Research Article: Time-resolved multi-omics reveals macrophage-centered immunometabolic remodeling in cutaneous dematiaceous fungal infection

Abstract:
Dematiaceous fungi cause chronic, invasive cutaneous infections that are difficult to eradicate and frequently relapse despite antifungal therapy. Although host immunity is critical for controlling these infections, the temporal organization of immune responses and the underlying immunometabolic programs remain poorly defined. In particular, how macrophage dynamics and chemokine signaling shape antifungal immunity over time is largely unknown. Using Phialophora verrucosa as a representative dematiaceous fungus, we established a murine subcutaneous infection model and performed time-resolved transcriptomic and proteomic analyses across the course of infection. Immune cell composition, pathway dynamics, and metabolic signatures were systematically characterized. To functionally validate key regulatory axes identified by multi-omics analyses, bone marrow–derived macrophages and dendritic cells from wild-type and Ccr2 knockout mice were subjected to in vitro fungus–cell coculture assays. Time-resolved multi-omics analysis revealed that days 7–14 post-infection constituted a critical transition phase of the host immune response, coinciding with lesion regression and pathogen clearance. This stage featured marked activation of pathways governing antigen presentation, phagosome formation and inflammatory signaling. Macrophages underwent dynamic changes in both abundance and phenotype during this period, accompanied by the upregulation of glycolysis- and lactate metabolism-related pathways. Co-expression and interaction network analysis further identified Ccr2 as a core hub within the chemokine signaling network. in vitro functional assays demonstrated that while Ccr2 deficiency did not compromise the phagocytic or fungicidal activity of macrophages, it significantly diminished their chemotactic capacity toward P. verrucosa conidia. Under infection stimulation, loss of Ccr2 also promoted M1-type polarization of macrophages, along with enhanced maturation of dendritic cells. This study elucidates the dynamic remodeling of immunometabolism centered on macrophages during P. verrucosa infection, and demonstrates that the CCL2/CCR2 biological axis contributes to host antifungal immunity mainly by modulating immune cell recruitment and the balance of inflammatory phenotypes. These findings provide a novel theoretical basis for understanding the immunoregulatory mechanisms of dematiaceous fungal infections and developing potential immunological intervention strategies.

Introduction:
Dematiaceous fungi cause chronic, invasive cutaneous infections that are difficult to eradicate and frequently relapse despite antifungal therapy. Although host immunity is critical for controlling these infections, the temporal organization of immune responses and the underlying immunometabolic programs remain poorly defined. In particular, how macrophage dynamics and chemokine signaling shape antifungal immunity over time is largely unknown.

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