide DNA methylation profiling shows a distinct epigenetic signature associated with lung macrophages in cystic fibrosis. Clin Epigenetics. 2018 Dec 10 10;(1)152.
   Google Scholar
• Armstrong DA, Nymon AB, Ringelberg CS, et al. Pulmonary microRNA profiling: implications in upper lobe predominant lung disease. Clin Epigenetics. 2017 Dec 30 9;(1)56.
   Google Scholar
• Cecil JD, O’Brien-Simpson NM, Lenzo JC, et al.Outer membrane vesicles prime and activate macrophage inflammasomes and cytokine secretion in vitro and in vivo.Front Immunol.8: 2017 Aug 25
   Google Scholar
• Smith EE, Buckley DG, Wu Z, et al. Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients. Proc Natl Acad Sci U S A. 2006 May 30 103;(22)8487–8492.
   Google Scholar
• Hoffman LR, Richardson AR, Houston LS, et al. Nutrient availability as a mechanism for selection of antibiotic tolerant Pseudomonas aeruginosa within the CF airway. PLoS Pathog. 2010 Jan;6(1): DOI:https://doi.org/10.1371/journal.ppat.1000712
   Google Scholar
• Kling T, Wenger A, Beck S, et al. Validation of the methylationEPIC beadChip for fresh-frozen and formalin-fixed paraffin-embedded tumours. Clin Epigenetics. 2017 Apr 4;91. https://doi.org/10.1186/s13148-017-0333-7
   Google Scholar
• Aryee MJ, Jaffe AE, Corrada-Bravo H, et al. Minfi: A flexible and comprehensive bioconductor package for the analysis of infinium DNA methylation microarrays. Bioinformatics. [2014 May 15];30(10):1363–1369.
   Google Scholar
• Zhou W, Laird PW, Shen H. Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes. Nucleic Acids Res. 2017 Feb 28;45(4):e22.
   Google Scholar
• Xu Z, Niu L, Li L, et al. ENmix: a novel background correction method for Illumina HumanMethylation450 BeadChip. Nucleic Acids Res. 2015;44(3):20.
   Google Scholar
• Ritchie ME, Phipson B, Wu D, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015 Apr 20 43;(7)e47.
   Google Scholar
• Storey JD, Bass AJ, Dabney A, et al. qvalue: Q-value estimation for false discovery rate control. [Internet]. R Package. 2019;2(18.0): Available from: http://github.com/jdstorey/qvalue
   Google Scholar
• Zhu LJ, Gazin C, Lawson ND, et al. ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics. 2010 Dec 11 11;(1)237.
   Google Scholar
• Robinson MD, McCarthy DJ, Smyth GK. edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2009 Jan 1; 26(1):139–140.
   Google Scholar
• Wang J, Vasaikar S, Shi Z, et al., A more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit.Nucleic Acids Res. 2017 [2017 Jul 3];45(W1):W130–7.
   Google Scholar