Validation of prognostic biomarkers for overall survival in melanoma patients undergoing autologous vaccination

Malignant Melanoma is deadliest type of skin cancer, seen with low frequency. Lack of diagnostic and prognostic markers are important obstacles during early detection and selection of appropriate adjuvant therapy for malignant melanoma patients. Upon early diagnosis of melanoma in patients with stage IA and IB, the survival rates for 5 to 10 years is above 85% based on American Cancer Society statistics. However, with increasing stage and low survival rates, selection of appropriate post surgical adjuvant therapy has high impact to increase the survival and life quality of patients. Immunotherapy trials targeting malignant melanoma (MM) patients have been developing in larger extents in the last 2 decades, considering melanoma is the most immugenic cancer type among all cancers. Based on these facts, we decided to search for prognostic biomarkers which will guide clinicians to define appropriate malignant melanoma patients to apply autologous vaccination as a post surgical adjuvant therapy. With the contribution of our collaborator research group, we were able to obtain 28 primary cell cultures of MM patients with known survival outcomes, and their gene expression profiles in Luminex platform. Grounding from the results of Unsupervised Survival Analysis Tool (USAT; a software designed to determine prognosis-associated mRNAs, developed in our laboratory), we decided to validate the expression profiles of prospective prognostic biomarker genes in the primary cell culture samples, with qRT-PCR. Subsequent to elimination of samples determined as being altered in culture over time, and thus no longer representing their expression profile, based on Sum of Absolute Rank Difference (SARD) analysis, 8 genes validated out of 10 in 21 samples were as follows; CT genes (SSX1, MAGEA1), EMT markers (CDX2, CLDN1), DNA repair genes (ERCC1, LIG3), transforming growth factor alpha (TGFα), A-kinase anchor protein 13 (AKAP13). Previous studies of our laboratory, concerning high immunogenic potential of CT genes in cancers, made SSX1 and MAGEA1 our major interest in autologous vaccinated MM patients. Our findings suggest that autologous vaccination might increase overall survival especially in malignant melanoma patients whose tumors show higher CT gene expression. We show that high expression of TGFα can also be used as a prognostic marker for identifying patients who will benefit from this treatment.