Head and neck squamous cell carcinomas (HNSCC) are highly immunosuppressive. Exosomes are small extracellular vesicles that mediate intercellular communication. HNSCC patient’s plasma is enriched in immunomodulatory exosomes which correlate with clinical parameters. We investigate the miRNA and mRNA signatures of plasma-derived exosomes as potential biomarkers for HNSCC.
Exosomes were isolated from plasma of 16 HNSCC patients and 12 healthy donors (HD) by ultrafiltration and differential (ultra)centrifugation (EV-Track ID 210344). Primary tumor cells were obtained from the same HNSCC patients. Total exosomal and tumor RNA was used for targeted profiling of 798 miRNAs and 730 mRNAs. Differential presence and discriminatory potential of exosomal RNAs between HNSCC and HD were analyzed by multiple Mann-Whitney test and unsupervised hierarchical clustering. Ingenuity pathway analysis was applied to predict downstream effects of miRNAs and identify related pathways.
Of all detected exosomal RNAs, 55% miRNAs and 31% mRNAs were HNSCC-exclusive, while 8% miRNAs and 48% mRNAs were HD-exclusive. 91 miRNAs and 347 mRNAs were significantly differentially present between HNSCC and HD exosomes. Both exosomal RNA signatures could successfully assign samples to “Tumor” or “Healthy”. 165 miRNAs and 146 mRNAs overlapped between corresponding tumor and exosomes and were considered as tumor-originating RNAs. These were filtered to 23 miRNAs inversely targeting 17 mRNAs, e.g. upregulated miR-421-3p targeting downregulated, anti-tumor IL15. Identified core hubs of tumor-originating RNAs were related to TLR, NF-κB and IFN signaling.
Exosomal miRNA and mRNA signatures have high discriminatory potential between HNSCC patients and HD. Final RNA candidates are currently validated in an independent cohort. Identified RNAs were related to pathways of immune regulation, inflammatory response and cellular development which highlights their relevance for disease pathogenesis.
The authors.
German Research Foundation.
All authors have declared no conflicts of interest.