Exosomes secreted by human cells transport largely mRNA fragments that are enriched in the 3'-untranslated regions

Abstract

Small secreted membrane vesicles called exosomes have recently attracted a great interest after the discovery that they transfer mRNA that can be translated into protein in recipient cells. Surprisingly, we found that for the majority of exosomal mRNAs only a fraction of their corresponding probes is detectable on the expression microarrays. Exosomal mRNA fragmentation is characterized with a specific structural pattern. The closer to the 3'-end of the transcript the fragments are localized, the larger fraction among the secreted RNAs they constitute. Since the 3'-ends of transcripts contain elements conferring subcellular localization of mRNA and are rich in miRNA-binding sites, exosomal RNA may act as competing RNA to regulate stability, localization and translation activity of mRNAs in recipient cells.

Reviewers: This article was reviewed by Neil Smalheiser and Sandor Pongor.

Figure 1

Detection of mRNA fragments in exosomes secreted by human cells. (A) Distribution of the transcripts by exosomal secretion of their fragments. Secreted transcripts were identified with ECER ≥ 3. Transcripts with all secreted probes were considered as secreted unfragmented. Fragmented transcripts were classified into three classes with i) majority, ii) minority and iii) exactly half of the probes secreted. (B) Cumulative fraction of fragmented transcripts in the total RNA measured in exosomes versus secretion magnitude (ECER cutoff). (C) Distribution of individual probe expression in exosomes by the magnitude of their secretion (ECER) and their location. The probes measure exosomal expression of specific fragments of the transcripts. Expression level is depicted with color ranging from red (low expression) to yellow (high expression). Relative location of the probes within their transcripts is represented by a number ranging from 0 (5’-end) to 1 (3’-end) with precision step 0.02 of the total relative length (1.0) of a transcript. (D) Dependence of probe localization relative to the 3’- and the 5’-ends of each individual transcript on the magnitude of its secretion (ECER). Only strongly secreted transcripts (ECER ≥ 10) are shown. Each dot represents a representative probe pair for an individual transcript (see details in Methods section). (E) Genomic view of CNDP2, RHO, and PPFIBP1 genes, along with the qPCR results for the SF295 intracellular and exosomal samples. The position of Agilent probes and the amplicons generated by PCR are shown in green and red. Expression was quantified by ΔCT between the genes of interest and that of a firefly luciferase cDNA spike-in control (See Additional file 3: Table S2 and Additional file 5). The potential post-transcriptional cleavage sites are designated by long dashed arrows.