Characterization of RNA in exosomes secreted by human breast cancer cell lines using next-generation sequencing

Abstract

Exosomes are nanosized (30–100 nm) membrane vesicles secreted by most cell types. Exosomes have been found to contain various RNA species including miRNA, mRNA and long non-protein coding RNAs. A number of cancer cells produce elevated levels of exosomes. Because exosomes have been isolated from most body fluids they may provide a source for non-invasive cancer diagnostics. Transcriptome profiling that uses deep-sequencing technologies (RNA-Seq) offers enormous amount of data that can be used for biomarkers discovery, however, in case of exosomes this approach was applied only for the analysis of small RNAs. In this study, we utilized RNA-Seq technology to analyze RNAs present in microvesicles secreted by human breast cancer cell lines.Exosomes were isolated from the media conditioned by two human breast cancer cell lines, MDA-MB-231 and MDA-MB-436. Exosomal RNA was profiled using the Ion Torrent semiconductor chip-based technology. Exosomes were found to contain various classes of RNA with the major class represented by fragmented ribosomal RNA (rRNA), in particular 28S and 18S rRNA subunits. Analysis of exosomal RNA content revealed that it reflects RNA content of the donor cells. Although exosomes produced by the two cancer cell lines shared most of the RNA species, there was a number of non-coding transcripts unique to MDA-MB-231 and MDA-MB-436 cells. This suggests that RNA analysis might distinguish exosomes produced by low metastatic breast cancer cell line (MDA-MB-436) from that produced by highly metastatic breast cancer cell line (MDA-MB-231). The analysis of gene ontologies (GOs) associated with the most abundant transcripts present in exosomes revealed significant enrichment in genes encoding proteins involved in translation and rRNA and ncRNA processing. These GO terms indicate most expressed genes for both, cellular and exosomal RNA.For the first time, using RNA-seq, we examined the transcriptomes of exosomes secreted by human breast cancer cells. We found that most abundant exosomal RNA species are the fragments of 28S and 18S rRNA subunits. This limits the number of reads from other RNAs. To increase the number of detectable transcripts and improve the accuracy of their expression level the protocols allowing depletion of fragmented rRNA should be utilized in the future RNA-seq analyses on exosomes. Present data revealed that exosomal transcripts are representative of their cells of origin and thus could form basis for detection of tumor specific markers.

Multiparameter Evaluation of the Heterogeneity of Circulating Tumor Cells Using Integrated RNA In Situ Hybridization and Immunocytochemical Analysis

“…Another hypothesis is that these bright, extracellular spots are extracellular vesicles. The extracellular vesicles secreted from some cancer cell lines have been found to contain many tumor-related mRNA sequences via RT-PCR and RNA microarrays (40, 41). Further work is needed to examine the hypotheses and better understand the phenomenon.…”

Functions of Exosomes and Microbial Extracellular Vesicles in Allergy and Contact and Delayed-Type Hypersensitivity

“…Importantly, functional mRNA and miRNAs can be a small percentage of the total exosome RNA [2,54,55]. However, functions of many of the miRNAs still have to be delineated.…”

“…However, functions of many of the miRNAs still have to be delineated. The remaining RNA cargo is usually made up of other classes of RNA, including long non-coding RNAs of unknown significance, along with numerous ribosomal RNA fragments and tRNAs, also of unknown functions [2,54,55]. Therefore, exosome exchange of molecules between cells is a sophisticated and potentially quite heterogeneous process of great complexity, with diverse functional consequences for mediation and modulation of cellular functions in immunity, allergy and hypersensitivity.…”

Exosomes: From Garbage Bins to Promising Therapeutic Targets

“…Notably, tumor cells have been shown to produce and secrete exosomes in greater numbers than normal cells [2]. Exosomes have been found in numerous body fluids, including blood, amniotic fluid, urine, malignant ascites, cerebrospinal fluid, breast milk, saliva, lymph, and bile, under both healthy and morbid conditions [3,4,5].…”