Biomarkers Discovery: The Benefit of the Study Exosomes Originated from Merkel Cell Carcinoma Cell Lines

Abstract

Merkel cell carcinoma (MCC) is a rare, aggressive neuroendocrine form of skin cancer with a rising incidence and a high mortality rate. The risk of developing Merkel cell carcinoma increased among a large number of immunosuppressed patients. The origin of cancer not known and the pathogenesis of MCC not fully understood. Two causes can initiate MCC tumorigenesis, such as accumulation of UV-induced mutations in the MCPyV-negative MCCs and Merkel cell polyomavirus (MCPyV)-encoded genes in MCPyV-positive tumor. Approximately 80% of all MCCs are positive for viral DNA of MCPyV. Immune therapy is a promising treatment for MCC patients, but it has failed to arrest the cancer progression. Precision medicine is needed. Precision medicine is a core of highly specific biomarkers disclose information for diagnosis, prognosis, and therapy. The usefulness of a biomarker lies in its ability to provide an early indication of a disease and its progression, and it should be easy to detect and measure. Our research aim was to investigate by high-throughput approaches for screening and analysis of two different types of MCC cell lines and their exosomes. Our proteomic investigation result showed that MCPyV-negative and –positive Merkel cell lines’ exosomes contain several proteins associated with tumor cell motility and metastasis. We identified a list of vesicular proteins derived from the extracellular region, which upregulated in exosome from MCPyV-negative MCC cell lines compare to MCPyV-positive MCC cell lines. We did the next-generation sequencing screening of exosomal small RNA from two groups of MCC cell lines. Main findings investigated in samples from healthy donors and MCC patients. The result showed the exosomal miR-222-3p presence in all type of samples derived from MCC cell lines, healthy donors and patients. The miR-222-3p selectively sorted in exosomes. The target genes’ screening indicates that the exosomal miR-222-3p play pleiotropic role dependent on recipient cells in health and disease. Then, the proteomic investigation and integrated analyses revealed the MCPyV-negative MCC cell lines loss the DNA, RNA and protein synthesis and their regulation system activity, and have an unusual event of protein expression at cell proliferation and post-translational modification sites. These may lead to transcription-associated mutation (TAM) and transcription-associated recombination (TAR), which gave a rise a high mutational burden. The MCPyV-positive MCC cell lines showed upregulated expression of proteins involved in DNA transcription initiation, termination, modification, and repair, harnesses of polyomaviruses for DNA integration. Following upregulated proteins of RNA, protein synthesis and post-translational modification machinery such as the protein acylation culminates in the viral proteins and genome synthesis. However, a fixed exosome-ER accession ability and a low activity on endocytosis and exocytosis sites indicate to reduce the chance of MCPyV spreading. Finally, transcriptomic and proteomic approaches are powerful tools for cell phenotyping and biomarkers discovery.