Comprehensive profiling of RNAs enriched in small extracellular vesicles of colorectal cancer patients

The main objective of this project was to determine RNA expression profiles in small extracellular vesicles isolated from low volumes of blood serum of colorectal cancer (CRC) patients and to compare the data with those of healthy controls (HC) in order to identify molecules (mainly lncRNAs and protein-coding genes) that could serve as novel non-invasive biomarkers for early diagnosis of CRC. In total, we have identified 4,014 transcripts to be differentially expressed between two studied groups (adjusted P < 0.05). From those, 1,469 were assigned to lncRNAs (36.6%), while protein-coding genes represented the second most common gene biotype (1,166 transcripts; 29%). The hierarchical clustering proved that it is possible to distinguish CRC samples from HC based on the expression of all significantly deregulated genes as well as protein coding genes and lncRNAs, separately or in combination. As this study was primarily focused on lncRNAs, more stringent criteria concerning several different parameters were set to identify lncRNAs with the highest potential to discriminate the two groups of samples. In total, we got 21 molecules, which met our requirements and thus were chosen for further evaluation in the training phase of the study by RT-qPCR. In total, 150 samples were involved in the study including 100 serum samples of CRC patients and 50 serum samples of HC. No replicates were involved.