Conserved and Tissue‐Specific RNA and Protein Cargos of Small Extracellular Vesicles From 120 Tissue Sites Across 34 Organs in a Single Pig

ABSTRACT Small extracellular vesicles (sEVs) carry diverse cargo essential for intercellular communication, but their organism‐wide characterization across all tissues is still limited. Here, we present a multi‐omics sEV atlas covering the whole‐body of 120 tissue sites, four body fluids and nine gastrointestinal contents from the same pig. We identified 7995 proteins, 337 miRNAs as well as 105,409 transcripts (93,409 full‐length) in sEVs by mass spectrometry, next‐ and third‐generation RNA sequencing. Among these, a conserved cargo set of 252 proteins, 18 miRNAs and 1227 transcripts was defined, including RNA‐binding proteins (ANXA2, ALIX and MVP), mitochondrial proteins (ATP5F1A, COX6C and VDACs), the let‐7 miRNA family and ferritin genes ( FTH1 / FTL ). Notably, sEV biogenesis‐associated ACTG1, CFL1 and ANXA2 were detected in all samples, suggesting their potential as novel sEV protein markers. In contrast, 2638 proteins, 152 miRNAs and 1000 transcripts showed organ‐specific expression patterns, which are likely to underpin organ‐specific biological processes. Moreover, by using this multi‐omic dataset and additional RIP assays, we found that HNRNPU participates in the sorting of hypoxia‐responsive EPAS1 into sEVs. This comprehensive sEV atlas establishes a foundation for future studies in sEV cell biology.