(164e) Leveraging Advances in Proteomics to Mathematically Model Cell Signaling Processes: A Case Study on TGF? Signaling in Valve Interstitial Cells

Background: With no pharmaceutical treatments that prevent or delay the onset of calcific aortic valve disease (CAVD), treatment options consist of interventional repair or replacement. Valve interstitial cells (VICs) are the predominant cell type contributing to increased extracellular matrix (ECM) deposition and remodeling as well as calcification in CAVD. A detailed understanding of the signaling network driving VIC activation and expression of ECM-related genes would facilitate the rational discovery of suitable drug targets for mitigating, preventing, and/or reversing CAVD.

Methods: Herein, we stimulated VIC activation with transforming growth factor beta 1 (TGFβ1) to induce their phenotypic transition to myofibroblasts. VIC lysates were collected at various time points and subjected to bottom-up (phospho-)proteomics analysis based on a data independent acquisition (DIA) strategy. We use a small sample of the VIC lysate prior to phosphoenrichment to determine the protein copies/cell and to normalize the phospho-enriched samples. The time course of a subset of the discovered phosphorylations were modeled as a dynamic reaction network.

Results: A suitable model of TGFβ1-induced VIC activation was identified from phosphoproteomics data. In addition to canonical signaling through SMAD2/3, we have incorporated numerous non-canonical mechanisms. Sensitivity analysis enables model simplification and the identification of key reactions that drive this phenotypic transition in response to TGFβ1.

Implications: By coupling (phospho-)proteomics experiments with scientific computing, we can develop large, predictive models that enable the rational identification of suitable drug targets for combatting CAVD. These models can be extended in the future with other stimuli and further validated with knockout/knockdown studies to enhance our understanding of the mechanisms of VIC phenotypic transitions in CAVD.