Human endogenous retrovirus profiling reveals heterogenous expression in cutaneous melanoma

Background Cutaneous melanoma (CM) is a cancer of the pigment-producing melanocytes of the skin. Advances in treatment with immune checkpoint inhibitors (ICI) have greatly improved the outcomes, although not all patients with CM respond to ICI. Emerging evidence shows that ICI responsiveness is correlated with the expression of certain human endogenous retroviruses (HERVs). We aimed to investigate the relationships between HERV expression and outcomes in patients with CM. Methods We characterized HERV expression from 330 patients with primary or metastatic CM using Telescope, a computational software package that calculates the expression of HERV loci from bulk RNA sequencing datasets. Results We found that HERVs expression differed between primary and metastatic CM. Using HERV expression alone, three subtypes of metastatic CM had distinct survival outcomes. Among the differentially expressed HERV loci in metastatic and treatment non-responders, we identified HERV-FRD which has the potential to produce the endogenous retrovirus group V Env polyprotein (syncytin-2) precursor. Conclusion Our analyses demonstrate the unique features of HERV expression in CM metastases and in ICI responsiveness. These exploratory findings identify modulated HERVs in CM, and further studies should be developed to determine whether HERV expression has any predictive or clinical utility.