Interferon-gamma-inducible protein 30 prevents IFN-γ-receptor 1 degradation to maintain PD-L1 and MHC-II levels in metastatic melanoma

Immunotherapies such as immune checkpoint inhibitors (ICIs) targeting programmed death protein 1 (PD-1) and programmed death-ligand 1 (PD-L1) have successfully improved outcomes in metastatic melanoma (MM) patients. PD-L1 and major histocompatibility complex class II (MHC-II) levels in tumor cells are critical in modulating ICI responses; however, the regulatory mechanisms controlling PD-L1 and MHC-II expression levels are still not fully characterized. Targeted mRNA sequencing data comparing tissue samples from MM patients (n = 25). Publicly available RNA-Seq [TCGA-SKCM (n = 383), PMID31792460 (n = 121), PRJEB23709 (n = 73)] and proteomic [PXD006003 (n = 63)] datasets from MM patients were utilized for bioinformatic analysis. Functional assays were performed on MM cell lines and multiplex immunofluorescence on tumor samples from MM patients to validate in-silico observations. Here, we showed that interferon gamma (IFN-γ) inducible factor 30 (IFI30) has a dual role in preventing PD-L1 and MHC-II lysosomal degradation mediated by cathepsin L (CTSL), and modulating IFN-γ pathway signaling. Briefly, IFI30, PD-L1, MHC-II and CTSL levels are stimulated by IFN-γ in MM cell lines. The basal and IFN-γ-stimulated protein/mRNA levels of PD-L1 and MHC-II dramatically decreased, while CTSL levels increased in MM with IFI30 knockdown. Blockage of lysosome acidification prevented PD-L1 protein degradation in MM with IFI30 knockdown. Conversely, CTSL knockdown significantly increased IFI30, PD-L1 and MHC-II levels. IFI30 knockdown decreased the levels of IFN-γ receptor 1 (IFNGR1) at the plasma membrane, blocked IFN-γ pathway downstream signaling, and decreased PD-L1 and MHC-II mRNA/protein levels. IFNGR1 knockdown in MM cells resembled the phenotype observed for IFI30 knockdown. Of clinical relevance, MM patients with high-IFI30 levels in tumor tissue samples showed a better progression-free survival and better responses to ICIs in three independent datasets (PMID31792460, PRJEB23709, and PXD006003). High-IFI30 levels in tumor tissue samples were associated with increased infiltration levels of M1 macrophages, CD8+ and CD4+ T cells. IFI30 exerts a negative modulation on CTSL to regulate IFNGR1, PD-L1, and MHC-II levels during IFN-γ stimulation. IFI30 levels may represent a key regulatory factor of IFN-γ pathway associated with ICI responses in MM patients.