Serum Extracellular Vesicle-Derived microRNAs as Potential Biomarkers for Pleural Mesothelioma in a European Prospective Study

Abstract

Malignant pleural mesothelioma (MPM) is an aggressive cancer with a dismal prognosis. Early therapeutic interventions could improve patient outcomes. We aimed to identify a pattern of microRNAs (miRNAs) as potential early non-invasive markers of MPM. In a case-control study nested in the European Prospective Investigation into Cancer and Nutrition cohort, we screened the whole miRNome in serum extracellular vesicles (EVs) of preclinical MPM cases. In a subgroup of 20 preclinical samples collected five years prior MPM diagnosis, we observed an upregulation of miR-11400 (fold change (FC) = 2.6, adjusted p-value = 0.01), miR-148a-3p (FC = 1.5, p-value = 0.001), and miR-409-3p (FC = 1.5, p-value = 0.04) relative to matched controls. The 3-miRNA panel showed a good classification capacity with an area under the receiver operating characteristic curve (AUC) of 0.81 (specificity = 0.75, sensitivity = 0.70). The diagnostic ability of the model was also evaluated in an independent retrospective cohort, yielding a higher predictive power (AUC = 0.86). A signature of EV miRNA can be detected up to five years before MPM; moreover, the identified miRNAs could provide functional insights into the molecular changes related to the late carcinogenic process, preceding MPM development.

Keywords: biomarkers; early changes; malignant pleural mesothelioma; microRNAs; next generation sequencing.

Figure 1

Volcano plot of differentially expressed miRNAs. Each dot represents a miRNA. The green dot represents miR-11400 significantly differentially expressed at FDR ≤ 0.05. The gray dots represent miRNAs that were not significantly differentially expressed at FDR.

Figure 2

Boxplots show expression levels of miR-11400 (a), miR-148a-3p (b), miR-409-3p (c), and miR-4508 (d), in pre-clinical MPM cases collected up to five years before diagnosis and matched controls. Above each boxplot, the p-values yielded by DESeq2 after adjustment for multiple testing (FDR) or nominal p-value.

Figure 3

Enrichment analysis of KEGG pathways relative to validated target genes of miR-409-3p and miR-148a-3p. Bar plots show the significantly enriched functional categories ordered by p-value.

Figure 4

KEGG enrichment analysis of KEGG pathways relative to predicted target genes of miR-11400. Bar plots depict the significantly enriched terms ordered by p-value.

Figure 5

Receiver operating characteristics (ROC) curves of the three miRNAs signature (miR-11400, miR-148a-3p, and miR-409-3p) for the discrimination between preclinical MPM and matched controls (solid line), as well as for discriminating between MPM at diagnosis and healthy controls (dashed line). The area under the curve (AUC) shows the percentage of correct discrimination associating sensitivity (Y) and 1-specificity (X).