Extracellular Vesicles Carry Distinct Proteo-Transcriptomic Signatures That are Different from Their Cancer Cell of Origin

Abstract

Circulating extracellular vesicles (EVs) contain molecular footprints from their cell of origin and may provide potential non-invasive access for detection, characterization, and monitoring of numerous diseases. Despite their growing promise, the integrated proteo-transcriptomic landscape of EVs and their donor cells remain poorly understood. To assess their cargo, we conducted small RNA sequencing and mass spectrometry (LC-MS/MS) of EVs isolated from in vitro cancer cell culture and prostate cancer patients serum. Here, we report that EVs enrich for distinct molecular cargo, and their proteo-transcriptome is predominantly different from their cancer cell of origin, implicating a coordinated disposal and delivery mechanism. We have discovered that EVs package their cargo in a non-random fusion, as their most enriched RNAs and proteins are not the most abundant cargo from their donor cells. We show that EVs enrich for 4 times more cytoskeletal and 2 times extracellular proteins than their donor cells. While the donor cells carry 10 times more mitochondrial and 3 times nuclear proteins than their EVs. EVs predominantly (40-60%) enrich for small RNA (~15-200 nucleotides) molecules that implicate cell differentiation, development, and signaling signatures. Finally, our integrated proteo-transcriptomic analyses reveal that EVs are enriched of RNAs (RNY3, vtRNA, and MIRLET-7) and their complementary proteins (YBX1, IGF2BP2, SRSF1/2), implicating an interrelated mechanism that may protect and regulate transcripts until a biological function is achieved. Based on these results, we envision that the next-generation clinical assays will take an integrative multi-omic (proteomic and transcriptomic) approach for liquid biopsy in numerous diseases.

A review of suspension trapping digestion method in bottom‐up proteomics

“…Recently, Chen et al. used the S‐Trap method to identify proteins in EVs isolated from cell culture media (human prostate cancer cell lines 22RV1) [91]. The authors found 422 proteins for EVs and 5630 proteins for donor cells.…”

Developmental Aspects of SARS-CoV-2, Potential Role of Exosomes and Their Impact on the Human Transcriptome

“…Exosomes are secreted by all cell types studied to date [62][63][64]. With respect to the placental lineage, exosomes have been investigated from mesenchymal, endothelial, and trophoblastic lineages and have been demonstrated to suppress T-cell expression [65].…”

“…Hence, exosomal transcriptome analysis has the potential to inform about some of the complexities that have been reported in pregnant women who have received COVID-19 vaccines [94]. Exosomes are also significant for other diseases, because their participation in signaling pathways and cell-to-cell communication impacts the tumor microenvironment [62,63,91,95].…”