HPV E5 Mediates Resistance to PD-1 Checkpoint Blockade Via Inhibition of MHC and IFN Pathway

Purpose/Objective(s) Objective response rates to PD-1 blockade in human papillomavirus (HPV) mediated Head and Neck Squamous cell carcinoma (HNSCC) are low and resistance mechanisms are unclear. HPV oncogenes are known to modulate immune responses; however, the role that they play in limiting responses to PD-1 blockade is poorly understood. Here we investigated HPV oncogenes and uncovered a novel mechanism by which HPV E5 suppresses immune responses and diminishes the activity of PD-1 blockade in HNSCC. Materials/Methods Human cell lines were engineered to express HPV E5 and RNAseq was performed to elucidate E5 mediated alterations in transcriptome. MHC class I pull downs and tandem MS/MS was performed to characterize the immunopeptidome and investigate the effect of HPV E5 on the repertoire of presented tumor antigens. Syngeneic murine models were used to dissect molecular mechanisms by which E5 modulates antigen presentation and IFN signaling pathways. Finally, a curated database of tumor RNAseq from 35 HPV-positive HNSCC patients was analyzed to determine the impact of E5 on HLA expression and patient outcomes. Results RNAseq revealed dramatic downregulation of antigen processing and type I interferon pathways in E5-expressing human cell lines. Immunopeptidome analysis revealed that E5-expressing cells have a significantly restricted antigen repertoire, indicating that E5 may help HPV mediated tumors escape from host immune surveillance. Remarkably, syngeneic murine tumors expressing HPV E5 were rendered entirely resistant to PD-1 blockade compared to responding parental lines without E5 expression. Mechanistically HPV E5 was demonstrated to suppress phosphorylation of IRF3 and type I interferon production, while directly binding MHC and preventing translocation to the cell surface. Ultimately, we observed a striking improvement in disease free survival (DFS) and overall survival (OS) in patients with low E5 and high HLA expression [Median DFS 50mo in E5 high/HLA-A low versus not reached in E5 low/HLA-A high; p=0.039]. Conclusion Our findings establish HPV E5 as a mediator of resistance to PD-1 checkpoint blockade via inhibition of HLA expression and IFN response pathways. These results have broad clinical relevance beyond HNSCC to other HPV-associated malignancies and reveal a powerful mechanism of HPV E5-mediated immunosuppression which can be exploited to improve response rates to PD-1 checkpoint blockade. Objective response rates to PD-1 blockade in human papillomavirus (HPV) mediated Head and Neck Squamous cell carcinoma (HNSCC) are low and resistance mechanisms are unclear. HPV oncogenes are known to modulate immune responses; however, the role that they play in limiting responses to PD-1 blockade is poorly understood. Here we investigated HPV oncogenes and uncovered a novel mechanism by which HPV E5 suppresses immune responses and diminishes the activity of PD-1 blockade in HNSCC. Human cell lines were engineered to express HPV E5 and RNAseq was performed to elucidate E5 mediated alterations in transcriptome. MHC class I pull downs and tandem MS/MS was performed to characterize the immunopeptidome and investigate the effect of HPV E5 on the repertoire of presented tumor antigens. Syngeneic murine models were used to dissect molecular mechanisms by which E5 modulates antigen presentation and IFN signaling pathways. Finally, a curated database of tumor RNAseq from 35 HPV-positive HNSCC patients was analyzed to determine the impact of E5 on HLA expression and patient outcomes. RNAseq revealed dramatic downregulation of antigen processing and type I interferon pathways in E5-expressing human cell lines. Immunopeptidome analysis revealed that E5-expressing cells have a significantly restricted antigen repertoire, indicating that E5 may help HPV mediated tumors escape from host immune surveillance. Remarkably, syngeneic murine tumors expressing HPV E5 were rendered entirely resistant to PD-1 blockade compared to responding parental lines without E5 expression. Mechanistically HPV E5 was demonstrated to suppress phosphorylation of IRF3 and type I interferon production, while directly binding MHC and preventing translocation to the cell surface. Ultimately, we observed a striking improvement in disease free survival (DFS) and overall survival (OS) in patients with low E5 and high HLA expression [Median DFS 50mo in E5 high/HLA-A low versus not reached in E5 low/HLA-A high; p=0.039]. Our findings establish HPV E5 as a mediator of resistance to PD-1 checkpoint blockade via inhibition of HLA expression and IFN response pathways. These results have broad clinical relevance beyond HNSCC to other HPV-associated malignancies and reveal a powerful mechanism of HPV E5-mediated immunosuppression which can be exploited to improve response rates to PD-1 checkpoint blockade.