Digital Spatial Profiling identifies distinct patterns of immuno-oncology-related gene expression within oropharyngeal tumours in relation to HPV and p16 status

Jill M Brooks; Yuanning Zheng; Kelly Hunter; Benjamin E Willcox; Janet Dunn; Paul Nankivell; Olivier Gevaert; Hisham Mehanna

doi:10.3389/fonc.2024.1428741

Digital Spatial Profiling identifies distinct patterns of immuno-oncology-related gene expression within oropharyngeal tumours in relation to HPV and p16 status

Front Oncol. 2024 Sep 12:14:1428741. doi: 10.3389/fonc.2024.1428741. eCollection 2024.

Authors

Jill M Brooks¹, Yuanning Zheng², Kelly Hunter³, Benjamin E Willcox⁴, Janet Dunn⁵, Paul Nankivell¹, Olivier Gevaert², Hisham Mehanna^{1

6}

Affiliations

¹ Institute of Head and Neck Studies and Education, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom.
² Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine, and Department of Biomedical Data Science, Stanford University, Stanford, CA, United States.
³ Propath, Hereford, United Kingdom.
⁴ Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom.
⁵ Warwick Clinical Trials Unit, University of Warwick, Coventry, United Kingdom.
⁶ National Institute for Health and Care Research (NIHR) Birmingham Biomedical Research Centre, University of Birmingham, Birmingham, United Kingdom.

Abstract

Background: The incidence of oropharyngeal cancer (OPC) is increasing, due mainly to a rise in Human Papilloma Virus (HPV)-mediated disease. HPV-mediated OPC has significantly better prognosis compared with HPV-negative OPC, stimulating interest in treatment de-intensification approaches to reduce long-term sequelae. Routine clinical testing frequently utilises immunohistochemistry to detect upregulation of p16 as a surrogate marker of HPV-mediation. However, this does not detect discordant p16-/HPV+ cases and incorrectly assigns p16+/HPV- cases, which, given their inferior prognosis compared to p16+/HPV+, may have important clinical implications. The biology underlying poorer prognosis of p16/HPV discordant OPC requires exploration.

Methods: GeoMx digital spatial profiling was used to compare the expression patterns of selected immuno-oncology-related genes/gene families (n=73) within the tumour and stromal compartments of formalin-fixed, paraffin-embedded OPC tumour tissues (n=12) representing the three subgroups, p16+/HPV+, p16+/HPV- and p16-/HPV-.

Results: Keratin (multi KRT) and HIF1A, a key regulator of hypoxia adaptation, were upregulated in both p16+/HPV- and p16-/HPV- tumours relative to p16+/HPV+. Several genes associated with tumour cell proliferation and survival (CCND1, AKT1 and CD44) were more highly expressed in p16-/HPV- tumours relative to p16+/HPV+. Conversely, multiple genes with potential roles in anti-tumour immune responses (immune cell recruitment/trafficking, antigen processing and presentation), such as CXCL9, CXCL10, ITGB2, PSMB10, CD74, HLA-DRB and B2M, were more highly expressed in the tumour and stromal compartments of p16+/HPV+ OPC versus p16-/HPV- and p16+/HPV-. CXCL9 was the only gene showing significant differential expression between p16+/HPV- and p16-/HPV- tumours being upregulated within the stromal compartment of the former.

Conclusions: In terms of immune-oncology-related gene expression, discordant p16+/HPV- OPCs are much more closely aligned with p16-/HPV-OPCs and quite distinct from p16+/HPV+ tumours. This is consistent with previously described prognostic patterns (p16+/HPV+ >> p16+/HPV- > p16-/HPV-) and underlines the need for dual p16 and HPV testing to guide clinical decision making.

Keywords: Digital Spatial Profiling; Human Papilloma Virus (HPV); dual p16/HPV testing; oropharyngeal cancer; p16; treatment de-intensification; tumour microenvironment.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was funded by Cancer Research UK (CRUK Centre funding) and National Institute for Health and Care Research (NIHR) UK.