Structural analysis of a Petri net model of oxidative stress in atherosclerosis

A new computational workflow to guide personalized drug therapy

OBJECTIVE

Computational models are at the forefront of the pursuit of personalized medicine thanks to their descriptive and predictive abilities. In the presence of complex and heterogeneous data, patient stratification is a prerequisite for effective precision medicine, since disease development is often driven by individual variability and unpredictable environmental events. Herein, we present GreatNectorworkflow as a valuable tool for (i) the analysis and clustering of patient-derived longitudinal data, and (ii) the simulation of the resulting model of patient-specific disease dynamics.

METHODS

GreatNectoris designed by combining an analytic strategy composed of CONNECTOR, a data-driven framework for the inspection of longitudinal data, and an unsupervised methodology to stratify the subjects with GreatMod, a quantitative modeling framework based on the Petri Net formalism and its generalizations.

RESULTS

To illustrate GreatNectorcapabilities, we exploited longitudinal data of four immune cell populations collected from Multiple Sclerosis patients. Our main results report that the T-cell dynamics after alemtuzumab treatment separate non-responders versus responders patients, and the patients in the non-responders group are characterized by an increase of the Th17 concentration around 36 months.

CONCLUSION

GreatNectoranalysis was able to stratify individual patients into three model meta-patients whose dynamics suggested insight into patient-tailored interventions.

Control of Cholesterol Metabolism Using a Systems Approach

Simple Summary

Cholesterol is the main sterol in mammals that is essential for healthy cell functionining. It plays a key role in metabolic regulation and signaling, it is a precursor molecule of bile acids, oxysterols, and all steroid hormones. It also contributes to the structural makeup of the membranes. Its homeostasis is tightly controlled since it can harm the body if it is allowed to reach abnormal blood concentrations. One of the diseases associated with elevated cholesterol levels being the major cause of morbidities and mortalities worldwide, is atherosclerosis. In this study, we have developed a model of the cholesterol metabolism taking into account local inflammation and oxidative stress. The aim was to investigate the impact of the interplay of those processes and cholesterol metabolism disturbances on the atherosclerosis development and progression. We have also analyzed the effect of combining different classes of drugs targeting selected components of cholesterol metabolism.

Abstract

Cholesterol is an essential component of mammalian cells and is involved in many fundamental physiological processes; hence, its homeostasis in the body is tightly controlled, and any disturbance has serious consequences. Disruption of the cellular metabolism of cholesterol, accompanied by inflammation and oxidative stress, promotes the formation of atherosclerotic plaques and, consequently, is one of the leading causes of death in the Western world. Therefore, new drugs to regulate disturbed cholesterol metabolism are used and developed, which help to control cholesterol homeostasis but still do not entirely cure atherosclerosis. In this study, a Petri net-based model of human cholesterol metabolism affected by a local inflammation and oxidative stress, has been created and analyzed. The use of knockout of selected pathways allowed us to observe and study the effect of various combinations of commonly used drugs on atherosclerosis. The analysis results led to the conclusion that combination therapy, targeting multiple pathways, may be a fundamental concept in the development of more effective strategies for the treatment and prevention of atherosclerosis.

Antioxidant and cytoprotective effects of avocado oil and extract (Persea americana Mill) against rotenone using monkey kidney epithelial cells (Vero)

Oxidative stress is known to be involved in development of numerous diseases including cardiovascular, respiratory, renal, kidney and cancer. Thus, investigations that mimic oxidative stress in vitro may play an important role to find new strategies to control oxidative stress and subsequent consequences are important. Rotenone, widely used as a pesticide has been used as a model to simulate oxidative stress. However, this chemical was found to produce several diseases. Therefore, the aim of this study was to investigate the antioxidant and cytoprotective effect of avocado (Persea americana Mill) extract and oil in monkey kidney epithelial cells (VERO) exposed to rotenone. VERO cells were exposed to IC₅₀ of rotenone in conjunction with different concentrations of avocado extract and oil (ranging from 1 to 1000 µg/ml), for 24 hr. Subsequently, cell viability and oxidative metabolism were assessed. Data demonstrated that avocado extract and oil in the presence of rotenone increased cellular viability at all tested concentrations compared to cells exposed only to rotenone. In addition, extract and avocado oil exhibited antioxidant action as evidenced by decreased levels of reactive oxygen species (ROS), superoxide ion, and lipid peroxidation, generated by rotenone. Further, avocado extract and oil appeared to be safe, since these compounds did not affect cell viability and or generate oxidative stress. Therefore, avocado appears to display a promising antioxidant potential by decreasing oxidative stress.