Biology subjects

Eldahshoury, M. K.

Publications and source records attributed to Eldahshoury, M. K..

4 recordsLinked to original sources

bioRxiv2026

Isolation Strategy Shapes the Matrisome Landscape of Cancer-Associated Fibroblast Extracellular Vesicles

Cancer-associated fibroblasts (CAFs) secrete small extracellular vesicles (sEVs) that mediate stromal remodelling, tumour progression, and pre-metastatic niche formation. A foundational assumption in EV research is that MISEV-compliant preparations from the same conditioned medium are biologically equivalent. Here, we directly challenged this assumption through a side-by-side comparison of ultracentrifugation (UC), size exclusion chromatography (SEC), and the EXODUS nanofiltration platform using breast CAF-conditioned media, characterised in accordance with MISEV2023 guidelines using nanoparticle tracking analysis, cryogenic transmission electron microscopy (Cryo-TEM), and quantitative proteomics. EXODUS and SEC recovered approximately 7-fold more particles per mL than UC. While Cryo-TEM confirmed intact vesicle morphology across all methods, UC preparations exhibited substantial non-vesicular background, with gene ontology analysis revealing significant enrichment of ribosomal, mitochondrial, and ER-derived proteins absent from EXODUS and SEC. Matrisome profiling further uncovered method-dependent divergence in the composition of core versus matrisome-associated proteins, highlighting differences extending beyond standard purity metrics. These findings demonstrate that MISEV2023 compliance is necessary but insufficient for methodological equivalence. The isolation method should be treated as a biological variable and selected according to the EV subpopulation or cargo class under investigation.

cancer biology↗

bioRxiv2025

Extracellular vesicles from a model of melanoma cancer-associated fibroblasts induce changes in brain microvascular cells consistent with pre-metastatic niche priming.

Malignant melanoma has one of the lowest 5-year survival rates of any cancer, and is recognised for being particularly invasive and metastatic, with the poorest survival outcomes in brain metastases patients. A key characteristic of these tumours is crosstalk between melanoma cells and cells of the tumour microenvironment (TME), such as cancer associated fibroblasts (CAFs). The role of melanoma-derived small extracellular vesicles (sEVs) in potentiating CAFs has been studied extensively, however the role of CAF sEVs in regulation of the local TME and distal pre-metastatic niche (PMN) is less clear. Here, we demonstrate that sEVs derived from an in vitro model of melanoma CAFs alter melanoma to promote oncogenic parameters within models of the TME and target a model of the brain PMN to promote changes associated with melanoma extravasation. Cargo profiling of these sEVs found significant differential expression of proteins, and RNA associated with pre-metastatic niche remodelling and unfavourable outcomes in patients. Together these data suggest a role for CAF sEVs in local and distal PMN formation, highlighting a potential therapeutic target for metastatic melanoma and identifying prospective liquid biomarker reservoirs.

cancer biology↗

bioRxiv2025

eRNAkit: Expanding the Functional Atlas of human Enhancer RNAs Beyond the Nucleus

Enhancer RNAs (eRNAs) are a class of non-coding RNAs transcribed from active enhancers that regulate various aspects of transcription. Although traditionally viewed as nuclear-localised and unstable transcripts, large transcriptomic studies reveal they vary widely in localisation and biochemical properties, including detectable accumulation in cytoplasmic compartments. These observations suggest potential non-nuclear functions for eRNAs, yet existing databases remain focused on nuclear, cis-regulatory roles, limiting systematic exploration of their broader regulatory repertoire. Here we present eRNAkit, a comprehensive and accessible resource designed to address this gap by integrating subcellular localisation, RNA-RNA interaction and expression data for annotated eRNAs. Leveraging fractionation-based RNA-Seq datasets, eRNAkit profiles eRNA distribution across nuclear and cytoplasmic compartments. It incorporates gene expression data spanning major human organs and primary cell types, enabling tissue-specific analysis of eRNA function. Crucially, eRNAkit includes experimentally derived RNA-RNA interaction data from RIC-Seq, PARIS, and KARR-Seq, supporting exploration of trans-acting and cytoplasmic roles for eRNAs grounded in physical interaction evidence. eRNAkit expands current eRNA resources beyond the enhancer-promoter paradigm, offering a robust platform for dissecting non-canonical functions of eRNAs and advancing our understanding of their full regulatory potential in human biology. The eRNAkit resource is available to download at https://github.com/AneneLab/eRNAkit.

molecular biology↗

bioRxiv2024

The two crystal structures of unloaded and cargo-loaded Vacuolar Sorting Receptor 1 lumenal domain (VSR1-Nt) reveal two cargo binding sites and a mechanism of transport.

Vacuolar sorting receptors (VSRs) are type I membrane proteins crucial for seed germination and plant development. While VSR trafficking has been extensively studied, the mechanism of cargo binding and release by the N-terminal lumenal region is less understood. We have elucidated the crystal structures of unloaded and cargo-loaded forms of the lumenal region of VSR1 containing the protease-associated domain, the Central domain and epidermal growth factor-like repeats. Calcium coordination induces remodeling of the linkers between domains, triggering large conformational changes that expose two binding sites, one across the PA and Central domain and a second site in the Central domain. Our findings provide a mechanistic model for cargo binding in a calcium rich environment, where VSR is locked in a conformation exposing the cargo binding sites, while cargo release is favoured by lower calcium concentrations and trimer formation. These results advance our current knowledge on VSRs and will inform future studies on vacuolar trafficking and cargo binding/release.

plant biology↗