Identification of HPV16 E1 and E2-specific T cells in the oropharyngeal cancer tumor microenvironment

Abstract

BackgroundHigh-risk human papillomavirus (HPV) is a primary cause of an increasing number of oropharyngeal squamous cell carcinomas (OPSCCs). The viral etiology of these cancers provides the opportunity for antigen-directed therapies that are restricted in scope compared with cancers without viral components. However, specific virally-encoded epitopes and their corresponding immune responses are not fully defined.MethodsTo understand the OPSCC immune landscape, we conducted a comprehensive single-cell analysis of HPV16+ and HPV33+ primary tumors and metastatic lymph nodes. We used single-cell analysis with encoded peptide-human leukocyte antigen (HLA) tetramers to analyze HPV16+ and HPV33+ OPSCC tumors, characterizing the ex vivo cellular responses to HPV-derived antigens presented in major Class I and Class II HLA alleles.ResultsWe identified robust cytotoxic T-cell responses to HPV16 proteins E1 and E2 that were shared across multiple patients, particularly in HLA-A*01:01 and HLA-B*08:01. Responses to E2 were associated with loss of E2 expression in at least one tumor, indicating the functional capacity of these E2-recognizing T cells and many of these interactions validated in a functional assay. Conversely, cellular responses to E6 and E7 were limited in quantity and cytotoxic capacity, and tumor E6 and E7 expression persisted.ConclusionsThese data highlight antigenicity beyond HPV16 E6 and E7 and nominate candidates for antigen-directed therapies.

The Tumor-Specific Immune Landscape in HPV+ Head and Neck Cancer

“…Surprisingly, most CD8+ T cell epitopes discovered in our study were derived from HPV E2 and E5, which also encompassed the most immunodominant responses, with little to no reactivity detected against HPV E6 and E7. Notably, a recent study identified CD8+ TIL responses against HPV E1, E2, and E6 [ 133 ], further supporting the notion that “non-classical” HPV antigens such as E1, E2, E4, and E5 are targeted by a substantial portion of HPV-specific CD8+ TILs and should thus not be neglected in the development of novel therapeutic interventions for HPV+ HNSCC. Importantly, our findings also confirmed previous studies demonstrating that HPV-specific CD8+ T cells are virtually undetectable in the peripheral blood of patients with HPV+ HNSCC [ 79 , 80 , 81 , 82 , 83 ], despite individual epitope-specific responses accounting for up to 10% of CD8+ T cells in the TME [ 78 ].…”

Preferential Expansion of HPV16 E1-Specific T Cells from Healthy Donors’ PBMCs after Ex Vivo Immunization with an E1E2E6E7 Fusion Antigen

“…A study by Eberhardt et al on patients with HPV-positive head and neck cancer showed that more patients had tumor-infiltrating CD8 + T cells towards E2 rather than E6 or E7 [18]. McInnis et al showed strong anti-E1 and E2 CD8 + T-cell responses in head-neck cancer patients and also reported that E1 was expressed in tumor biopsies from all patients enrolled in their study [20]. Similarly, Peng et al reported an E1 expression in all enrolled cervical cancer patients.…”

“…We have previously shown that such a vaccine design is capable of inducing strong T-cell responses in outbred mouse strains and have seen indications that E1-specific T cells may enhance tumor control in C57BL/6 mice. The use of E1 and E2 as targets for HPV therapeutic vaccines is also supported by recent studies on patients with cervical cancer or OPSCC [18][19][20].…”

Bioinformatics analysis of immune characteristics in tumors with alternative carcinogenesis pathways induced by human papillomaviruses

“…Therapeutic vaccines against HPV-associated tumors are usually based only on the E7 and/or E6 oncoproteins, which are considered indispensable for maintaining the malignant transformation of cells [ 63 ]. However, the detection of specific immunity against HPV in HNSCC has shown a broad response of CD4 and CD8 T cells against viral antigens E1, E2, E4, E5, E6, E7, and L1 [ 64 ], and E1, E2 and E5 have been identified as major targets of intratumoral CD8 T cells [ 65 , 66 ]. T-cell responses to E2 are also common in cervical premalignant and malignant lesions [ 67 , 68 ].…”