Tuliakova, A. | bioRxiv Science

bioRxiv2024

Cell state transition analysis reveals a causal network that controls critical limb ischemia

Increased endothelial cell (EC) permeability significantly contributes to peripheral arterial disease and its severe manifestation, critical limb ischemia (CLI). CLI remains refractory to current pharmacological interventions, often requiring limb amputation and showing how limited our knowledge is about signaling pathways that control EC states. Here, we utilize a two-pronged approach, employing cell State Transition Assessment and Regulation (cSTAR) analyses to both the published knowledge (e.g., LINCS data portal) and our own transcriptomics data collected from CLI patients and healthy adult (HA) control. We identified CLI and HA transcriptomics patterns and reconstructed causal network that controls transitions between EC states associated with CLI and HA. Contrary to general belief, our study demonstrates that VEGF administration slightly promotes the CLI EC states, indicating VEGF ineffectiveness in enhancing perfusion of CLI tissue. Based on the unveiled control network, we suggest targets whose inhibition would reverse CLI EC states closer to HA states.

bioinformatics↗

bioRxiv2023

cSTAR analysis identifies endothelial cell cycle as a key regulator of flow-dependent artery remodeling

Fluid shear stress (FSS) from blood flow is sensed by vascular endothelial cells (ECs) to determine vessel stability, remodeling and susceptibility to atherosclerosis and other inflammatory diseases but the regulatory networks that govern these behaviors are only partially understood. We used cSTAR, a powerful new computational method, to define EC transcriptomic states under low shear stress (LSS) that triggers vessel inward remodeling, physiological shear stress (PSS) that stabilizes vessels, high shear stress (HSS) that triggers outward remodeling, and oscillatory shear stress (OSS) that confers disease susceptibility, all in comparison to cells under static conditions (STAT). We combined these results with the LINCS database where EC transcriptomic responses to drug treatments to define a preliminary regulatory network in which the cyclin-dependent kinases CDK1/2 play a central role in promoting vessel stability. Experimental analysis showed that PSS induced a strong late G1 cell cycle arrest in which CDK2 was activated. EC deletion of CDK2 in mice resulted in inward artery remodeling and both pulmonary and systemic hypertension. These results validate use of cSTAR to determine EC state and in vivo vessel behavior, reveal unexpected features of EC phenotype under different FSS conditions, and identify CDK2 as a key element within the EC regulatory network that governs artery remodeling.

cell biology↗