Quan, M. | Search bioRxiv

bioRxiv2025

Capturing Multi-Scale Dynamics of Aortic Valve Calcification With a Coupled Fluid Structure and Systems Biology Model

Calcific aortic valve disease (CAVD) arises from coupled interactions between blood flow, tissue mechanics, and cellular signaling. Hemodynamic forces influence endothelial and interstitial cell behavior, while the resulting tissue remodeling alters valve motion and flow patterns. Capturing this two-way feedback requires models that integrate fluid-structure mechanics with biochemical regulation, yet such multiscale coupling remains technically challenging. Previous computational models have focused on isolated aspects of the disease: fluid-structure interaction (FSI) simulations reproduce valve deformation and flow, and systems biology (SB) models describe molecular signaling that drives fibrosis and calcification. However, without coupling, these approaches cannot predict how mechanical dysfunction initiates biochemical remodeling or how biochemical changes feed back on mechanics. Here, we present a proof-of-principle, multi-physics computational framework that couples three-dimensional FSI simulations of aortic valve dynamics with a mechanistic SB model of calcification signaling. The FSI module resolves pulsatile blood flow and leaflet deformation, yielding local wall shear stresses and tissue strains throughout the cardiac cycle. These mechanical quantities are used as inputs to the SB module, which comprises key biochemical pathways governing inflammation, TGF-{beta}/SMAD signaling, and nitric-oxide (NO)-mediated inhibition within valvular cells. Simulations predict long-term calcification trajectories for valves of varying thickness, showing that fibrosis-induced stiffening lowers shear stress, reduces NO synthesis, and enhances TGF-{beta} activation, thereby accelerating calcification. While the current one-way coupling implementation is not intended yet for clinical applications, the framework is modular and extensible, allowing for future enhancements that will advance towards this goal. These include the incorporation of additional biological pathways in the SB model and implementation of a fully two-way coupling scheme between the FSI and SB models that will increase accuracy and predictive capability of the framework. By integrating physics-based hemodynamics with systems-level biochemistry, this study demonstrates the utility of a next-generation, multi-scale modeling platform for studying cardiovascular disease that unites blood flow dynamics and biochemical signaling.

systems biology↗

bioRxiv2025

Themis dominates T cell exhaustion by regulation of TCR and PD-1 signaling

T cell exhaustion is important to protect the host from immunopathology during chronic viral infection, but it also impairs T cell anti-tumor immunity1-5. A fundamental unresolved question is whether and how T cell exhaustion is determined at the onset of TCR signaling6-8. Here we report an unexpected role of Themis, a TCR-proximal signaling molecule9, in T cell exhaustion. Chronic viral infection in mice usually leads to T cell exhaustion and survival of the host. Surprisingly, Themis T-cell conditional knockout mice died from severe CD8+-dependent lung immunopathology in chronic viral infection, showing Themis importance in establishing T cell exhaustion. We found that Themis-deficient CD8+ T cells were hyperactivated at the single-cell level - producing more TNF and IFN{gamma} compared to wild-type counterparts - but defective in population-level expansion. Moreover, TCF-1 and TOX expression were inhibited in Themis-deficient CD8+ T cells, thereby impairing differentiation of exhausted T cell precursors (T-pex) and maintenance of terminally exhausted T cells (T-ex), respectively. Mechanistically, Themis initially promotes TCR signaling to induce PD-1 expression and subsequently mediates PD-1 signaling. In the latter, Themis binds to PD-1 and promotes PD-1 phosphorylation and its recruitment of SHP2, thereby acting as a negative regulator to inhibit T cell effector functions. Without Themis, the orderly regulation of TCR and PD-1 signaling, and therefore exhaustion, is disrupted. Thus, our results unequivocally demonstrate that Themis-mediated early TCR signaling plays a decisive role in T cell exhaustion and provide a novel mechanism of PD-1 signaling through Themis.

immunology↗