DNA analysis of low- and high-density fractions defines heterogeneous subpopulations of small extracellular vesicles based on their DNA cargo and topology

J Extracell Vesicles. 2019 Aug 27;8(1):1656993. doi: 10.1080/20013078.2019.1656993. eCollection 2019.

Abstract

Extracellular vesicles have the capacity to transfer lipids, proteins, and nucleic acids between cells, thereby influencing the recipient cell's phenotype. While the role of RNAs in EVs has been extensively studied, the function of DNA remains elusive. Here, we distinguished novel heterogeneous subpopulations of small extracellular vesicles (sEVs) based on their DNA content and topology. Low- and high-density sEV subsets from a human mast cell line (HMC-1) and an erythroleukemic cell line (TF-1) were separated using high-resolution iodixanol density gradients to discriminate the nature of the DNA cargo of the sEVs. Paired comparisons of the sEV-associated DNA and RNA molecules showed that RNA was more abundant than DNA and that most of the DNA was present in the high-density fractions, demonstrating that sEV subpopulations have different DNA content. DNA was predominately localised on the outside or surface of sEVs, with only a small portion being protected from enzymatic degradation. Whole-genome sequencing identified DNA fragments spanning all chromosomes and mitochondrial DNA when sEVs were analysed in bulk. Our work contributes to the understanding of how DNA is associated with sEVs and thus provides direction for distinguishing subtypes of EVs based on their DNA cargo and topology.

Keywords: DNA topology; Small extracellular vesicles; cell-free DNA; density gradient; exosomes; extracellular DNA; histones; sEVs.

Grant support

This work was funded by grants from the Swedish Research Council, the Swedish Cancer Foundation, VBG Group Herman Krefting Foundation for Asthma and Allergy Research, and the Swedish Heart and Lung Foundation. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The authors also thank the Cost Action BM1202 MEHAD for the Short-Term Scientific Missions (STSMs) Grant (ME-HaD) for ELI to visit the Krefting Research Centre at the University of Gothenburg;Hjärt-Lungfonden;Cost Action BM1202 MEHAD for the Short Term Scientific Missions (STSMs) Grant (ME-HaD).