High Level Expression of MHC-II in HPV+ Head and Neck Cancers Suggests that Tumor Epithelial Cells Serve an Important Role as Accessory Antigen Presenting Cells

Abstract

High-risk human papillomaviruses (HPVs) are responsible for a subset of head and neck squamous cell carcinomas (HNSCC). Expression of class II major histocompatibility complex (MHC-II) is associated with antigen presenting cells (APCs). During inflammation, epithelial cells can be induced to express MHC-II and function as accessory APCs. Utilizing RNA-seq data from over 500 HNSCC patients from The Cancer Genome Atlas, we determined the impact of HPV-status on the expression of MHC-II genes and related genes involved in their regulation, antigen presentation, and T-cell co-stimulation. Expression of virtually all MHC-II genes was significantly upregulated in HPV+ carcinomas compared to HPV- or normal control tissue. Similarly, genes that encode products involved in antigen presentation were also significantly upregulated in the HPV+ cohort. In addition, the expression of CIITA and RFX5-regulators of MHC-II-were significantly upregulated in HPV+ tumors. This coordinated upregulation of MHC-II genes was correlated with higher intratumoral levels of interferon-gamma in HPV+ carcinomas. Furthermore, genes that encode various co-stimulatory molecules involved in T-cell activation and survival were also significantly upregulated in HPV+ tumors. Collectively, these results suggest a previously unappreciated role for epithelial cells in antigen presentation that functionally contributes to the highly immunogenic tumor microenvironment observed in HPV+ HNSCC.

Keywords: MHC-II; T-cell; antigen presentation; co-stimulatory molecules; head and neck carcinoma; human papillomavirus; major histocompatibility complex; survival signals.

Figure 1

Expression of classical class II major histocompatibility complex (MHC-II) α- and β-chain genes in head and neck squamous cell carcinomas stratified by high-risk human papillomaviruses (HPV)-status. RNA-Seq by Expectation Maximization (RSEM)-normalized RNA-seq data for the indicated MHC-II genes was extracted from The Cancer Genome Atlas (TCGA) database for the head and neck squamous cell carcinoma (HNSC) cohort for HPV+, HPV−, and normal control tissues. Numbers in brackets refer to the number of samples included in each analysis. Statistical analysis was performed using a two-tailed non-parametric Mann–Whitney U test. ** p ≤ 0.01, *** p ≤ 0.001, **** p ≤ 0.0001, ns—not significant.

Figure 2

Expression of the invariant chain and MHC class II-like genes in head and neck carcinomas stratified by HPV-status. RSEM normalized RNA-seq data for the indicated genes involved in MHC-II-dependent antigen processing and presentation was extracted from the TCGA database for the HNSC cohort for HPV+, HPV−, and normal control tissues. Numbers in brackets refer to the number of samples included in each analysis. Statistical analysis was performed using a two-tailed non-parametric Mann–Whitney U test. ** p ≤ 0.01, *** p ≤ 0.001, **** p ≤ 0.0001, ns—not significant.

Figure 3

Expression of class II major histocompatibility complex transactivator (CIITA), regulatory factor X5 (RFX5), and interferon-gamma (IFNG) mRNA in head and neck carcinomas stratified by HPV-status. RSEM normalized RNA-seq data for the CIITA, RFX5, and IFNG genes were extracted from the TCGA database for the HNSC cohort for HPV+, HPV−, and normal control tissues. Numbers in brackets refer to the number of samples included in each analysis. Statistical analysis was performed using a two-tailed non-parametric Mann–Whitney U test. ** p ≤ 0.01, *** p ≤ 0.001, **** p ≤ 0.0001, ns—not significant.

Figure 4

Correlation matrix of genes involved in the MHC-II antigen presentation pathway in head and neck carcinomas stratified by HPV-status. RSEM normalized RNA-seq data for the genes listed above were extracted from the TCGA database for the HNSC cohort for HPV+ (upper triangle) and HPV− samples (lower triangle). Pairwise spearman correlation was performed followed by hierarchical clustering to group based on correlation. Number in boxes indicate Spearman’s rank correlation coefficient of analyzed gene pairs.

Figure 5

Expression of genes that encode for T-cell co-stimulatory molecules in head and neck carcinomas stratified by HPV-status. RSEM normalized RNA-seq data for genes that encode T-cell specific co-stimulatory molecules was extracted from the TCGA database for the HNSC cohort for HPV+, HPV−, and normal control tissues. Statistical analysis was performed using a two-tailed non-parametric Mann–Whitney U test. Numbers in brackets refer to the number of samples included in each analysis. **** p ≤ 0.0001, ns—not significant.

Figure 6

Expression of inducible T-cell survival signal molecules in head and neck carcinomas stratified by HPV-status. RSEM normalized RNA-seq data for inducible genes that encode for T-cell survival molecules was extracted from the TCGA database for the HNSC cohort for HPV+, HPV−, and normal control tissues. Statistical analysis was performed using a two-tailed non-parametric Mann–Whitney U test. Numbers in brackets refer to the number of samples included in each analysis. * p ≤ 0.05, ** p ≤ 0.01, *** p ≤ 0.001, **** p ≤ 0.0001, ns—not significant.