Mass Spectrometry-Based Multiomic Profiling Defines Proteome, Lipidome, and Metabolome Remodeling in IFN-γ and LPS-Stimulated BV-2 Microglial Cells

Abstract

Microglial inflammatory activation is accompanied by extensive molecular remodeling, yet proteomic, lipidomic, and metabolomic responses are often analyzed independently. Here, we applied a mass spectrometry-based multiomic workflow to characterize proteomic, lipidomic, and polar metabolomic remodeling from matched biological replicates of immortalized murine BV-2 microglial cells following stimulation with interferon-γ (IFN-γ) and lipopolysaccharide (LPS). Pro-inflammatory activation was confirmed by increased nitrite accumulation, elevated TNF-α and IL-6 secretion, and treatment-associated morphological changes. Discovery proteomics quantified 8,676 proteins and identified 562 significantly altered proteins, including 344 increased and 218 decreased proteins. Increased proteins were enriched for interferon-responsive, innate immune, inflammatory effector, and antigen-associated pathways, whereas decreased proteins were associated with cellular organization, protein biogenesis, vesicular trafficking, and metabolic regulation. Targeted lipidomics identified 237 significantly altered lipids, including increased triacylglycerols and diacylglycerols and broad remodeling of glycerophospholipids, lysophospholipids, and sphingolipid-related species. Targeted polar metabolomics identified 75 significantly altered metabolites, including changes in nucleotide/NAD-related metabolism, amino acid metabolism, methylation-associated metabolites, acylcarnitine abundance, phospholipid precursors, polyamine metabolism, arginine/nitric oxide-associated metabolism, and redox-associated metabolites. Process-level integration of significant features revealed coordinated remodeling of inflammatory protein programs with lipid storage, membrane remodeling, nucleotide metabolism, amino acid availability, phospholipid precursor abundance, nitric oxide-associated metabolism, and redox/osmolyte pathways. These findings demonstrate that IFN-γ and LPS-induced activation of BV-2 cells involves complementary immune, lipid, and metabolic adaptation rather than isolated induction of canonical inflammatory mediators. This multiomic framework provides a resource for investigating how lipid and metabolic remodeling regulate microglial inflammatory states.