Unraveling the molecular mechanisms of Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD): Leveraging Proteomics and PTMs analysis for the development of precision medicine

Steatotic Liver Disease (SLD) is a pathology characterized by an excessive accumulation of fat in hepatic tissue. This abnormal concentration of lipids in hepatocytes produces damage and subsequently activates the inflammatory response. Persistent inflammation can lead to further liver damage and the development of more severe outcomes such as scarring (fibrosis), cirrhosis, or even hepatic cancer. Several risk factors have been associated with the development of this pathology, including obesity, heavy alcohol consumption, type 2 diabetes, high levels of triglycerides in the blood, and genetics, among others. Metabolic (dysfunction)-Associated Steatotic Liver Disease (MASLD) is a type of SLD in which the steatosis is not associated with high alcohol consumption, but it can also lead to other complications like cardiovascular disease.

In hepatocytes, an excess of glucose and free fatty acids promotes de novo lipogenesis. As a result of excessive lipid accumulation, the b-oxidation decreases, and the mitochondria become dysfunctional, increasing the production of reactive oxygen species (ROS). This accumulation of oxidative stress damages lipids, proteins, and DNA, promoting inflammation and fibrosis, and in advanced stages, cellular apoptosis or necrosis.

In this study, we analyzed the proteomic profile of liver biopsies from patients with MASLD under different conditions (Obesity, Type 2 Diabetes, Steatosis, and Fibrosis). The results revealed which key proteins involved in sucrose, lipid, and amino acid metabolism, as well as signaling, are differentially implicated across the various patient types.

In addition, we utilized our lab-developed softwares (Comet-PTM, ReCom, iSanXoT, and a new PTMs analysis package) to conduct an open-search proteomic analysis, aiming to obtain a detailed map of the molecular alterations occurring under each of the conditions analyzed, including a comprehensive study of the post-translationally modified peptidome. This analysis provided an additional layer of information regarding the changes taking place in the studied proteomes. The majority of the differential PTMs were oxidative and exhibited varying abundances, enabling differentiation between patient groups.

Overall, this study identified differential proteins with the potential for use as biomarkers for the diagnosis of MASLD. Additionally, the utilization of a new open-search analysis tool enabled the localization of PTM differences across the patients, providing a more comprehensive representation of protein changes in liver tissue. This will aid researchers in the development of targeted therapy strategies.