Nucleic Acids on the Surface and Lumen of Tumor-Derived Small Extracellular Vesicles as Potential Cancer Biomarkers

TL;DR

This study shows that tumor-derived small extracellular vesicles (TEX) contain DNA on their surface and inside, which could be used as cancer biomarkers.

Contribution

The study reveals that TEX have surface and luminal nucleic acids with tumor-specific mutational signatures, offering new biomarker potential.

Findings

Nucleic acids on the TEX surface support vesicle integrity and are disrupted by DNase/RNase.

The TEX lumen contains protected genomic DNA with a mutational signature matching the parent tumor.

TEX morphology changes after prolonged DNase/RNase treatment, forming smaller membrane-bound vesicles.

Abstract

Background: Tumor-derived small extracellular vesicles (sEV), which we call TEX, carry a cargo of molecules that resembles the producer tumor cells. Circulating freely in body fluids, TEX potentially serve as a liquid tumor biopsy. TEX horizontally transfer their cargo to various recipient cells, imparting to them pro-tumor activity. Mechanisms of TEX-driven reprogramming might involve nucleic acids, especially double-stranded (ds)DNA. Methods: TEX isolated from supernatants of human tumor cells were identified as sEV, based on their size, endocytic origin and morphology. TEX treated with DNase/RNase cocktail were examined by transmission and cryo-electron microscopy and tested for biologic activity. DNA was extracted from enzyme-treated TEX, quantified by Qubit and analyzed for fragment sizes. The presence of genomic DNA in TEX was confirmed by PCR, and sequencing of the TP53 gene fragment for a mutational signature was performed. Results: Enzymatic and microscopic studies of TEX showed that nucleic acids are present in the biocorona on the outer surface. Their removal interfered with the biocorona integrity. A short TEX exposure to DNase/RNase altered their morphology without impairing vesicle functions; longer treatments induced TEX re-organization into smaller membrane-bound vesicles. The TEX lumen contained long fragments of protected genomic DNA with a mutational signature reflecting that of the tumor. Conclusions: Nucleic acids present on the TEX surface support the vesicular integrity. The TEX lumen contains membrane-protected large (ds)DNA fragments with the mutational signature of the parent tumor. The presence of surface and luminal nucleic acids in TEX, and especially their mutational signature, suggests that TEX may serve as highly promising cancer-specific biomarkers.

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