Abstract
BACKGROUND: Obesity is a major risk factor for type 2 diabetes (T2D); however, the molecular links between these conditions are not fully understood. METHODS: We performed an integrative serum proteomics study on samples from 134 individuals (healthy controls, patients with obesity and/or T2D) using both data-independent (DIA) and data-dependent (DDA) liquid chromatography-mass spectrometry approaches, complemented by phosphopeptide enrichment, kinase activity prediction, network and pathway analyses to get more information on the different proteoforms involved in the pathophysiology of the diseases. RESULTS: We identified 235 serum proteins, including 13 differentially abundant proteins (DAPs) between groups. Both obesity and T2D were characterized by activation of complement and coagulation cascades, as well as alterations in lipid metabolism. Ingenuity Pathway Analysis(®) (IPA) revealed shared canonical pathways, while phosphorylation-based regulation differentiated the two conditions. Elevated hemopexin (HPX), vitronectin (VTN), kininogen-1 (KNG1) and pigment epithelium-derived factor (SERPINF1), along with decreased adiponectin (ADIPOQ) and apolipoprotein D (APOD), indicated a pro-inflammatory, pro-coagulant serum profile. Network analyses of antimicrobial and immunomodulatory peptides (AMPs) revealed strong overlaps between immune regulation and lipid metabolism. Phosphoproteomics and kinase prediction highlighted altered CK2 and AGC kinase activities in obesity, suggesting signaling-level modulation. CONCLUSIONS: Our comprehensive proteomic and phosphoproteomic profiling reveals overlapping yet distinct molecular signatures in obesity and T2D, emphasizing inflammation, complement activation and phosphorylation-driven signaling as central mechanisms that potentially contribute to disease progression and therapeutic targeting.