Exosomes and Extracellular Vesicles: ncRNA Biomarkers, Therapeutic Delivery and Network Analysis

Aim

Workshop Objectives

Workshop Structure

📅 Day 1: Extracellular-Vesicle Biology, Isolation and Database Exploration

• Introduction to extracellular vesicles and intercellular communication
• Differences between exosomes, microvesicles, and apoptotic bodies
• Extracellular-vesicle biogenesis, secretion, cellular uptake, and biological functions
• EV cargo: miRNA, lncRNA, mRNA, proteins, lipids, and metabolites
• Principles of EV isolation and purification
• Differential ultracentrifugation, size-exclusion chromatography, precipitation, and immunoaffinity capture
• EV characterisation using nanoparticle tracking analysis, electron microscopy, flow cytometry, and Western blotting
• Importance of standardised EV reporting and experimental guidelines
• Introduction to extracellular-vesicle databases and data resources

🛠️ Hands-on:

• Explore extracellular-vesicle cargo using Vesiclepedia and ExoCarta
• Search for exosomal miRNAs, proteins, and genes associated with a selected disease
• Review EV isolation and characterisation information using EV-TRACK
• Prepare a curated list of disease-associated extracellular-vesicle molecules

🧰 Tools Covered:

Vesiclepedia, ExoCarta, EV-TRACK, extracellular-vesicle datasets, and data-curation templates

📅 Day 2: Exosomal ncRNA Biomarkers and Disease-Network Analysis

• Biological roles of exosomal miRNAs and lncRNAs
• Exosomal ncRNA-mediated regulation of gene expression
• miRNA–mRNA and lncRNA–miRNA–mRNA regulatory relationships
• Identification of disease-associated exosomal biomarkers
• Principles of miRNA target prediction
• Construction of miRNA–gene and ncRNA-regulatory networks
• Gene Ontology and pathway-enrichment analysis
• Protein–protein interaction-network analysis
• Cancer, inflammation, wound-healing, and immune-regulation case studies
• Interpretation of hub genes, regulatory miRNAs, and disease-associated pathways

🛠️ Hands-on:

• Select candidate exosomal miRNAs from the Day 1 dataset
• Predict miRNA target genes using miRDB and TargetScan
• Perform functional and pathway-enrichment analysis using Enrichr
• Analyse protein–protein interactions using STRING
• Construct and visualise a miRNA–gene–pathway network in Cytoscape

🧰 Tools Covered:

miRNet, miRDB, TargetScan, Enrichr, STRING, Cytoscape, and exosomal ncRNA datasets

📅 Day 3: Exosome-Based Therapeutics, Liquid Biopsy and Biomarker-Panel Development

• Exosomes as natural therapeutic-delivery vehicles
• Loading of RNA, drugs, proteins, and genome-editing components into exosomes
• Native and engineered exosome-delivery systems
• Exosome surface modification and tissue-specific targeting
• Exosomal biomarkers for liquid-biopsy applications
• Candidate miRNA and lncRNA prioritisation
• Therapeutic-target and regulatory-network analysis
• Evaluation of biomarker specificity, biological relevance, and clinical potential
• Challenges in exosome manufacturing, standardisation, scalability, and clinical translation
• Development of multi-marker exosomal diagnostic panels

🛠️ Hands-on:

• Integrate exosomal ncRNA, target-gene, pathway, and interaction data
• Rank candidate miRNAs using biological and network-based criteria
• Identify hub genes and key regulatory pathways
• Develop a preliminary exosomal biomarker panel
• Prepare a therapeutic or diagnostic network for a selected disease
• Generate data summaries and visualisations in Google Colab

🧰 Tools Covered:

Google Colab, Python, pandas, miRNet, Enrichr, STRING, Cytoscape, and biomarker-ranking templates

Who Should Enrol?

Important Dates

Workshop Outcomes