miRNome sequencing of a large cohort of vascular Ehlers-Danlos syndrome patients' dermal fibroblasts reveals aberrantly expressed miRNAs involved in pathways relevant for the disease pathophysiology
Non-coding RNA profiling by high throughput sequencing
Summary
To investigate the potential role of miRNAs in disease mechanisms, we conducted a thorough analysis by comparing the entire miRNome of 18 vEDS dermal fibroblasts to those of 18 control cells. To improve statistical reliability, we sequenced each sample from both groups as biological replicates. By applying a log2 fold change threshold of greater than 1 or less than -1, and an adjusted p-value of less than 0.05, we identified 137 DE-miRNAs in patient vs. control fibroblasts. Among these, 71 miRNAs exhibited decreased expression, while 66 miRNAs were upregulated. To explore the functional relationship between DE-miRNAs and the altered gene expression profile of vEDS cells, we conducted an extensive review of the literature and consulted several bioinformatics databases. Our search involved utilizing data from four miRNA-target prediction databases (microT-CDS, Targetscan, miRTarBase, and miRwalk) in addition to relevant literature sources providing information on the functional roles of these miRNAs. We thus focused our research on a specific subset of DE-miRNAs, known as miR-15b-5p, miR-16-5p, miR-21-3p, miR-24-3p, miR-29a-3p, miR-29b-3p, miR-138-5p, miR-145-5p, and miR-195-5p, which may play a biological role in dysregulated molecular mechanisms underlying disease pathogenesis. Our initial emphasis was on miR-29a-3p and miR-29b-3p due to their involvement in regulating critical cellular processes such as ECM remodeling into the vascular network, autophagy, cell proliferation, and apoptosis. To study how miR-29a-3p and miR-29b-3p contribute to the dysregulated cellular processes observed in patient cells, we performed GO and pathway enrichment analyses on their predicted target DEGs. GO analysis revealed that both these miRNAs may disturb fundamental biological functions, such as regulation of transcription by RNA polymerase II, negative gene expression regulation, miRNA-mediated gene silencing, translation regulation, heterochromatin organization, and ECM organization. This comphrensive transcriptome analysis of a large cohort of dermal fibroblasts from patients with vEDS reveals deregulated biological functions potentially involved in the disease pathogenesis. Taken together, the abnormal expression of several miRNAs suggests the presence of epigenetic control in vEDS cells, which could influence the transcriptional regulation of numerous target DEGs and related biological processes, potentially influencing disease mechanisms.
This work was supported by Fondazione Telethon and the “Associazione con Giacomo contro vEDS”, (Grant number: GSA21F001, Seed Grant Fall 2021 vEDS) to Nicola Chiarelli.
Overall design
Comparative gene expression profiling analysis of miRNome sequencing data of fibroblast cell strains derived from 18 vEDS patients and 18 healthy donors
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