Transcriptomic immune profiling for cervical squamous cell carcinoma: Does HPV type matter?

Objectives: Immunotherapy (IO) has shown initial promise in treating metastatic or recurrent cervical cancer. However, response rates have been modest, and PD-L1 has shown limited value as a predictive marker. Recently-presented data exploring transcriptomic immune profiling (TIP) in cervical cancer suggested that (a) far more immune-relevant signals in cervical cancer can be evaluated and (b) squamous cell carcinoma (SCC) has increased immunogenicity than adenocarcinoma. Given the near-universal HPV+ status of cervical SCC, we sought to explore whether TIP signals vary with respect to HPV variants. Methods: Cervical SCC tumors were analyzed using next-generation sequencing and whole-exome sequencing (NGS: NextSeq, 45 or 592 Genes and NovaSEQ, WES), immunohistochemistry (IHC), and WTS (NovaSeq) (Caris Life Sciences, Phoenix, AZ). PD-L1 expression was tested by IHC (positive: CPS ≥1). Microsatellite instability (MSI) was tested by FA, IHC, and NGS. Tumor mutational burden (TMB) was measured by totaling all somatic mutations per tumor (TMB-h: ≥10 mutations/MB). Immune cell infiltration was calculated by QuantiSeq. HPV16/18 status was determined using WES. Significance was tested by Chi-square and Wilcoxon rank-sum test and adjusted for multiple comparisons (q<0.05). Results: Total 89 cervical SCC tumors with available HPV16/18 status were included: 63 (71%) were HPV16+ or 18+ while 26 (29%) were non-HPV16/18. HPV16/18+ had significantly fewer TP53 alterations compared to non-HPV16/18 tumors (1.7% vs 33%, q=0.01). There was a trend toward increased regulatory T cell infiltration in HPV16/18+ tumors (2.2% vs 1.9%) (p=0.02; q=0.2) accompanied with a trend towards increased immune checkpoint (IC) gene expression: CD86 (1.4-fold, p=0.05/q=0.5), IFNG (2.2-fold, p=0.03; q=0.3) and IDO1 (2.5-fold, p=0.03; q=0.3). Additionally, there was a trend towards increased T cell inflammation (32% vs 19%, p=0.16) in HPV16/18+ tumors (Table 1). Among prevalent mutations/pathways in this dataset, there were no significant differences in PI3K (42% vs 42%), Telomerase Maintenance (12% vs 15%) or RTK RAS (22% vs 27%) pathway alterations (q=1). There were no significant differences in IO-related biomarkers: PD-L1 (92% vs 82%), dMMR/MSI-H (4.8% vs 3.7%) or TMB (25% vs 19%) (q=1). No significant genomic, transcriptomic or immune differences were seen between HPV16+ and HPV18+ tumors. Conclusions: Individual TIP markers were not significantly different with respect to high-risk HPV types for cervical SCC. Besides TP53 alterations, major cancer-relevant mutations/pathways were not significantly different for the HPV16/18+ versus non-HPV16/18 groups. The HPV16/18+ group had trends of increased regulatory T cell infiltration and IC gene expression. These data are hypothesis-generating for the concept that HPV16/18+ cervical SCC tumors might have differentially modulated immune activity compared to non-HPV16/18 cervical SCC tumors.