FFPE Validation of a Survival Gene Signature in HPV-Negative Oral Cavity Cancer

口腔和口咽部鳞状细胞癌（OSCC）是一个重大的全球健康负担，2012年估计有529,000例新病例和超过292,000例死亡。OSCC可进一步细分为预后不同的实体。例如，人乳头瘤病毒（HPV）阳性的口咽癌（OPC）患者往往比HPV阴性的口咽癌患者有更好的生存。然而，口腔癌的预后主要基于临床分期，可用于临床实践的分子标志物尚未确定，口腔癌占OSCC的大部分，且大多数为hpv阴性。迫切需要开发更好的预后标记物，以便对这些患者进行个性化的临床管理。我们的长期目标是开发简单、可靠、具有成本效益的基因表达特征来指导OSCC患者的管理。在我们之前的工作中（Oralchip研究，5 R01 CA095419, PI: Chu Chen），我们已经在肿瘤组织中发现了一个预后基因表达特征，它显示出比肿瘤分期更能预测hpv阴性OSCC患者的OSCC特异性生存，与治疗类型无关。我们通过MD安德森癌症中心的一组独立的口腔癌患者验证了这一特征。这是基因表达标记的首次展示，该标记为口腔癌患者提供了AJCC分期以外的预后信息。拟议研究的具体目的是利用现有的诊断肿瘤块、人口统计学和临床信息以及五项头颈癌研究中口腔癌患者的生存结果(Fred Hutchinson癌症研究中心/Univ。华盛顿;卡尔加里大学；密歇根大学；犹他大学；1)验证我们的9基因标记对hpv阴性OSCC患者的预后预测能力的假设，该假设是利用快速冷冻新鲜肿瘤组织和Affymetrix基因表达阵列开发和验证的，可以运输到hpv阴性、p16阴性口腔癌患者的福尔马林固定石蜡包埋（FFPE）医院肿瘤块和NanoString nCounter技术。并建立整体和口腔癌症特异性生存的预测模型；2)使用hpv阴性、p16阴性口腔癌患者的独立队列验证预测模型；3)评估基因标记预测生存的能力，总体上是oscc特异性的，是否会受到治疗方式（单独手术；手术+放疗；手术+放疗+化疗）的影响，这些治疗方式共同给予约90%的研究参与者。这项研究意义重大且新颖，因为它有可能首次提供一种快速、廉价、可靠的多标记物检测方法，可以在医院诊断性FFPE样本上运行，医院在手术时常规制备，以提高hpv阴性口腔癌患者的生存预测，从而改善对这种通常致命疾病患者的临床护理。

DESCRIPTION (provided by applicant): Squamous cell carcinoma of the oral cavity and oropharynx (OSCC) is a substantial global health burden, with an estimate of 529,000 new cases and over 292,000 deaths in 2012. OSCC can be further subclassified into entities with a different prognosis. For example, patients with human papillomavirus (HPV)-positive oropharyngeal cancer (OPC) tend to have better survival than those with HPV-negative OPC. However, prognostication for oral cavity cancer, which comprises the majority of OSCC and is mostly HPV-negative, is largely based on clinical staging, and molecular markers that could be used in clinical practice have not been identified. There is an urgent need to develop better prognostic markers for personalized clinical management of these patients. Our long-term goal is to develop simple, reliable, and cost-effective gene expression signatures to guide the management of OSCC patients. In our prior work (the Oralchip study, 5 R01 CA095419, PI: Chu Chen), we have identified a prognostic gene expression signature in tumor tissue that showed a greater ability than tumor stage to predict OSCC-specific survival for patients with HPV-negative OSCC, irrespective of types of treatment. We validated this signature using an independent set of patients with oral cavity cancer from the MD Anderson Cancer Center. This was the first demonstration of a gene expression signature that provides prognostic information beyond AJCC stage for oral cavity cancer patients. The specific aims of the proposed study are to leverage the available diagnostic tumor blocks, demographic and clinical information and survival outcomes of oral cavity cancer patients from five head and neck cancer studies (Fred Hutchinson Cancer Research Center/Univ. of Washington; Univ. of Calgary; Univ. of Michigan; Univ. of Utah; and the International Agency of Research on Cancer) to 1) test the hypothesis that the prognostic ability of our 9-gene signature for HPV-negative OSCC patients, that was developed and validated using snap frozen fresh tumor tissue and Affymetrix gene expression arrays, can be transported to formalin-fixed paraffin embedded (FFPE) hospital tumor blocks of HPV-negative, p16-negative oral cavity cancer patients and NanoString nCounter technology, and to build prediction models for overall and oral cavity cancer-specific survival; 2) validate th prediction models using independent cohorts of HPV-negative, p16-negative oral cavity cancer patients; and 3) evaluate whether the ability of the gene signature to predict survival, overall an OSCC-specific, would be influenced by treatment modalities (surgery alone; surgery + radiation; and surgery + radiation + chemotherapy) that collectively were administered to ~90% of the study participants. This study is significant and novel because it has the potential to deliver, fr the first time, a rapid, inexpensive, and reliable multi-marker assay that can be run on hospital diagnostic FFPE samples, routinely prepared by the hospital at the time of surgery, to improve survival prediction of HPV-negative oral cavity cancer patients, and thus lead to improved clinical care of patients with this often lethal disease.