exoRBase 3.0: an updated resource for extracellular RNAs from human biofluids

Area of Science:

• Biochemistry
• Genomics
• Bioinformatics

Background:

• Extracellular RNAs (exRNAs) in biofluids are key noninvasive biomarkers for disease detection.
• Understanding the distinct origins of exRNAs (e.g., vesicle-bound vs. cell-free) is crucial for optimizing liquid biopsy.
• Existing databases lack comprehensive comparative analysis of different extracellular RNA fractions.

Purpose of the Study:

• To present exoRBase 3.0, an expanded database integrating and comparing extracellular long RNAs (exLRs).
• To provide the first large-scale platform for distinguishing between EVP-associated and cell-free exLRs.
• To facilitate comparative analysis of RNA expression, pathways, and origins for improved liquid biopsy strategies.

Main Methods:

• Systematic integration of exLR data from extracellular vesicles and particles (EVPs) and cell-free fractions.
• Development of a comparative analysis platform distinguishing between EVP-associated and cell-free exLRs.
• Inclusion of interactive visualizations and expanded pathway analysis for 12,981 gene sets.

Main Results:

• exoRBase 3.0 integrates 19,927 mRNAs, 15,961 lncRNAs, and 126,816 circRNAs from 2,913 samples (blood, urine, CSF, bile).
• The database enables large-scale comparison of exLRs from EVP and cell-free fractions.
• Enhanced pathway analysis facilitates understanding of functional roles and tissue origins.

Conclusions:

• exoRBase 3.0 is a valuable resource for comparative analysis of exLRs from different biofluid fractions.
• This resource supports the identification of context-specific RNA biomarkers for precision medicine.
• The findings advance noninvasive disease diagnosis, monitoring, and therapeutic applications using liquid biopsies.