Introduction: The number of tumor-infiltrating lymphocytes (TIL) correlates with better survival and is increased in HPVpos OPSCC. The expression of immune checkpoint molecules (ICM) affects anti-tumor T-cell function and immune response. To determine the extent to which HPVpos differs from HPVneg OPSCC, single-cell RNA sequencing data from oropharyngeal carcinomas (OPSCC) were analyzed in addition to a transcription analysis of a TCGA and an Ulm/Southampton RNA sequencing data set.
Material and methods: The complete TCGA transcriptome data set, selected TCGA OPSCC cases (n = 66), and OPSCC cases from Ulm and Southampton (n = 51) were analyzed using the DeSeq2 pipeline in R. In addition, raw data from a published scRNA sequencing dataset from 26 OPSCC (18 HPVneg and 8 HPVpos) patients with blood samples (PBMC) and paired TIL samples (GSE139324) were bioinformatically processed and analyzed with the Seurat pipeline in R.
Results: In the transcriptome analysis, CD27 and TIM3 showed a statistically significant different expression depending on the HPV status. The scRNA analysis showed a statistically higher expression of VSIR in the PBMC and TILs of HPVneg OPSCC. The LAG3 expression on PBMCs was reduced in HPVneg OPSCC while there was no difference found on the TILs. Other differences were seen in the TILs: CD27, CD28, TIGIT, PD-1, BTLA, TNFRSF9 (CD137), and CD40 were elevated in HPVpos OPSCC, while ICOS, TNFRSF4 (OX40), TNFRSF18 (GITR), and ENTPD1 (CD39) were increasingly expressed in HPVneg OPSCC.
Conclusion: In this project, we describe the importance of ICM expression analysis for OPSCC depending on their HPV status. The identified expression profiles underpin the immunological differences of HPVpos OPSCCs with enhanced T cell basal activation and point to a possible distinction in therapy and checkpoint inhibitor selection in the future.