鉴定和验证与自噬、细胞凋亡和焦亡相关基因的头颈部鳞状细胞癌预后标志物：提示 HPV 阴性患者的治疗选择。

INTRODUCTION: An effective tool is needed to predict the prognosis of head and neck squamous cell carcinoma (HNSCC). Human papillomavirus (HPV) positive HNSCC patients generally have a favorable survival and a promising responsiveness to radiotherapy, chemoradiotherapy and checkpoint blockades. However, HPV negative patients, the majority of HNSCC patients, have been largely overlooked. Cell death has been involved in the therapeutic resistance of cancers. To this end, we aimed to identify the association of autophagy, apoptosis and pyroptosis-related genes with the prognosis of HNSCC, and construct a prognostic signature to predict the prognosis for HNSCC, especially for HPV negative HNSCC. METHODS: Autophagy and apoptosis-related genes were obtained from Gene Set Enrichment Analysis (GSEA) website, and pyroptosis-related genes were obtained from GSEA and Gene Ontology (GO) database. We established the cell death index (CDI) based on RNA sequencing (RNA-seq) data and clinicopathological information from The Cancer Genome Atlas (TCGA) dataset. The prognostic value of CDI was verified by Kaplan-Meier, receiver operating characteristic (ROC) and univariate and multivariate Cox regression analyses in TCGA dataset, and validated with the datasets from Gene Expression Omnibus (GEO) and Qilu Hospital of Shandong University. We further assessed the immune microenvironment of patients with high and low CDI scores. Moreover, the expression of the signature genes in HNSCC cell lines were explored. RESULTS: We found that CDI was an independent prognostic indicator for overall survival (hazard ratio 3.80, 95% confidential interval: 2.70-5.40, < 0.001). Furthermore, HNSCC patients with high CDI scores obtained increased overall survival post radiation indicating benefits from radiotherapy of this subgroup. On the other hand, HPV negative HNSCC patients with low CDI exhibited increased checkpoint gene expressions, an inflamed tumor microenvironment and an enriched immune response-related functions, suggesting the potential benefits from checkpoint immunotherapies of this subgroup. Moreover, we validated the baseline and induced expressions of above 16 genes in two HPV negative HNSCC cell lines, CAL27 and SCC-15. DISCUSSION: We established a prognostic signature and emphasized its implements in the therapeutic choices of HPV negative HNSCC patients, the majority and the poor outcome population of HNSCC.

简介：需要一种有效的工具来预测头颈部鳞状细胞癌（HNSCC）的预后。人乳头瘤病毒（HPV）阳性 HNSCC 患者的生存预后通常较好，对放疗、放化疗和检查点阻断治疗反应良好。然而，HPV 阴性患者，即大多数 HNSCC 患者，在很大程度上被忽视了。细胞死亡与癌症的治疗耐药性有关。为此，我们旨在确定自噬、凋亡和细胞焦亡相关基因与 HNSCC 预后的相关性，并构建一个预测 HNSCC 预后的签名，特别是用于预测 HPV 阴性 HNSCC 的预后。

方法：自噬和凋亡相关基因从基因集富集分析（GSEA）网站获得，细胞焦亡相关基因从 GSEA 和基因本体论（GO）数据库获得。我们基于来自癌症基因组图谱（TCGA）数据集的 RNA 测序（RNA-seq）数据和临床病理信息，建立了细胞死亡指数（CDI）。在 TCGA 数据集、基因表达综合数据库（GEO）和山东大学齐鲁医院数据集通过 Kaplan-Meier、受试者工作特征（ROC）和单因素及多因素 Cox 回归分析验证 CDI 的预后价值。我们还进一步评估了 CDI 高、低评分患者的免疫微环境。此外，还探讨了 HNSCC 细胞系中签名基因的表达。

结果：我们发现 CDI 是总生存期的独立预后指标（危险比 3.80，95%置信区间：2.70-5.40，<0.001）。此外，CDI 评分较高的 HNSCC 患者在接受放疗后总生存期延长，提示该亚组从放疗中获益。另一方面，CDI 评分较低的 HPV 阴性 HNSCC 患者表现出更高的检查点基因表达、炎症肿瘤微环境和丰富的免疫反应相关功能，提示该亚组可能从检查点免疫治疗中获益。此外，我们还验证了两个 HPV 阴性 HNSCC 细胞系（CAL27 和 SCC-15）中上述 16 个基因的基础和诱导表达。

讨论：我们建立了一个预后签名，并强调了其在 HPV 阴性 HNSCC 患者的治疗选择中的应用，包括大多数 HNSCC 患者和预后不良的患者。