Immune checkpoint expression on tumor-infiltrating lymphocytes (TIL) is dependent on HPV status in oropharyngeal carcinoma (OPSCC) – A single-cell RNA sequencing analysis

Introduction

A substantial proportion of head and neck squamous cell carcinoma (HNSCC), particularly oropharyngeal squamous cell carcinoma (OPSCC), is associated with human papillomavirus (HPV), resulting in distinct molecular phenotypes. In this study, we investigated differential immune checkpoint molecule (ICM) expression by HPV status using RNA sequencing data to identify additional ICM targets that may complement anti-PD1 antibodies.

Material and methods

RNA sequencing was performed on 51 OPSCC cases and validated using the TCGA HNSCC dataset. Unsupervised clustering and differential gene expression analyses in R were conducted based on HPV status. Additionally, a published single-cell RNA sequencing (scRNA) dataset of tumor-infiltrating lymphocytes (TIL) and peripheral immune cells (PBMC) (GSE139324) was analyzed with a Seurat pipeline grouped by HPV status.

Results

Our study identified a significant upregulation of all examined ICM in HPV-positive OPSCC through bulk RNA sequencing, validated by the TCGA cohort. Unsupervised clustering revealed a strong association between HPV-positive/-negative and high/low ICM expression cases respectively, indicating overlap between ICM and HPV status. In scRNA analysis, CD27, PD-1, OX-40, and BTLA were significantly more highly expressed on TILs of HPV-positive OPSCC. Conversely, VSIR was increased in PBMC and TILs of HPV-negative OPSCC, while LAG3 expression on PBMC was reduced in HPV-negative OPSCC.

Conclusion

Our study unveils the intricate interplay of ICMs in OPSCC, emphasizing the necessity for personalized therapeutic approaches based on HPV status and immune profiles. The identified ICMs, including PD1, CD27, and CTLA4, are promising candidates for further investigation and may enhance immunotherapeutic interventions in the HPV-dependent treatment strategies for OPSCC.