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Review

Clinical epigenetics and multidrug-resistant bacterial infections: host remodelling in critical illness

ORCID Icon, ORCID Icon, , , ORCID Icon &
Pages 1021-1034 | Received 11 Jan 2020, Accepted 25 Mar 2020, Published online: 14 Apr 2020

References

  • Kollef MH, Bassetti M, Francois B, et al. The intensive care medicine research agenda on multidrug-resistant bacteria, antibiotics, and stewardship. Intensive Care Med. 2017;43:1187–1197.
  • Jasovský D, Littmann J, Zorzet A, et al. Antimicrobial resistance-a threat to the world’s sustainable development. Ups J Med Sci. 2016;121:159–164.
  • Magiorakos AP, Srinivasan A, Carey RB, et al. Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin Microbiol Infect. 2012;18:268–281.
  • Bassetti M, Poulakou G, Timsit JF. Focus on antimicrobial use in the era of increasing antimicrobial resistance in ICU. Intensive Care Med. 2016;42:955–958.
  • Blair JM, Webber MA, Baylay AJ, et al. Molecular mechanisms of antibiotic resistance. Nat Rev Microbiol. 2015;13:42–51.
  • Motta SS, Cluzel P, Aldana M. Adaptive resistance in bacteria requires epigenetic inheritance, genetic noise, and cost of efflux pumps. PLoS One. 2015;10:e0118464.
  • Cohen NR, Lobritz MA, Collins JJ. Microbial persistence and the road to drug resistance. Cell Host Microbe. 2013;13:632–642.
  • Kauffman SA. The epigenetic landscape and clinical implications. J Crit Care. 2011;26:e15.
  • Casadesús J, Low DA. Programmed heterogeneity: epigenetic mechanisms in bacteria. J Biol Chem. 2013;288:13929–13935.
  • Day T. Interpreting phenotypic antibiotic tolerance and persister cells as evolution via epigenetic inheritance. Mol Ecol. 2016;25:1869–1882.
  • Fernández L, Breidenstein EB, Hancock RE. Creeping baselines and adaptive resistance to antibiotics. Drug Resist Updat. 2011;14:1–21.
  • Netea MG, Joosten LA, Latz E, et al. Trained immunity: a program of innate immune memory in health and disease. Science. 2016;352:aaf1098.
  • Crimi E, Cirri S, Benincasa G, et al. Epigenetics mechanisms in multiorgan dysfunction syndrome. Anesth Analg. 2019;129:1422–1432. doi:10.1213/ANE.0000000000004331
  • van der Wijst MG, Venkiteswaran M, Chen H, et al. Local chromatin microenvironment determines DNMT activity: from DNA methyltransferase to DNA demethylase or DNA dehydroxymethylase. Epigenetics. 2015;10:671–676.
  • Greenberg MVC, Bourc’his D. The diverse roles of DNA methylation in mammalian development and disease. Nat Rev Mol Cell Biol. 2019;20:590–607.
  • Cedar H, Bergman Y. Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet. 2009;10:295–304.
  • Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012;13(7):484–492.
  • Fritz KS. Chemical acetylation and deacetylation. Methods Mol Biol. 2013;1077:191–201.
  • Taniguchi Y. BET Bromodomain as a target of epigenetic therapy. Chem Pharm Bull (Tokyo). 2016;64:540–547.
  • Seto E, Yoshida M. Erasers of histone acetylation: the histone deacetylase enzymes. Cold Spring Harb Perspect Biol. 2014;6:a018713.
  • Greer EL, Shi Y. Histone methylation: a dynamic mark in health, disease and inheritance. Nat Rev Genet. 2012;13:343–357.
  • Holoch D, Moazed D. RNA-mediated epigenetic regulation of gene expression. Nat Rev Genet. 2015;16:71–84.
  • Chan AO, Lam SK, Wong BC, et al. Promoter methylation of E-cadherin gene in gastric mucosa associated with Helicobacter pylori infection and in gastric cancer. Gut. 2003;52:502–506.
  • Bussiere FI, Michel V, Memet S, et al. H. pylori-induced promoter hypermethylation downregulates USF1 and USF2 transcription factor gene expression. Cell Microbiol. 2010;12:1124–1133.
  • Yan J, Zhang M, Zhang J, et al. Helicobacter pylori infection promotes methylation of WWOX gene in human gastric cancer. Biochem Biophys Res Commun. 2011;408:99–102.
  • Yao Y, Tao H, Park DI, et al. Demonstration and characterization of mutations induced by helicobacter pylori organisms in gastric epithelial cells. Helicobacter. 2006;11:272–286.
  • Ando T, Yoshida T, Enomoto S, et al. DNA methylation of microRNA genes in gastric mucosae of gastric cancer patients: its possible involvement in the formation of epigenetic field defect. Int J Cancer. 2009;124:2367–2374.
  • Tolg C, Sabha N, Cortese R, et al. Uropathogenic E. coli infection provokes epigenetic downregulation of CDKN2A (p16INK4A) in uroepithelial cells. Lab Invest. 2011;91:825–836.
  • Pacis A, Tailleux L, Morin AM, et al. Bacterial infection remodels the DNA methylation landscape of human dendritic cells. Genome Res. 2015;25:1801–1811.
  • Sharma G, Sowpati DT, Singh P, et al. Genome-wide non-CpG methylation of the host genome during M. tuberculosis infection. Sci Rep. 2016;6:25006.
  • Napoli C, Benincasa G. Loscalzo J epigenetic inheritance underlying pulmonary arterial hypertension. Arterioscler Thromb Vasc Biol. 2019;39:653–664. doi:10.1213/ANE.0000000000004331
  • Napoli C, Benincasa G, Schiano C, et al. Differential epigenetic factors in the prediction of cardiovascular risk in diabetic patients. Eur Heart J Cardiovasc Pharmacother. 2019. DOI:10.1093/ehjcvp/pvz062
  • de Nigris F, Cacciatore F, Mancini FP, et al. Epigenetic hallmarks of fetal early atherosclerotic lesions in humans. JAMA Cardiol. 2018;3:1184–1191. doi:10.1001/jamacardio.2018.3546
  • Napoli C, Crudele V, Soricelli A, et al. Primary prevention of atherosclerosis: a clinical challenge for the reversal of epigenetic mechanisms? Circulation. 2012;125:2363–2373. doi:10.1161/CIRCULATIONAHA.111.085787
  • Bobetsis YA, Barros SP, Lin DM, et al. Bacterial infection promotes DNA hypermethylation. J Dent Res. 2007;86:169–174.
  • Grabiec M, Potempa J. Epigenetic regulation in bacterial infections: targeting histone deacetylases. Crit Rev Microbiol. 2018;44:336–3350.
  • Bierne H, Hamon M, Cossart P. Epigenetics and bacterial infections. Cold Spring Harb Perspect Med. 2012;2:a010272.
  • Schmeck B, Beermann W, van Laak V, et al. Intracellular bacteria differentially regulated endothelial cytokine release by MAPK-dependent histone modification. J Immunol. 2005;175:2843–2850.
  • Bandyopadhaya A, Tsurumi A, Maura D, et al. A quorum-sensing signal promotes host tolerance training through HDAC1-mediated epigenetic reprogramming. Nat Microbiol. 2016;1:16174.
  • Descamps HC, Herrmann B, Wiredu D, et al. The path toward using microbial metabolites as therapies. EBioMedicine. 2019;44:747–754.
  • Saeed S, Quintin J, Kerstens HH, et al. Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity. Science. 2014;345:1251086.
  • Rolando M, Sanulli S, Rusniok C, et al. Legionella pneumophila effector RomA uniquely modifies host chromatin to repress gene expression and promote intracellular bacterial replication. Cell Host Microbe. 2013;13:395–405.
  • Qi Y, Cui L, Ge Y, et al. Altered serum microRNAs as biomarkers for the early diagnosis of pulmonary tuberculosis infection. BMC Infect Dis. 2012;12:384.
  • Cui JY, Liang HW, Pan XL, et al. Characterization of a novel panel of plasma microRNAs that discriminates between mycobacterium tuberculosis infection and healthy individuals. PLoS One. 2017;12:e0184113.
  • Alipoor SD, Tabarsi P, Varahram M, et al. Serum exosomal miRNAs are associated with active pulmonary tuberculosis. Dis Markers. 2019;2019:1907426.
  • Wang Y, Wang C. MicroRNA-211-3p has a role in the effects of lipopolysaccharide on endoplasmic reticulum stress in cultured human skin fibroblasts. Med Sci Monit Basic Res. 2019;25:164–168.
  • Yan H, Xu R, Zhang X, et al. Identifying differentially expressed long non-coding RNAs in PBMCs in response to the infection of multidrug-resistant tuberculosis. Infect Drug Resist. 2018;11:945–959.
  • Parmeciano Di Noto G, Molina MC, Quiroga C. Insights into non-coding RNAs as novel antimicrobial drugs. Front Genet. 2019;10:57.
  • Li W, Sun Z. Mechanism of action for HDAC inhibitors-insights from omics approaches. Int J Mol Sci. 2019;20:1616.
  • Fischer N, Sechet E, Friedman R, et al. Histone deacetylase inhibition enhances antimicrobial peptide but not inflammatory cytokine expression upon bacterial challenge. Proc Natl Acad Sci U S A. 2016;113:2993–3001.
  • Ariffin JK, Das Gupta K, Kapetanovic R, et al. Histone deacetylase inhibitors promote mitochondrial reactive oxygen species production and bacterial clearance by human macrophages. Antimicrob Agents Chemother. 2015;60:1521–1529.
  • Zhang T, Yu J, Zhang Y, et al. Salmonella enterica serovar enteritidis modulates intestinal epithelial miR-128 levels to decrease macrophage recruitment via macrophage colony-stimulating factor. J Infect Dis. 2014;209:2000–2011.
  • Vincent JL, Rello J, Marshall J, et al. International study of the prevalence and outcomes of infection in intensive care units. JAMA. 2009;302:2323–2329.
  • Zilahi G, Artigas A, Martin-Loeches I. What’s new in multidrug-resistant pathogens in the ICU? Ann Intensive Care. 2016;6:96.
  • Eichenberger EM, Thaden JT. Epidemiology and mechanisms of resistance of extensively drug resistant gram-negative bacteria. Antibiotics (Basel). 2019;8. DOI:10.3390/antibiotics8020037
  • Lioy VS, Goussard S, Guerineau V, et al. Aminoglycoside resistance 16S rRNA methyltransferases block endogenous methylation, affect translation efficiency and fitness of the host. RNA. 2014;20:382–391.
  • Liao J, Tsai C, Patel S, et al. Acetylome of Acinetobacter baumanni SK17 reveals a highly-conserved modification of histone-like protein HU. Front Mol Biosci. 2017;4:77.
  • Len O, Garzoni C, Lumbreras C, et al. Recommendations for screening of donor and recipient prior to solid organ transplantation and to minimize transmission of donor-derived infections. Clin Microbiol Infect. 2014;20:10–18.
  • Westphal GA, Garcia VD, Souza RL, et al. Guidelines for the assessment and acceptance of potential brain-dead organ donors. Rev Bras Ter Intensiva. 2016;28:220–255.
  • Grossi PA. Donor-derived infections, lessons learnt from the past, and what is the future going to bring us. Curr Opin Organ Transplant. 2018;23:417–422.
  • Fishman JA. Infection in organ transplantation. Am J Transplant. 2017;17:856.
  • Franci G, Folliero V, Cammarota M, et al. Epigenetic modulator UVI5008 inhibits MRSA by interfering with bacterial gyrase. Sci Rep. 2018;8:13117.
  • Choi SW, Braun T, Chang L, et al. Vorinostat plus tacrolimus and mycophenolate to prevent graft-versus-host disease after related-donor reduced-intensity conditioning allogeneic haemopoietic stem-cell transplantation: a phase 1/2 trial. Lancet Oncol. 2014;15:87–95.
  • Cole J, Morris P, Dickman MJ, et al. The therapeutic potential of epigenetic manipulation during infectious diseases. Pharmacol Ther. 2016;167:85–99.
  • Ostuni R, Piccolo V, Barozzi I, et al. Latent enhancers activated by stimulation in differentiated cells. Cell. 2013;152:157–171.
  • Quintin J, Saeed S, Martens JHA, et al. Candida albicans infection affords protection against reinfection via functional reprogramming of monocytes. Cell Host Microbe. 2012;12:223–232.
  • Glant TT, Besenyei T, Kádár A, et al. Differentially expressed epigenome modifiers, including aurora kinases A and B, in immune cells in rheumatoid arthritis in humans and mouse models. Arthritis Rheum. 2013;65:1725–1735.
  • Brasacchio D, Okabe J, Tikellis C, et al. Hyperglycemia induces a dynamic cooperativity of histone methylase and demethylase enzymes associated with gene-activating epigenetic marks that coexist on the lysine tail. Diabetes. 2009;58:1229–1236.
  • Kleinnijenhuis J, Quintin J, Preijers F, et al. Bacille Calmette-Guerin induces NOD2-dependent nonspecific protection from reinfection via epigenetic reprogramming of monocytes. Proc Natl Acad Sci U S A. 2012;109:17537–17542.
  • van Splunter M, van Osch TLJ, Brugman S, et al. Induction of trained innate immunity in human monocytes by bovine milk and milk-derived immunoglobulin G. Nutrients. 2018;10. DOI:10.3390/nu10101378
  • Benincasa G, Mansueto G, Napoli C. Fluid-based assays and precision medicine of cardiovascular diseases: the ‘hope’ for Pandora’s box? J Clin Pathol. 2019;72:785–799. doi:10.1136/jclinpath-2019-206178
  • Sommese L, Zullo A, Mancini FP, et al. Clinical relevance of epigenetics in the onset and management of type 2 diabetes mellitus. Epigenetics. 2017;12:401–415. doi:10.1080/15592294.2016.1278097
  • Benincasa G, Marfella R, Della Mura N, et al. Strengths and opportunities of network medicine in cardiovascular diseases. Circ J. 2020;84:144–152. doi:10.1253/circj.CJ-19-0879
  • Miryala SK, Ramaiah S. Exploring the multi-drug resistance in Escherichia coli O157: h7by gene interaction network: a systems biology approach. Genomics. 2019;111:958–965.

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