Epigenome Alterations and 3D Chromatin Architecture Remodeling in Inflammatory Macrophage Activation under Diabetic Conditions

Aberrant monocyte/macrophage activation in diabetes drives chronic inflammation and diabetic complications. Although epigenetic mechanisms are implicated in these processes, the contribution of three-dimensional (3D) chromatin reorganization remains unclear. Here, we use integrated multi-omics approaches to profile gene expression, chromatin accessibility and 3D chromatin architecture in human CD14⁺ monocyte-derived macrophages exposed to high glucose and TNF-α (HT), mimicking the diabetic milieu. HT induces inflammatory transcription programs that recapitulate those observed in diabetes and dynamically remodel chromatin accessibility, enhancer-promoter interactions, and topologically associated domains. Inflammatory genes exhibit increased chromatin accessibility, whereas cell cycle and metabolic genes display reduced accessibility and weakened enhancer-promoter interactions. These architectural changes promote the convergence of lineage-determining and signal-dependent transcription factors at enhancer-promoter loops, generating distinct regulatory hubs that orchestrate pro-inflammatory responses. Similar enhancer-promoter interactions are observed in peripheral blood derived monocytes from individuals with diabetes. Furthermore, perturbing chromatin interactions via CRISPR interference targeting HT-induced enhancers suppresses nearby CCL2 and other chemokine genes. Collectively, this first comprehensive enhancer connectome map of macrophages under diabetic conditions advances the field by revealing extensive disease-associated rewiring of the 3D epigenome, highlighting chromatin architecture and epigenetic mechanisms as potential therapeutic target for diabetes-associated inflammation.