Xylosyltransferase-II deficiency rewires innate immune signaling and destabilizes polarization in human macrophages

Xylosyltransferase-II (XT-II), encoded by XYLT2, catalyzes the rate-limiting step of proteoglycan biosynthesis, yet its role in macrophage biology and innate immune regulation remains poorly defined. Given the central role of macrophages in inflammatory signaling and tissue homeostasis, we investigated the transcriptional consequences of XYLT2 deficiency in human primary macrophages across distinct polarization states (M0, M1, M2). Bulk mRNA sequencing revealed that XYLT2 deficiency induces a conserved and robust transcriptional reprogramming independent of polarization state. Differential expression analysis identified a shared interferon-associated gene signature, characterized by the upregulation of interferon-stimulated genes, including STAT1, IRF7, and multiple IFIT family members. Pathway enrichment analysis demonstrated significant activation of innate immune sensing pathways, including RIG-I-like, NOD-like, and Toll-like receptor signaling, alongside strong enrichment of JAK–STAT and cytokine signaling pathways. In parallel, pathways such as NF-κB, PI3K–Akt, and MAPK signaling exhibited bidirectional regulation, indicating complex network rewiring rather than uniform activation. Notably, osteoclast differentiation pathways were enriched among upregulated genes, suggesting a shift toward a pro-osteoclastogenic transcriptional state. Collectively, these findings demonstrate that XYLT2 deficiency drives a global, interferon-dominated transcriptional program associated with enhanced innate immune activation and altered macrophage functional identity, providing a mechanistic link between impaired proteoglycan biosynthesis and dysregulated immune signaling.