Biology subjects

Cifarelli, V.

Publications and source records attributed to Cifarelli, V..

4 recordsLinked to original sources

bioRxiv2026

Computational modeling of VEGF-A signaling predicts lymphatic junction state

Lymphatic endothelial cell (LEC) junctions switch between continuous zippers and discontinuous buttons to control fluid, cell and lipid uptake, but how the strength and timing of signaling set junction state is unknown. Here we present, to our knowledge, the first mechanistic signaling model calibrated to LEC data, linking VEGF-A-induced activation of VEGFR2 homodimers and VEGFR2/VEGFR3 heterodimers to the balance of active RAC1 and RhoA, summarized as a predicted zippering propensity. Calibrated to human dermal LEC time courses and validated against independent receptor knockdowns, the model predicts that VEGF-A dose primarily determines how long zippering-favoring signaling lasts following stimulation, and it identifies which of the parameters related to RAC1-RhoA kinetics control this duration. Using single-cell transcriptomes from high-fat-diet-fed mice, the model predicts that obesity shortens this response in mesenteric capillary and epididymal collector LECs but prolongs it in epididymal capillary LECs. Tuning RAC1-RhoA kinetics restores baseline in each population but requires opposite adjustments, suggesting that targeting this axis must be context-specific.

systems biology↗

bioRxiv2026

Loss of E3 ligase Ube4A disrupts colon homeostasis and accelerates experimental colitis via altered lipid handling

BackgroundUbiquitin-dependent signaling is essential for maintaining intestinal homeostasis and its dysregulation contributes to chronic intestinal disorders, such as Inflammatory Bowel Disease (IBD). Ube4A is a U-box E3/E4 ubiquitin ligase involved in lipid metabolism and insulin signaling in metabolic tissues. Autoantibodies against Ube4A have been identified in patients with IBD and are associated with disease long-term complications. Despite these clinical associations, the physiological role of Ube4A in the gastrointestinal tract remains unknown. This study aimed to define the function of Ube4A in the colon and determine how its loss influences susceptibility to experimental colitis. MethodsUBE4A expression in human colonic tissue from healthy individuals and patients with IBD was analyzed using publicly available single-cell RNA sequencing datasets. The role of Ube4A in colonic homeostasis and colitis pathogenesis was examined using global Ube4A knockout (UKO) mice subjected to dextran sulfate sodium (DSS)-induced colitis. UKO colon phenotypes were characterized using transcriptomic analyses, immunofluorescence, and flow cytometry. ResultsUBE4A is highly expressed in human colonic epithelial cells, and its expression is reduced from healthy to IBD inflamed tissues. In mice, Ube4A deficiency significantly exacerbated DSS-induced colitis, as evidenced by increased weight loss, disease activity scores, shortened colon length, and more severe histological injury. Transcriptomic profiling revealed enhanced inflammatory signaling, alongside dysregulation of lipid transport and storage, as well as antimicrobial defense pathways. DSS-treated UKO mice also exhibited increased mast cell activation and elevated expression of matrix metalloproteinases. Importantly, colons from UKO mice displayed baseline transcriptional alterations indicative of epithelial stress and disrupted lipid metabolic programs, even in the absence of injury. ConclusionsUbe4A is a previously unrecognized regulator of colon homeostasis. Its loss induces existing epithelial stress and metabolic reprogramming that sensitize the colon to exaggerated inflammatory responses during injury such as experimental colitis.

pathology↗

bioRxiv2025

Sex Differences in VEGF and PDGF Ligand and Receptor Protein Expression during Adipose Tissue Expansion and Regression

Inadequate angiogenesis in obesogenic adipose tissue (AT) has been implicated in disrupted adipogenesis and metabolic disorders. Yet, key cellular and molecular regulators of AT angiogenesis remain largely unidentified. This study sought to identify the dysregulated elements within the Vascular Endothelial Growth Factor (VEGF) and Platelet-Derived Growth Factor (PDGF) systems during obesity progression. We employ a mouse model, comprising both male and female mice, to investigate the changes in the VEGF/PDGF concentration and their receptor distribution in AT during short- and long-term weight gain and weight loss. Our results reveal pronounced sex-specific differences in obesity progression, with male and female mice exhibiting distinct angiogenic ligand and receptor profiles under identical dietary interventions. This data also lays the groundwork for developing computational models of VEGF/PDGF signaling networks in AT, allowing for the simulation of complex biological interactions and the prediction of therapeutic outcomes.

cell biology↗

bioRxiv2024

Insulin regulates lymphatic endothelial function via palmitoylation

Lipid metabolism plays a critical role in lymphatic endothelial cell (LEC) development and maintenance. Altered lipid metabolism is associated with loss of lymphatic vessel integrity, which compromises organ function, protective immunity, and metabolic health. However, the role of lipid metabolism in LEC function is not well understood. Insulin is a key regulator of lipid metabolism and protein palmitoylation, the reversible post-translational protein modification by palmitate that affects protein stability, trafficking, protein-protein, and protein-membrane interactions. Human LECs are highly sensitive to insulin and can develop insulin resistance in vitro, but whether insulin regulates LEC protein palmitoylation and function is unknown. To examine the role of palmitoylation in LEC function, we generated the first palmitoylation proteomics profile in human LECs, validated insulin regulated targets and profiled differences in palmitoylation between lymphatic and blood endothelial cells. Palmitoylation occurred primarily in proteins involved in LEC vesicular or membrane trafficking, translation initiation, and in those found in membrane rafts. Insulin enriched palmitoylation of LEC proteins involved in GTPase signaling, ubiquitination, and junctional anchoring. We also determined that the long-chain fatty acid receptor CD36 mediates optimal lymphatic palmitoylation. CD36 silencing in LECs doubled palmitoylation targets involving proteins related to inflammation and neutrophil degranulation contributing to an activated inflamed endothelium. These results suggest that the coordination of the process of palmitoylation is critical for normal lymphatic endothelial function.

physiology↗