{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,18]],"date-time":"2025-12-18T06:50:23Z","timestamp":1766040623727,"version":"3.48.0"},"reference-count":34,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,12,18]],"date-time":"2025-12-18T00:00:00Z","timestamp":1766016000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82172454"],"award-info":[{"award-number":["82172454"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Mol. Biosci."],"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>MicroRNA-155 (miR-155) is a key regulator of macrophage function, and its abnormal expression is closely associated with the pathogenesis of tuberculosis (TB)\u2014a disease where impaired macrophage autophagy weakens anti-mycobacterial immunity. Exosomes are promising nucleic acid carriers due to their biocompatibility and cell-targeting ability. Here, we constructed exosome-based miR-155 delivery systems (Exo-miR155-ago\/Exo-miR155-antago; \u201cago\u201d = agomir, a miR-155 agonist that enhances its expression; \u201cantago\u201d = antagomir, a miR-155 antagonist that inhibits its expression) to modulate macrophage autophagy and remold anti-TB immune responses.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Exosomes were isolated from the supernatant of bone marrow mesenchymal stem cells using differential centrifugation. The miR155-5p agomir and antagomir were transfected into exosomes via the Exosome Transfection Kit, followed by co-incubation with macrophages. Transcriptomics and proteomics were employed to screen for differentially expressed genes and proteins. Western blot was employed to detect autophagy-related proteins and phosphorylated proteins in signaling pathways (p- denotes phosphorylation, a key post-translational modification regulating protein activity). Techniques including transmission electron microscopy (TEM), Monodansylcadaverine (MDC) staining, and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) were applied to detect the autophagic level of macrophages.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Transcriptome sequencing identified 704 differentially expressed genes, with significant enrichment in TNF and NF-\u03baB pathways, differential expression of NF-\u03baB target genes (e.g., autophagy core gene Beclin1), and expression changes in key genes of the energy metabolism-related AMPK\/mTOR pathway; proteomic analysis found 164 differentially expressed proteins, including key molecules of the \u201cPathogen Recognition-TLR4-NF-\u03baB-Autophagy-Related Gene Transcription\u201d pathway (TLR4, p-p65) and core proteins of the AMPK\/mTOR pathway (p-AMPK, p-mTOR); functional verification showed the Exo-miR155-ago group had more autophagosomes (TEM), higher autophagic vacuole accumulation (MDC staining), upregulated mRNA\/protein of autophagy-related molecules (LC3B, Beclin1), downregulated mRNA\/protein of p62 (RT-qPCR\/Western blot), activated p-p65 (NF-\u03baB pathway), and increased p-AMPK with decreased p-mTOR (AMPK\/mTOR pathway), and all results confirmed Exo-miR155-ago promotes macrophage autophagy via the synergistic effect of the two pathways.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>This study provides multi-omics evidence for autophagy modulation mediated by the exosomal nucleic acid delivery system, verifies that this system regulates macrophage autophagy by controlling the TLR4-NF-\u03baB pathway and AMPK\/mTOR pathway, and clarifies the application potential of this system in tuberculosis (TB) and other macrophage-associated.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmolb.2025.1711082","type":"journal-article","created":{"date-parts":[[2025,12,18]],"date-time":"2025-12-18T06:45:38Z","timestamp":1766040338000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Decoding the exosomal nucleic acid delivery system axis of macrophage autophagy and immune reprogramming via multi-omics analysis"],"prefix":"10.3389","volume":"12","author":[{"given":"Zhoujun","family":"Zhu","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Xiang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pengchao","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Parhat","family":"Yasin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinghua","family":"Song","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2025,12,18]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1016\/j.cell.2009.01.002","article-title":"MicroRNAs: target recognition and regulatory functions","volume":"136","author":"Bartel","year":"2009","journal-title":"Cell"},{"key":"B2","doi-asserted-by":"publisher","first-page":"1062963","DOI":"10.3389\/fcimb.2023.1062963","article-title":"Mycobacterium tuberculosis-macrophage interaction: molecular updates","volume":"13","author":"Bo","year":"2023","journal-title":"Front. 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