Multi-OMICs analysis on tridimensional fibroblast spheroids to model vascular Ehlers-Danlos syndrome pathogenesis

Three-dimensional (3D) spheroids are an innovative cellular model mimicking tissue-like properties for a more effective replication of physiological cellular environment. Vascular Ehlers-Danlos syndrome (vEDS) is a rare hereditary connective tissue disorder caused by heterozygous deleterious variants in COL3A1. Affected individuals are at increased risk of early death due to ruptures of arteries, large intestine, and gravid uterus. vEDS cellular pathogenesis is only partially understood and the disease remains without effective treatment. We integrated transcriptomic and proteomic data generated from 2D fibroblast cultures and 3D spheroids from ten patients and four controls. Transcriptomic analysis revealed upregulation of genes related to mitochondrial function, organellar ribosomal subunits, and biosynthesis processes, to indicate an augmented adaptive metabolic response, while downregulation of genes involved in cell migration, differentiation, and stress response highlighted abnormalities in cellular signaling and extracellular matrix maintenance. Proteomic analysis found that induced proteins were significantly enriched for the mitochondrial matrix and minichromosome maintenance complex as well as in biological processes involving low-density lipoprotein particles, and cellular response to catabolic processes and DNA damage stimuli. Ultrastructural analysis and high-content imaging documented an endoplasmic reticulum dilation, increased autophagosomes and lipofuscin deposits. Our findings expand current knowledge on the multi-OMIC profile of vEDS by highlighting potential convergent mechanisms and novel features acting as master regulators of the emerging phenotype. This study supports, for the first time, 3D fibroblast spheroids as a suitable experimental tool to dissect vEDS pathogenesis and a crucial model for identifying new therapeutic targets.