Genetic Factors Associated with a Poor Outcome in Head and Neck Cancer Patients Receiving Definitive Chemoradiotherapy

Abstract

About half of advanced stage head and neck squamous cell carcinoma (HNSCC) patients can be cured by chemoradiotherapy. Patient outcome may be partially determined by the genetic alterations in HNSCC, rendering these alterations promising candidate prognostic factors and/or therapeutic targets. However, their relevance in patient outcome prognosis remains to be assessed in patients that receive standard-of-care chemoradiotherapy. We therefore tested whether frequent genetic alterations were associated with progression free survival (PFS) in advanced stage HNSCC patients who were uniformly treated with definitive platinum-based chemoradiotherapy. To this end, we performed targeted DNA sequencing on frozen pre-treatment tumor biopsy material from 77 patients with advanced stage oro- and hypopharyngeal carcinoma. This provided somatic point mutation and copy number aberration data of 556 genes. The most frequently mutated genes, TP53 (62%), CCND1 (51%), CDKN2A (30%) and PIK3CA (21%), were not associated with PFS. However, co-occurring CCND1 and CDKN2A mutations were associated with short PFS (HR 2.24, p = 0.028) in HPV-negative tumors. Furthermore, tumor mutational burden (sum of somatic point mutations) showed a trend towards decreased PFS (HR 1.9, p = 0.089), and chromosomal instability (CIN) was associated with shorter PFS (HR 2.3, p = 0.023), independent of HPV status. Our results show that tumor mutational burden, CIN markers, and co-occurring CCND1 and CDKN2A mutations are associated with chemoradiotherapy outcomes in advanced stage oro- and hypopharyngeal HNSCC patients, thereby highlighting their prognostic potential. Given their poor prognosis association and link to biological targets, they may also identify patients for novel targeted therapies and immunotherapies.

Biological Determinants of Chemo-Radiotherapy Response in HPV-Negative Head and Neck Cancer: A Multicentric External Validation

“…Some, such as tumor mutational burden (TMB) are prevalent in laryngeal and HPV-negative pharyngeal HNSCC (14) but require DNA sequencing data. TMB was found to be associated with poor prognosis in HPV-negative chemo-radiotherapy treated patients in our previous study (36) and more strongly so in a cohort of patients that also included oral cavity cancers and HPV-positive oropharyngeal (107). Interestingly, low immune cell infiltration or CD8+ T cell values, as assessed by gene expression, have been assigned to HNSCC high in TMB or mutational signatures related to smoking (56,107).…”

“…While the success of accelerated radiotherapy schedules (34) highlight the important role of tumor repopulation in HNSCC, there is a lack of biomarker data showing a link to cellular proliferation (35). Based on genetic mutation data, we find a small role for co-occurring CCND1 and CDKN2A mutations in HPV-negative chemo-radiotherapy treated HNSCC that was however not visible in the locoregional control endpoints (36). Yet, the combination of radiotherapy with the epidermal growth factor receptor (EGFR) binding antibody cetuximab has shown efficacy and EGFR expression has been associated with poor survival, preferentially in non-accelerated schedules arguing for a role in tumor repopulation (37)(38)(39)(40).…”

Analysis of HPV-Positive and HPV-Negative Head and Neck Squamous Cell Carcinomas and Paired Normal Mucosae Reveals Cyclin D1 Deregulation and Compensatory Effect of Cyclin D2

“…It is presumed that the increase in the cyclin D expression is an early oncogenic event that causes tumor formation and continuous uncontrolled proliferation of tumor cells [18,19,41]. Concordantly, with these studies, the analysis of almost 500 HNSCC samples showed amplification of chromosomal region 11q13 containing the CCND1 gene in 31% of cases [15], although the CCND1 amplification frequency has been reported to range from 17% to 50% [33,34]. The amplified 11q13 locus harbors several other genes that could promote tumorigenesis.…”

“…The observed low number of tumors with upregulated CCND1 expression was unexpected, as CCND1 overexpression was generally reported in up to 70% of patients at the protein level [21,22]. The common mechanism underlying CCND1 upregulation is its gene locus amplification, with frequency ranging from 17% to 50% of cases [33,34]. While we do not possess direct data on the amplification, we analyzed changes in the expression of genes surrounding the CCND1 gene as its surrogate marker [15,22].…”

Identifying predictors of HPV‐related head and neck squamous cell carcinoma progression and survival through patient‐derived models

“…A list of genetic differences between HPV− and HPV+ HNSCCs was curated to include alterations that differed significantly in frequency in direct comparison of HPV+ to HPV− HNSCCs within a study or have been reported to be highly enriched in one subtype but not the other (Table S5). 10,19,[25][26][27][28][29][30][31][32][33] These differences were broadly preserved between the two groups of PDXs ( Figure 1A, left). The alterations less common in HPV+ cases were markedly underrepresented in HPV+ PDXs, and the more common alterations were significantly overrepresented ( Figure 1A, right).…”