Proteomic evaluation and comparison of native and decellularized human saphenous vein extracellular matrices

The growing prevalence of cardiovascular diseases (CVDs) has created an increasing demand for alternative biologically functional vascular grafts. Among the explored tissue engineering strategies, decellularization provides a means to generate suitable acellular scaffolds from donor tissues with preserved complex extracellular matrix (ECM) architecture and vascular basement membrane (BM), both of which are critical for graft endothelialization and function. To assess decellularization efficiency and quality, proteomic profiling offers high-resolution characterization of tissue composition, enabling systematic analysis of extracellular matrix subgroups and residual proteins with the aid of open-access annotation tools, thus providing critical insights beyond conventional methods.

Human saphenous vein segments were decellularized using a CHAPS-based protocol, and decellularization efficiency was evaluated by DNA and glycosaminoglycan (GAG) quantification, together with histological evaluation. A subset of samples (n = 9) was further subjected to label-free quantitative proteomic profiling using LC-MS/MS to assess ECM composition, BM integrity, and residual cellular content.

Decellularization led to 99.96% DNA removal and 53.78% GAG retention, with well-preserved tissue morphology. Decellularization efficiency was further assessed by label-free quantitative proteomics, which showed well-preserved ECM composition. Collagens, proteoglycans, and BM proteins were largely well-maintained, whereas ECM glycoproteins and matrisome-affiliated proteins were moderately reduced. The strongest decrease in protein abundance was observed among cellular proteins, and Gene Ontology analysis confirmed the reduction of key cellular protein groups.

In this study, we provide a comprehensive proteomic evaluation of decellularized human saphenous veins, demonstrating selective preservation and loss across ECM subgroups and cellular proteins. The findings highlight proteomics as a valuable complement to conventional assays for assessing decellularization efficiency and establishing a reference framework for optimizing protocols in vascular tissue engineering.