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

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.