Exosomal cargo genes as biomarkers and potential mediators of exosome-driven cell communication in Pleural Mesothelioma

Pleural mesothelioma (PM) is a rare yet aggressive and heterogeneous cancer type with very poor survival rates. Due to its long latency period and nonspecific symptoms, the disease is usually detected at advanced stages, limiting available treatment options and leading to poor survival rates. So far, the disease can only be confirmed through invasive thoracoscopic biopsy. Moreover, the proposed circulating protein biomarkers lack sensitivity and specificity, highlighting the urgent need for novel approaches. In our previous work, we characterized the transcriptomic profile of extracellular vesicles secreted by PM cells and demonstrated their feasibility as a source of circulating biomarkers. To further investigate the role of circulating RNA in tumor progression and its potential use in non-invasive testing for PM, here we present a detailed characterization of RNA cargo carried by PM exosomes - a distinct subset of extracellular vesicles known to serve as key mediators of intercellular communication. By utilizing primary cell cultures established from tissue samples of 11 PM and 6 non-PM patients, followed by exosome isolation, and total RNA sequencing of RNA from isolated exosomes, matching cells, and tissues, we provide new evidence on exosomal RNA secretion, regulation of PM-exosome cargo genes, and their potential functions in recipient cells. We show that PM-exosomal cargo is enriched in genes associated with proliferation, whose key transcriptional factors are SETDB1, FOXM1 and GATA2. We identified Pcbp2, Srsf1 and Srsf9, RNA-binding proteins, which may be involved in selective cargo sorting into PM-exosomes. Our analysis identified six secreted genes, including GAS5, AL031666.3, RSLD1D1, AC103740.2, ADAM10, and AC020892.1, whose exosomal expression was associated with patient survival, as promising biomarkers for patient diagnosis, stratification, and prognosis assessment. Finally, we identify potential target genes of candidate LncRNAs biomarkers and processes in which they are involved.