Detection of candidate melanoma blood biomarkers by RNA-Sequencing

Abstract

Due to the high lethality of melanoma, the prediction and non-invasive confirmation of potential melanoma patients of disease-free states is of great interest. The detection of circulating melanoma cells in human blood is a non-invasive surrogate marker of melanoma. We used the publicly available RNA-Sequencing (RNA-Seq) datasets from peripheral blood cells of a melanoma patient and healthy primary melanocytes cells as controls. Differentially expressed genes (DEGs) between peripheral blood from melanoma patients and normal melanocytes were identified by HTSeq followed by DESeq. A total of 2,470 DEGs were obtained, which was analyzed by Gene Set Enrichment Analysis. We indicated that the Gene Ontology term neurogenesis is significantly over-represented by the DEG list, which is consistent with the rapid formation of melanoma. In addition, the pathway analysis revealed that several cancer-related pathways are over-represented. We also found several over-represented transcription factors, such as SMAD3, NFAT, which may be important upstream regulators to influence the dysregulation of the DEGs. Finally, we used available publications to validate top two genes in DEG list, while other DEGs may still need further investigation including computational and experimental efforts. Altogether, the top ranked DEGs may represent clinically useful biomarkers from blood, which would help the early diagnosis of melanoma.