RNA-sequencing reveals an immune “hot” gene expression signature in oropharyngeal squamous cell carcinoma which is upregulated upon decitabine treatment in cell lines

Content Introduction A significant percentage of oropharyngeal squamous cell carcinoma (OPSCC) is human papillomavirus (HPV) driven. HPV-positive OPSCC have a prognostic advantage likely due to cancer-specific immunity. We aimed to identify expression patterns of immune-related genes to assign “hot”and “cold” tumors.

Material and Methods RNA sequencing was performed in 51 patients (Cohort 1, HPV-: n=19, HPV+: n=32), and in 6 HNSCC cell lines (HPV-: n=3, HPV+: n=3). Cell lines were treated with 2µM decitabine (DAC) or control-treated (DMSO). A validation cohort was obtained from The Cancer Genome Atlas (TCGA, Cohort 2, HPV-: n=18, HPV+: n=48). Differential gene expression analysis was performed using deseq2 (1.29.16), and gene ontology using clusterProfiler (3.18.0) R packages.

Results An immune signature (n=32 genes) was developed based on the comparison of CD8^high/low and CD103^high/low tumors in Cohort 1 and validated in cohort 2. The signature was cross-validated and refined using a previously established signature to define “hot”and “cold” tumors resulting in a 47 gene immune signature. Differential gene expression analysis confirmed an upregulation of immune-related genes in “hot”tumors (n=428 genes). That gene set was further analyzed in HNSCC cell lines +/- DAC treatment. Differential gene expression analysis showed that DAC treatment leads to an increase of immune-related gene expression in-vitro, which was confirmed by gene ontology analysis.

Conclusions Based on our findings, it seems that DAC treatment causes an increase in expression of immune-relate genes which could lead to increased tumor immunogenicity and may enhance immunotherapy results.

Poster-PDF A-1581.pdf

Publication History

Article published online:
13 May 2021