Functional proteomics investigation of biomarkers and molecular pathways suggestive of onset, development, and therapeutic monitoring of different lung disorders

Proteomics is the large-scale study of proteins and their post-translational modifications, aiming to characterize molecular and cellular dynamics of the biological system. The proteomic approach allows to understand molecular mechanisms and pathways and to identify critical diagnostic and prognostic biomarkers for different physiological states and their disease alteration. Moreover, by global investigation of the proteome, proteomics facilities drug target discovery and it is also useful for the evaluation of drug action, toxicity, resistance, or its efficacy. The first study reported in this thesis regards the follow-up investigations of two biological therapies recently approved for severe eosinophilic asthma (SEA) control, benralizumab and mepolizumab. SEA is the major subtype of severe asthma associated with a higher risk of severe exacerbations and characterized by hypereosinophilia in peripheral blood and sputum dependent on IL-5 release. Benralizumab binds the IL-5 receptor, while mepolizumab blocks circulating IL-5. Intending to investigate the response to therapies at molecular levels, we performed functional proteomic analysis on SEA serum samples collected before and after 1 and 6 months of mepolizumab or benralizumab, and serum from healthy donors. After one month of therapy, serum protein patterns were differently influenced by treatments, while after 6 months of both therapies, serum protein patterns become similar to the healthy ones. In particular, among differential proteins after six months of both treatments, there were increased levels of plasminogen, apolipoproteins and ceruloplasmin. These proteins are related to blood coagulation, lipid metabolism and transport, inflammation response and extracellular matrix remodelling, well known to be involved in SEA physiopathology, suggesting as their modulation counteracts the pathology. Curiously, apolipoproteins resulted negatively correlated with peripheral eosinophilia highlighting their anti-inflammatory and anti-allergic effects in protecting the lung. The second study reported characterizes the bronchoalveolar lavage fluid (BALF) proteomic signature of lung cancer (LC) in idiopathic pulmonary fibrosis (IPF) patients. IPF is a chronic and irreversible fibrosing interstitial pneumonia sharing similarities in terms of risk factors, and pathogenic pathways with lung cancer that is difficult to diagnose in a fibrotic lung. This is reflected in the lack of optimal therapeutic strategies for patients with both diseases. We performed a functional proteomic study on BALF samples from IPF, LC associated with IPF (LC-IPF) patients, and healthy controls (CTRLs) aiming to highlight biomarkers of LC onset in a IPF contest. To this purpose our analysis revealed an up-regulation of proteins involved in inflammation, immune response and cell adhesion in LC-IPF condition also revealing a relationship between inflammation- and lipid metabolism-related proteins where NAMPT, which we found down-regulated in LC-IPF serum, stands at the crossroad between these two molecular pathways. Since the compromised situation of IPF patients, it was relevant the evaluation of the BAL differential proteins at the serum level to permit future less invasive diagnostic procedures. This confirms calgranulin, apolipoprotein A1 and NAMPT as potential serum biomarkers of LC onset in IPF lung.