Modulation of antimicrobial activity in macrophages

Thesis

Host protective immunity within the gastrointestinal tract depends on the antimicrobial functions of macrophages and neutrophils, and on tightly regulated, context-specific inflammatory responses. Macrophages contribute to mucosal defence through various antimicrobial mechanisms, including reactive oxygen species production, phagolysosome acidification, antimicrobial peptide secretion, and autophagy. These functions are shaped by host–microbiota interactions. Among microbial metabolites, short-chain fatty acids, particularly butyrate, act as key immunomodulators that regulate barrier integrity and immune function. Previous work from our group demonstrated that butyrate enhances macrophage antimicrobial responses by inhibiting histone deacetylase 3, leading to transcriptional and metabolic reprogramming. This includes increased expression of antimicrobial peptides such as calprotectin (S100A8/S100A9), reduced glycolysis, inhibition of mTOR signalling, and enhanced LC3–mediated bacterial clearance. However, the mechanisms linking histone deacetylase 3 inhibition to butyrate-induced antimicrobial activity in macrophages remain incompletely understood.

This thesis investigates how butyrate enhances macrophage antimicrobial activity by regulating histone modification dynamics and intracellular vesicle trafficking. Using transcriptomic and proteomic analyses, functional assays, and super-resolution imaging, it was found that butyrate induces histone H3 acetylation at lysine 18 and 23 and promotes its accumulation in the cytoplasm. Histone H3 colocalises to CD63-positive vesicles that accumulate in lysosomes, where it is cleaved by cathepsin L to generate an N-terminal histone H3 peptide with antimicrobial properties. In parallel, butyrate enhances RAB7-dependent trafficking of the antimicrobial peptide LL37. These vesicles fuse with pathogen-containing phagosomes, delivering their antimicrobial contents and promoting bacterial clearance. This butyrate-driven mechanism, termed the Histone Acetylation-Mediated Macrophage Microbe Effector Response, represents a macrophage-specific intracellular killing mechanism. While it shares antimicrobial features with neutrophil extracellular traps, it is distinct in its mechanism. This work identifies a novel link between microbial metabolites, chromatin modification, and intracellular immunity, and expands current understanding of how host–microbial interactions regulate macrophage function.

Authors: Lam, Y

• DOI: 10.5287/ora-vqgabed79
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford
• Language: English