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

• Understand extracellular-vesicle biogenesis, cargo, isolation, characterisation, and biological functions.
• Explore disease-associated exosomal miRNAs, genes, proteins, and experimental information using EV databases.
• Analyse miRNA targets, biological pathways, and protein-interaction networks related to selected diseases.
• Apply bioinformatics tools to construct and interpret ncRNA–gene–pathway regulatory networks.
• Develop a preliminary exosomal biomarker panel or therapeutic network using integrated molecular data.

📅 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:

• Differentiate exosomes, microvesicles, and apoptotic bodies based on their origin and biological roles.
• Retrieve and curate disease-associated extracellular-vesicle molecules from specialised databases.
• Predict miRNA target genes and perform functional and pathway-enrichment analysis.
• Construct and visualise miRNA–gene and protein-interaction networks using STRING and Cytoscape.
• Prepare a preliminary exosomal ncRNA biomarker panel or therapeutic-network framework for a selected disease.

• Graduate and postgraduate students in biotechnology, bioinformatics, molecular biology, biochemistry, microbiology, pharmacy, and life sciences
• PhD scholars, research fellows, and academicians
• Faculty members and laboratory researchers
• Biotechnology, pharmaceutical, diagnostic, and healthcare industry professionals
• Researchers working in cancer biology, regenerative medicine, liquid biopsy, ncRNA therapeutics, or drug delivery