{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T22:08:13Z","timestamp":1789682893350,"version":"4.0.1"},"reference-count":107,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,6,5]],"date-time":"2026-06-05T00:00:00Z","timestamp":1780617600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003336","name":"Bulgarian National Science Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003336","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Immunol."],"abstract":"<jats:p>\n                    Gram-negative bacteria are clinically significant pathogens responsible for life-threatening infections, including respiratory infections. These can be acute or persistent and can exacerbate existing chronic diseases, such as cystic fibrosis, COPD and lung cancer. In this review, we use\n                    <jats:italic>Pseudomonas aeruginosa<\/jats:italic>\n                    as a model organism that demonstrates the molecular complexity of host-pathogen interactions during lower airway infection. Specifically, we focus on RNA modifications and show that they, on the one hand, regulate bacterial fitness and pathogenicity, and on the other control the execution of an effective host innate immune response. Furthermore, we examine the role of epigenetic and epitranscriptomic modifications in the immune dysregulation observed in sepsis, with an emphasis on sepsis-induced lung injury. Innate immune memory -\u00a0a cellular adaptation mechanism to primary microbial stimulation - results in training or tolerization of host cells towards secondary immune challenges. While fundamentally grounded in epigenetic and metabolic reprogramming, we propose that it can crosstalk with epitranscriptomic regulation. To overcome limitations imposed by animal models when investigating microbe-induced epitranscriptomic dynamics, we highlight physiologically-relevant\n                    <jats:italic>in vitro<\/jats:italic>\n                    tissue models that can complement work performed\n                    <jats:italic>in vivo<\/jats:italic>\n                    . Ultimately, a detailed understanding of the RNA modification landscape regulating host-pathogen interactions will help us identify new therapeutic targets and molecular pathways to better manage the clinical symptoms of bacterial respiratory infections and address the growing challenge of antimicrobial resistance.\n                  <\/jats:p>","DOI":"10.3389\/fimmu.2026.1845134","type":"journal-article","created":{"date-parts":[[2026,6,5]],"date-time":"2026-06-05T05:05:21Z","timestamp":1780635921000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["RNA modifications shape innate immunity and cellular adaptation during bacterial respiratory infection"],"prefix":"10.3389","volume":"17","author":[{"given":"Martina M.","family":"Ivanova","sequence":"first","affiliation":[{"name":"Department of Immunology, Laboratory of Experimental Immunotherapy, Stephan Angeloff Institute of Microbiology","place":["Sofia, Bulgaria"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Petya A.","family":"Dimitrova","sequence":"additional","affiliation":[{"name":"Department of Immunology, Laboratory of Experimental Immunotherapy, Stephan Angeloff Institute of Microbiology","place":["Sofia, Bulgaria"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Milena N.","family":"Leseva","sequence":"additional","affiliation":[{"name":"Department of Immunology, Laboratory of Experimental Immunotherapy, Stephan Angeloff Institute of Microbiology","place":["Sofia, Bulgaria"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,6,5]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.2139\/ssrn.6712818","article-title":"Global burden of bacterial antimicrobial resistance 1990-2021: a systematic analysis with forecasts to 2050","volume":"404","year":"2024","journal-title":"Lancet"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaf1284","article-title":"MODOMICS: a database of RNA modifications and related information. 2025 update and 20th anniversary","volume":"54","author":"Sordyl","year":"2026","journal-title":"Nucleic Acids Res"},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.1016\/s1473-3099(25)00118-5","article-title":"The WHO Bacterial Priority Pathogens List 2024: a prioritisation study to guide research, development, and public health strategies against antimicrobial resistance","volume":"25","author":"Sati","year":"2025","journal-title":"Lancet Infect Dis"},{"key":"B4","article-title":"Cystic Fibrosis Foundation Patient Registry. 2024 Annual Data Report","year":"2025"},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.1007\/s40265-021-01635-6","article-title":"The epidemiology and pathogenesis and treatment of Pseudomonas aeruginosa infections: an update","volume":"81","author":"Reynolds","year":"2021","journal-title":"Drugs"},{"key":"B6","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1186\/s12879-025-12272-9","article-title":"Pathogenic mechanisms and resistance profiles of microbial pulmonary infections in lung cancer: a systematic review","volume":"26","author":"Sheervalilou","year":"2025","journal-title":"BMC Infect Dis"},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.1158\/0008-5472.can-20-1994","article-title":"Lipopolysaccharide-mediated chronic inflammation promotes tobacco carcinogen-induced lung cancer and determines the efficacy of immunotherapy","volume":"81","author":"Liu","year":"2021","journal-title":"Cancer Res"},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms13040913","article-title":"Antibiotic-resistant Pseudomonas aeruginosa: current challenges and emerging alternative therapies","volume":"13","author":"Hu","year":"2025","journal-title":"Microorganisms"},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.1126\/science.abi4882","article-title":"Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution","volume":"373","author":"Dar","year":"2021","journal-title":"Science"},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.1016\/j.cyto.2023.156135","article-title":"Immune escape strategies of Pseudomonas aeruginosa to establish chronic infection","volume":"163","author":"Marzhoseyni","year":"2023","journal-title":"Cytokine"},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2020.01722","article-title":"Pulmonary innate immune response determines the outcome of inflammation during pneumonia and sepsis-associated acute lung injury","volume":"11","author":"Kumar","year":"2020","journal-title":"Front Immunol"},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2025.1730702","article-title":"Editorial: Emerging mechanisms of host-pathogen interactions and immune responses","volume":"15","author":"Hussain","year":"2025","journal-title":"Front Cell Infect Microbiol"},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2023.1249098","article-title":"Role of toll-like receptors and nod-like receptors in acute lung infection","volume":"14","author":"Le","year":"2023","journal-title":"Front Immunol"},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.1152\/ajplung.00303.2020","article-title":"Inflammasome activation in acute lung injury","volume":"320","author":"McVey","year":"2021","journal-title":"Am J Physiol Lung Cell Mol Physiol"},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-immunol-101721-031732","article-title":"Effector-triggered immunity","volume":"41","author":"Remick","year":"2023","journal-title":"Annu Rev Immunol"},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.1016\/j.it.2022.10.004","article-title":"Effector-triggered immunity in mammalian antiviral defense","volume":"43","author":"Orzalli","year":"2022","journal-title":"Trends Immunol"},{"key":"B17","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1016\/j.chom.2009.06.007","article-title":"Patterns of pathogenesis: discrimination of pathogenic and nonpathogenic microbes by the innate immune system","volume":"6","author":"Vance","year":"2009","journal-title":"Cell Host Microbe"},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.1002\/iub.2041","article-title":"To be or not to be modified: miscellaneous aspects influencing nucleotide modifications in tRNAs","volume":"71","author":"Barraud","year":"2019","journal-title":"IUBMB Life"},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1038\/s41580-021-00342-0","article-title":"The expanding world of tRNA modifications and their disease relevance","volume":"22","author":"Suzuki","year":"2021","journal-title":"Nat Rev Mol Cell Biol"},{"key":"B20","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1011027","article-title":"tRNA modification enzyme MiaB connects environmental cues to activation of Pseudomonas aeruginosa type III secretion system","volume":"18","author":"Lin","year":"2022","journal-title":"PloS Pathog"},{"key":"B21","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2025.169020","article-title":"5-Methyluridine is ubiquitous in Pseudomonas aeruginosa tRNA and modulates antimicrobial resistance and virulence","volume":"437","author":"Chittrakanwong","year":"2025","journal-title":"J Mol Biol"},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.1079710","article-title":"Pseudomonas aeruginosa GidA modulates the expression of catalases at the posttranscriptional level and plays a role in virulence","volume":"13","author":"Srimahaeak","year":"2022","journal-title":"Front Microbiol"},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2312874121","article-title":"tRNA epitranscriptome determines pathogenicity of the opportunistic pathogen Pseudomonas aeruginosa","volume":"121","author":"Krueger","year":"2024","journal-title":"Proc Natl Acad Sci USA"},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2015.05.022","article-title":"Optimization of codon translation rates via tRNA modifications maintains proteome integrity","volume":"161","author":"Nedialkova","year":"2015","journal-title":"Cell"},{"key":"B25","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaf719","article-title":"tRNA hydroxylation is an epitranscriptomic modulator of metabolic states affecting Pseudomonas aeruginosa pathogenicity","volume":"53","author":"Frommeyer","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz702","article-title":"TrmB, a tRNA m7G46 methyltransferase, plays a role in hydrogen peroxide resistance and positively modulates the translation of katA and katB mRNAs in Pseudomonas aeruginosa","volume":"47","author":"Thongdee","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.1261\/rna.080004.124","article-title":"The modification landscape of Pseudomonas aeruginosa tRNAs","volume":"30","author":"Mandler","year":"2024","journal-title":"RNA"},{"key":"B28","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaf696","article-title":"tRNA modification profiling reveals epitranscriptome regulatory networks in Pseudomonas aeruginosa","volume":"53","author":"Sun","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"B29","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0511100103","article-title":"An ordered, nonredundant library of Pseudomonas aeruginosa strain PA14 transposon insertion mutants","volume":"103","author":"Liberati","year":"2006","journal-title":"Proc Natl Acad Sci USA"},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2025.115878","article-title":"Extensive natural variation in bacterial ribosomal drug-binding sites","volume":"44","author":"Ekemezie","year":"2025","journal-title":"Cell Rep"},{"key":"B31","doi-asserted-by":"publisher","first-page":"26484","DOI":"10.1038\/s41598-024-78296-4","article-title":"16S rRNA methyltransferase KsgA contributes to oxidative stress and antibiotic resistance in Pseudomonas aeruginosa","volume":"14","author":"Phatinuwat","year":"2024","journal-title":"Sci Rep"},{"key":"B32","doi-asserted-by":"publisher","DOI":"10.1016\/j.vaccine.2024.126476","article-title":"Pseudomonas aeruginosa elongation factor-Tu (EF-Tu) is an immunogenic protective protein antigen","volume":"42","author":"Moustafa","year":"2024","journal-title":"Vaccine"},{"key":"B33","doi-asserted-by":"publisher","DOI":"10.1021\/acsinfecdis.5c00297","article-title":"Discovery of first-in-class inhibitors targeting a pathogen-associated aminoglycoside-resistance 16S rRNA methyltransferase","volume":"11","author":"Dey","year":"2025","journal-title":"ACS Infect Dis"},{"key":"B34","doi-asserted-by":"publisher","first-page":"3484","DOI":"10.1016\/j.molcel.2022.08.015","article-title":"An ADP-ribosyltransferase toxin kills bacterial cells by modifying structured non-coding RNAs","volume":"82","author":"Bullen","year":"2022","journal-title":"Mol Cell"},{"key":"B35","doi-asserted-by":"publisher","DOI":"10.3390\/biom13071060","article-title":"Infection meets inflammation: N6-methyladenosine, an internal messenger RNA modification as a tool for pharmacological regulation of host-pathogen interactions","volume":"13","author":"Leseva","year":"2023","journal-title":"Biomolecules"},{"key":"B36","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1016\/j.stem.2017.11.016","article-title":"METTL14 inhibits hematopoietic stem\/progenitor differentiation and promotes leukemogenesis via mRNA m6A modification","volume":"22","author":"Weng","year":"2018","journal-title":"Cell Stem Cell"},{"key":"B37","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2023.112259","article-title":"METTL3-mediated m6A mRNA methylation regulates neutrophil activation through targeting TLR4 signaling","volume":"42","author":"Luo","year":"2023","journal-title":"Cell Rep"},{"key":"B38","doi-asserted-by":"publisher","first-page":"1898","DOI":"10.1038\/s41467-019-09903-6","article-title":"Mettl3-mediated mRNA m 6 A methylation promotes dendritic cell activation","volume":"10","author":"Wang","year":"2019","journal-title":"Nat Commun"},{"key":"B39","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abd4742","article-title":"Pooled CRISPR screening identifies m 6 A as a positive regulator of macrophage activation","volume":"7","author":"Tong","year":"2021","journal-title":"Sci Adv"},{"key":"B40","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1038\/s41419-023-06407-6","article-title":"METTL14 contributes to acute lung injury by stabilizing NLRP3 expression in an IGF2BP2-dependent manner","volume":"15","author":"Cao","year":"2024","journal-title":"Cell Death Dis"},{"key":"B41","doi-asserted-by":"publisher","DOI":"10.1001\/jama.2016.0287","article-title":"The third international consensus definitions for sepsis and septic shock (Sepsis-3)","volume":"315","author":"Singer","year":"2016","journal-title":"JAMA"},{"key":"B42","doi-asserted-by":"publisher","first-page":"596","DOI":"10.1038\/s41577-024-00998-7","article-title":"Made to order: emergency myelopoiesis and demand-adapted innate immune cell production","volume":"24","author":"Swann","year":"2024","journal-title":"Nat Rev Immunol"},{"key":"B43","doi-asserted-by":"publisher","DOI":"10.1097\/ccm.0b013e3181692c0b","article-title":"Gene-expression profiling of gram-positive and gram-negative sepsis in critically ill patients","volume":"36","author":"Tang","year":"2008","journal-title":"Crit Care Med"},{"key":"B44","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1038\/s41423-023-01115-9","article-title":"The RNA m6A demethylase ALKBH5 drives emergency granulopoiesis and neutrophil mobilization by up-regulating G-CSFR expression","volume":"21","author":"Liu","year":"2024","journal-title":"Cell Mol Immunol"},{"key":"B45","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-019-1678-1","article-title":"Metabolic regulation of gene expression by histone lactylation","volume":"574","author":"Zhang","year":"2019","journal-title":"Nature"},{"key":"B46","doi-asserted-by":"publisher","DOI":"10.1007\/s40121-025-01232-0","article-title":"The roles of histone H3K18 lactylation, acetylation, and lactylation\/acetylation ratio as potential biomarkers in the diagnosis and severity assessment of sepsis and septic shock","volume":"14","author":"Di","year":"2025","journal-title":"Infect Dis Ther"},{"key":"B47","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.201201-0134oc","article-title":"Interleukin 5 is protective during sepsis in an eosinophil-independent manner","volume":"186","author":"Linch","year":"2012","journal-title":"Am J Respir Crit Care Med"},{"key":"B48","doi-asserted-by":"publisher","first-page":"1660","DOI":"10.1016\/j.molcel.2022.02.033","article-title":"Lactylation-driven METTL3-mediated RNA m6A modification promotes immunosuppression of tumour-infiltrating myeloid cells","volume":"82","author":"Xiong","year":"2022","journal-title":"Mol Cell"},{"key":"B49","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2409132121","article-title":"Lactylation of RNA m6A demethylase ALKBH5 promotes innate immune response to DNA herpesviruses and mpox virus","volume":"121","author":"Li","year":"2024","journal-title":"Proc Natl Acad Sci USA"},{"key":"B50","doi-asserted-by":"publisher","DOI":"10.1016\/j.redox.2024.103194","article-title":"Histone lactylation-regulated METTL3 promotes ferroptosis via m6A-modification on ACSL4 in sepsis-associated lung injury","volume":"74","author":"Wu","year":"2024","journal-title":"Redox Biol"},{"key":"B51","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2022.897487","article-title":"METTL3-mediated N6-methyladenosine modification of Trim59 mRNA protects against sepsis-induced acute respiratory distress syndrome","volume":"13","author":"Chen","year":"2022","journal-title":"Front Immunol"},{"key":"B52","doi-asserted-by":"publisher","DOI":"10.3389\/fcell.2025.1682283","article-title":"Research advances in m6A methylation and sepsis","volume":"13","author":"Zhang","year":"2025","journal-title":"Front Cell Dev Biol"},{"key":"B53","doi-asserted-by":"publisher","DOI":"10.1016\/j.micpath.2025.107364","article-title":"NAT10 induces mitochondrial dysfunction in lung epithelial cells by acetylating HMGB1 to exacerbate Pseudomonas aeruginosa-induced acute lung injury","volume":"200","author":"Huang","year":"2025","journal-title":"Microb Pathog"},{"key":"B54","doi-asserted-by":"publisher","first-page":"1872","DOI":"10.1016\/j.cell.2018.10.030","article-title":"Acetylation of cytidine in mRNA promotes translation efficiency","volume":"175","author":"Arango","year":"2018","journal-title":"Cell"},{"key":"B55","doi-asserted-by":"publisher","first-page":"916","DOI":"10.1038\/s42003-022-03868-x","article-title":"NAT10 regulates neutrophil pyroptosis in sepsis via acetylating ULK1 RNA and activating STING pathway","volume":"5","author":"Zhang","year":"2022","journal-title":"Commun Biol"},{"key":"B56","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1186\/s10020-024-00912-w","article-title":"NAT10-mediated ac4C acetylation of TFRC promotes sepsis-induced pulmonary injury through regulating ferroptosis","volume":"30","author":"Xing","year":"2024","journal-title":"Mol Med"},{"key":"B57","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2013.09.049","article-title":"Cyclic dinucleotides trigger ULK1 (ATG1) phosphorylation of STING to prevent sustained innate immune signaling","volume":"155","author":"Konno","year":"2013","journal-title":"Cell"},{"key":"B58","doi-asserted-by":"publisher","first-page":"2912","DOI":"10.1016\/j.molcel.2022.05.016","article-title":"Direct epitranscriptomic regulation of mammalian translation initiation through N4-acetylcytidine","volume":"82","author":"Arango","year":"2022","journal-title":"Mol Cell"},{"key":"B59","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3000411","article-title":"Reporting animal research: Explanation and elaboration for the ARRIVE guidelines 2.0","volume":"18","author":"Percie du Sert","year":"2020","journal-title":"PloS Biol"},{"key":"B60","doi-asserted-by":"publisher","DOI":"10.1111\/mmi.14817","article-title":"Precision-cut lung slices: A powerful ex vivo model to investigate respiratory infectious diseases","volume":"117","author":"Viana","year":"2022","journal-title":"Mol Microbiol"},{"key":"B61","doi-asserted-by":"publisher","DOI":"10.1183\/13993003.01530-2025","article-title":"Label-free four-dimensional live imaging of immune-stromal interactions in human alveolar tissue using higher harmonic generation microscopy","volume":"66","author":"Ma","year":"2025","journal-title":"Eur Respir J"},{"key":"B62","doi-asserted-by":"publisher","DOI":"10.1152\/ajplung.00401.2020","article-title":"Isolation of high-yield and -quality RNA from human precision-cut lung slices for RNA-sequencing and computational integration with larger patient cohorts","volume":"320","author":"Stegmayr","year":"2021","journal-title":"Am J Physiol Lung Cell Mol Physiol"},{"key":"B63","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2020.598636","article-title":"Early cytokine induction upon Pseudomonas aeruginosa infection in murine precision cut lung slices depends on sensing of bacterial viability","volume":"11","author":"Kolbe","year":"2020","journal-title":"Front Immunol"},{"key":"B64","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1186\/s12931-023-02609-w","article-title":"Age-dependent inflammatory response is altered in an ex vivo model of bacterial pneumonia","volume":"25","author":"Sommer","year":"2024","journal-title":"Respir Res"},{"key":"B65","doi-asserted-by":"publisher","DOI":"10.1152\/physiol.00012.2022","article-title":"What can an organ-on-a-chip teach us about human lung pathophysiology","volume":"37","author":"Bai","year":"2022","journal-title":"Physiol (Bethesda)"},{"key":"B66","doi-asserted-by":"publisher","DOI":"10.1038\/s41551-025-01491-9","article-title":"An immune-competent lung-on-a-chip for modelling the human severe influenza infection response","author":"Ringquist","year":"2025","journal-title":"Nat BioMed Eng"},{"key":"B67","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcf.2021.10.004","article-title":"Modeling pulmonary cystic fibrosis in a human lung airway-on-a-chip","volume":"21","author":"Plebani","year":"2022","journal-title":"J Cyst Fibros"},{"key":"B68","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2025.1592597","article-title":"Revealing the impact of Pseudomonas aeruginosa quorum sensing molecule 2'-aminoacetophenone on the human bronchial-airway epithelium and pulmonary endothelium using a human airway-on-a-chip","volume":"16","author":"Aggarwal","year":"2025","journal-title":"Front Immunol"},{"key":"B69","doi-asserted-by":"publisher","first-page":"16174","DOI":"10.1038\/nmicrobiol.2016.174","article-title":"A quorum-sensing signal promotes host tolerance training through HDAC1-mediated epigenetic reprogramming","volume":"1","author":"Bandyopadhaya","year":"2016","journal-title":"Nat Microbiol"},{"key":"B70","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.00159-23","article-title":"Quorum-sensing signaling molecule 2-aminoacetophenone mediates the persistence of Pseudomonas aeruginosa in macrophages by interference with autophagy through epigenetic regulation of lipid biosynthesis","volume":"14","author":"Chakraborty","year":"2023","journal-title":"mBio"},{"key":"B71","doi-asserted-by":"publisher","DOI":"10.7554\/elife.97568.3","article-title":"The bacterial quorum sensing signal 2'-aminoacetophenone rewires immune cell bioenergetics through the Ppargc1a\/Esrra axis to mediate tolerance to infection","volume":"13","author":"Chakraborty","year":"2024","journal-title":"Elife"},{"key":"B72","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3002209","article-title":"Pseudomonas aeruginosa type IV pili actively induce mucus contraction to form biofilms in tissue-engineered human airways","volume":"21","author":"Rossy","year":"2023","journal-title":"PloS Biol"},{"key":"B73","doi-asserted-by":"publisher","DOI":"10.1101\/318444","article-title":"Long-term expanding human airway organoids for disease modeling","volume":"38","author":"Sachs","year":"2019","journal-title":"EMBO J"},{"key":"B74","doi-asserted-by":"publisher","DOI":"10.26508\/lsa.202101320","article-title":"Measuring cystic fibrosis drug responses in organoids derived from 2D differentiated nasal epithelia","volume":"5","author":"Amatngalim","year":"2022","journal-title":"Life Sci Alliance"},{"key":"B75","doi-asserted-by":"publisher","DOI":"10.1016\/j.xpro.2023.102337","article-title":"Protocol for generating airway organoids from 2D air liquid interface-differentiated nasal epithelia for use in a functional CFTR assay","volume":"4","author":"Rodenburg","year":"2023","journal-title":"STAR Protoc"},{"key":"B76","doi-asserted-by":"publisher","first-page":"1170","DOI":"10.1016\/j.stem.2025.05.013","article-title":"Human airway submucosal gland organoids to study respiratory inflammation and infection","volume":"32","author":"Lin","year":"2025","journal-title":"Cell Stem Cell"},{"key":"B77","doi-asserted-by":"publisher","first-page":"779","DOI":"10.1016\/j.stem.2018.04.007","article-title":"Submucosal gland myoepithelial cells are reserve stem cells that can regenerate mouse tracheal epithelium","volume":"22","author":"Lynch","year":"2018","journal-title":"Cell Stem Cell"},{"key":"B78","doi-asserted-by":"publisher","first-page":"668","DOI":"10.1016\/j.stem.2018.03.018","article-title":"Myoepithelial cells of submucosal glands can function as reserve stem cells to regenerate airways after injury","volume":"22","author":"Tata","year":"2018","journal-title":"Cell Stem Cell"},{"key":"B79","doi-asserted-by":"publisher","first-page":"2222","DOI":"10.1038\/s41598-024-82500-w","article-title":"Dual RNA sequencing of a co-culture model of Pseudomonas aeruginosa and human 2D upper airway organoids","volume":"15","author":"Pleguezuelos-Manzano","year":"2025","journal-title":"Sci Rep"},{"key":"B80","doi-asserted-by":"publisher","first-page":"496","DOI":"10.1038\/nature16547","article-title":"Dual RNA-seq unveils noncoding RNA functions in host-pathogen interactions","volume":"529","author":"Westermann","year":"2016","journal-title":"Nature"},{"key":"B81","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1186\/s13059-016-1054-5","article-title":"Time-resolved dual RNA-seq reveals extensive rewiring of lung epithelial and pneumococcal transcriptomes during early infection","volume":"17","author":"Aprianto","year":"2016","journal-title":"Genome Biol"},{"key":"B82","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-024-01718-6","article-title":"Pseudomonas aeruginosa breaches respiratory epithelia through goblet cell invasion in a microtissue model","volume":"9","author":"Swart","year":"2024","journal-title":"Nat Microbiol"},{"key":"B83","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-immunol-102119-073855","article-title":"Trained immunity: Reprogramming innate immunity in health and disease","volume":"39","author":"Bekkering","year":"2021","journal-title":"Annu Rev Immunol"},{"key":"B84","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2011.04.006","article-title":"Trained immunity: A memory for innate host defense","volume":"9","author":"Netea","year":"2011","journal-title":"Cell Host Microbe"},{"key":"B85","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0813192106","article-title":"Cytokine-induced memory-like natural killer cells","volume":"106","author":"Cooper","year":"2009","journal-title":"Proc Natl Acad Sci USA"},{"key":"B86","doi-asserted-by":"publisher","first-page":"3933","DOI":"10.1016\/j.celrep.2019.11.043","article-title":"H3K4me1 supports memory-like NK cells induced by systemic inflammation","volume":"29","author":"Rasid","year":"2019","journal-title":"Cell Rep"},{"key":"B87","doi-asserted-by":"publisher","first-page":"899","DOI":"10.1016\/j.immuni.2019.10.010","article-title":"Tissue-specific macrophage responses to remote injury impact the outcome of subsequent local immune challenge","volume":"51","author":"Hoyer","year":"2019","journal-title":"Immunity"},{"key":"B88","doi-asserted-by":"publisher","first-page":"1634","DOI":"10.1016\/j.cell.2018.09.042","article-title":"Induction of autonomous memory alveolar macrophages requires T cell help and is critical to trained immunity","volume":"175","author":"Yao","year":"2018","journal-title":"Cell"},{"key":"B89","doi-asserted-by":"publisher","DOI":"10.1128\/cvi.00688-13","article-title":"Trained immunity or tolerance: Opposing functional programs induced in human monocytes after engagement of various pattern recognition receptors","volume":"21","author":"Ifrim","year":"2014","journal-title":"Clin Vaccine Immunol"},{"key":"B90","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2012.06.006","article-title":"Candida albicans infection affords protection against reinfection via functional reprogramming of monocytes","volume":"12","author":"Quintin","year":"2012","journal-title":"Cell Host Microbe"},{"key":"B91","doi-asserted-by":"publisher","DOI":"10.1038\/nature24271","article-title":"Inflammatory memory sensitizes skin epithelial stem cells to tissue damage","volume":"550","author":"Naik","year":"2017","journal-title":"Nature"},{"key":"B92","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-018-0449-8","article-title":"Allergic inflammatory memory in human respiratory epithelial progenitor cells","volume":"560","author":"Ordovas-Montanes","year":"2018","journal-title":"Nature"},{"key":"B93","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2019.00013","article-title":"Mechanisms of trained innate immunity in oxLDL primed human coronary smooth muscle cells","volume":"10","author":"Schnack","year":"2019","journal-title":"Front Immunol"},{"key":"B94","doi-asserted-by":"publisher","DOI":"10.1016\/j.jaut.2017.07.001","article-title":"The epigenetic architecture at gene promoters determines cell type-specific LPS tolerance","volume":"83","author":"Klein","year":"2017","journal-title":"J Autoimmun"},{"key":"B95","doi-asserted-by":"publisher","DOI":"10.1016\/j.stemcr.2024.03.007","article-title":"Survivors of polymicrobial sepsis are refractory to G-CSF-induced emergency myelopoiesis and hematopoietic stem and progenitor cell mobilization","volume":"19","author":"Biswas","year":"2024","journal-title":"Stem Cell Rep"},{"key":"B96","doi-asserted-by":"publisher","DOI":"10.1126\/science.1251086","article-title":"Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity","volume":"345","author":"Saeed","year":"2014","journal-title":"Science"},{"key":"B97","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2012.12.018","article-title":"Latent enhancers activated by stimulation in differentiated cells","volume":"152","author":"Ostuni","year":"2013","journal-title":"Cell"},{"key":"B98","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.01211","article-title":"NF-\u03baBp50 and HDAC1 interaction is implicated in the host tolerance to infection mediated by the bacterial quorum sensing signal 2-aminoacetophenone","volume":"8","author":"Bandyopadhaya","year":"2017","journal-title":"Front Microbiol"},{"key":"B99","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1016\/j.cell.2018.04.033","article-title":"Time-resolved analysis reveals rapid dynamics and broad scope of the CBP\/p300 acetylome","volume":"174","author":"Weinert","year":"2018","journal-title":"Cell"},{"key":"B100","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1186\/s13059-022-02775-y","article-title":"H3K18 lactylation marks tissue-specific active enhancers","volume":"23","author":"Galle","year":"2022","journal-title":"Genome Biol"},{"key":"B101","doi-asserted-by":"publisher","first-page":"2992","DOI":"10.1016\/j.cell.2025.03.048","article-title":"Long-term histone lactylation connects metabolic and epigenetic rewiring in innate immune memory","volume":"188","author":"Ziogas","year":"2025","journal-title":"Cell"},{"key":"B102","doi-asserted-by":"publisher","DOI":"10.15252\/emmm.201910264","article-title":"Predicting antimicrobial resistance in Pseudomonas aeruginosa with machine learning-enabled molecular diagnostics","volume":"12","author":"Khaledi","year":"2020","journal-title":"EMBO Mol Med"},{"key":"B103","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaf128","article-title":"Toward the use of nanopore RNA sequencing technologies in the clinic: challenges and opportunities","volume":"53","author":"Katopodi","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"B104","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2025.169107","article-title":"Are bacterial processes dependent on global ribosome pausing affected by tRNA modification defects","volume":"437","author":"de Cr\u00e9cy-Lagard","year":"2025","journal-title":"J Mol Biol"},{"key":"B105","doi-asserted-by":"publisher","first-page":"894","DOI":"10.1182\/blood-2013-02-485771","article-title":"Comparing cancer vs normal gene expression profiles identifies new disease entities and common transcriptional programs in AML patients","volume":"123","author":"Rapin","year":"2014","journal-title":"Blood"},{"key":"B106","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0164985","article-title":"MicroRNA-941 expression in polymorphonuclear granulocytes is not related to granulomatosis with polyangiitis","volume":"11","author":"Svendsen","year":"2016","journal-title":"PloS One"},{"key":"B107","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad993","article-title":"BloodSpot 3.0: a database of gene and protein expression data in normal and Malignant haematopoiesis","volume":"52","author":"G\u00edslason","year":"2024","journal-title":"Nucleic Acids Res"}],"container-title":["Frontiers in Immunology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2026.1845134\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,5]],"date-time":"2026-06-05T05:05:23Z","timestamp":1780635923000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2026.1845134\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,5]]},"references-count":107,"alternative-id":["10.3389\/fimmu.2026.1845134"],"URL":"https:\/\/doi.org\/10.3389\/fimmu.2026.1845134","relation":{},"ISSN":["1664-3224"],"issn-type":[{"value":"1664-3224","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,5]]},"article-number":"1845134"}}