Proteomic approaches to complex health challenges: insights into vascular, metabolic, and neurodegenerative pathways, including alternative nutrition strategies

Lifestyle habits and dietary patterns are major determinants of population health, influencing cardiovascular risk, metabolic balance, and susceptibility to disease. In parallel, rare and complex pathologies with limited therapeutic options represent an additional challenge due to their biological heterogeneity and poorly defined etiological mechanisms. In this work, the biomolecular bases underlying that diverse health-related conditions were investigated using proteomic approaches combined with functional assays, bioinformatic network analysis, and statistical integration, with the aim of defining biochemical alterations associated with tissue dysfunction, disease susceptibility, and heterogeneous pathological responses. The first research line addressed cardiovascular risk associated with cigarette smoking and alternative nicotine delivery systems. Using murine and human aortic smooth muscle cell models, functional assays integrated with gene expression analysis, immunoblotting, and mass spectrometry-based proteomics showed that cigarette smoke induces phenotypic modulation toward a transdifferentiated, pro-inflammatory, and migratory state, involving regulation of the myocardin/KLF4 axis and matrix remodelling pathways. Comparative analyses indicated that traditional cigarettes, electronic cigarettes, and heated tobacco products elicit distinct molecular responses that may converge on shared vascular pathological phenotypes through partially divergent signalling mechanisms. The second research line focused on nutritional quality and food safety of diverse dietary sources, even within the context of the protein transition, toward more sustainable food systems. Proteomic profiling of Triticum monococcum and Triticum aestivum (heritage and modern varieties) was used to evaluate differences in protein composition potentially associated with reduced immunogenicity in ancient wheat. In Cicer arietinum, the effects of wood distillate application were assessed on yield, nutritional composition, antioxidant capacity, carbohydrate and amino acid profiles, and proteomic stability, addressing both crop quality and consumer safety. In parallel, dietary supplementation with heat-inactivated Lactobacillus plantarum was investigated in Caenorhabditis elegans under basal and glucose-induced obesogenic conditions, modelling the metabolic consequences of poor diet and lifestyle. This intervention aimed to assess whether postbiotic administration can, at least in part, support general health under basal conditions and improve homeostasis disrupted by obesogenic stress, revealing diet-dependent modulation of metabolic and inflammatory pathways. The final research line investigated rare and complex diseases characterised by high phenotypic heterogeneity, limited understanding of underlying molecular mechanisms, and scarce therapeutic options. This work applied functional proteomics and bioinformatic approaches to Krabbe disease (globoid cell leukodystrophy, KD), medication-related osteonecrosis of the jaw (MRONJ), and pituitary adenomas (PitNETs), analysing serum, bone tissue, and tumour biopsies, respectively. In KD, we identified candidate non-invasive serum biomarkers, detectable at early stages, in the Twitcher mouse, including in heterozygous carriers, revealing subtle systemic alterations preceding overt pathology. In MRONJ, our study highlighted coordinated dysregulation of angiogenesis, bone remodelling, and cell adhesion pathways, providing mechanistic insight into tissue dysfunction and impaired regeneration. Finally, in PitNETs, differential proteomic profiling uncovered alterations in protein homeostasis, mitochondrial function, energy metabolism, and oxidative stress pathways, offering molecular explanations for tumour behaviour and identifying potential therapeutic targets. By integrating multivariate statistics, network analysis, and functional correlation of protein changes, our research generated a comprehensive overview of molecular patterns across diverse biological contexts, including lifestyle and diet associated alterations as well as rare and complex diseases, highlighting candidate biomarkers and pathways with translational relevance, and demonstrating the value of the applied approach for understanding mechanisms underlying health and disease.