Extracellular vesicle (EV) microRNAs are of major interest as potential diagnostic biomarkers in all cancer types. Researchers at La Trobe University aimed to identify miRNA profiles of shed microvesicles (sMVs) and exosomes (Exos) secreted from the isogenic colorectal cancer (CRC) cell lines SW480 and SW620 and evaluate their ability to predict CRC. Deep sequencing of miRNAs in parental cell lysates (CLs) and highly-purified sMVs and Exos was performed.
The researchers focused on miRNAs enriched in EVs and dysregulated miRNAs in metastatic cells (SW620) relative to primary cancer cells (SW480). They investigated the ability of EV miRNA signatures to predict CRC tumours using 594 tumours (representing different pathological stages) and 11 normal samples obtained from TCGA. In SW480 and SW620 cells we identified 345 miRNAs, of which 61 and 73 were upregulated and downregulated in SW620-CLs compared to SW480-CLs, respectively. Selective distribution of cellular miRNAs into EVs results in distinct miRNA signatures for sMVs and Exos in each cell line. Cross cell line comparisons of EV miRNA profiles reveal a subset of miRNAs critical in CRC progression from primary carcinoma to metastasis. Many miRNAs non-detectable (<5 TPM) in CLs were significantly enriched (>1000 TPM) in secreted EVs. Strikingly, miR-7641 which is non-detectable in SW480-CL but upregulated in SW620-CL is highly enriched in EVs secreted from both cell lines. Pearson correlation analysis demonstrated that EV miRNA profiles can be used to predict CRC tumours with ~96% accuracy. These findings suggest that EV miRNA profiles from CRC cell lines may allow prediction of CRC tumours, and that miR-7641 may serve as an attractive candidate for the specific, non-invasive diagnosis and prognosis of CRC.
Analysis of cellular miRNAs in human colon cancer cell models
A, Venn diagrams of miRNAs identified in SW480/ SW620 cell lysates (biological replicates combined) and for each cell line the number of unique miRNAs that selectively distribute to secreted EVs: sMVs and Exos. B, Correlation coefficient heat map shows limited variability between biological replicates (R1-2) and illustrates differences between miRNA profiles of SW480/SW620-CLs and their secreted EV subtypes. C, Differential miRNA expression analysis (log2 FC >1 or <-1, p-value <0.05, FDR <0.05) in SW480/SW620 cell lines by edgeR revealed 134 dysregulated miRNAs. Of these, 73 are miRNAs down-regulated in SW620-CL and 61 up-regulated, relative to SW480-CL; the Venn diagrams show the number of dysregulated miRNAs that selectively distribute to SW480/SW620 secreted EVs.