Saba Nabil F, Wilson Malania, Doho Gregory, DaSilva Juliana, Benjamin Isett R, Newman Scott, Chen Zhuo Georgia, Magliocca Kelly, Rossi Michael R
Department of Otolaryngology and Head and Neck Oncology Program, Winship Cancer Institute of Emory University, Emory University School of Medicine, Atlanta, GA, USA,
Head Neck Pathol. 2015 Jun;9(2):223-35. doi: 10.1007/s12105-014-0566-0. Epub 2014 Sep 19.
The role of molecular methods in the diagnosis of head and neck cancer is rapidly evolving and holds great potential for improving outcomes for all patients who suffer from this diverse group of malignancies . However, there is considerable debate as to the best clinical approaches, particularly for Next Generation Sequencing (NGS). The choices of NGS methods such as whole exome, whole genome, whole transcriptomes (RNA-Seq) or multiple gene resequencing panels, each have strengths and weakness based on data quality, the size of the data, the turnaround time for data analysis, and clinical actionability. There have also been a variety of gene expression signatures established from microarray studies that correlate with relapse and response to treatment, but none of these methods have been implemented as standard of care for oropharyngeal squamous cell carcinoma (OPSCC). Because many genomic methodologies are still far from the capabilities of most clinical laboratories, we chose to explore the use of a combination of off the shelf targeted mutation analysis and gene expression analysis methods to complement standard anatomical pathology methods. Specifically, we have used the Ion Torrent AmpliSeq cancer panel in combination with the NanoString nCounter Human Cancer Reference Kit on 8 formalin-fixed paraffin embedded (FFPE) OPSCC tumor specimens, (4) HPV-positive and (4) HPV-negative. Differential expression analysis between HPV-positive and negative groups showed that expression of several genes was highly likely to correlate with HPV status. For example, WNT1, PDGFA and OGG1 were all over-expressed in the positive group. Our results show the utility of these methods with routine FFPE clinical specimens to identify potential therapeutic targets which could be readily applied in a clinical trial setting for clinical laboratories lacking the instrumentation or bioinformatics infrastructure to support comprehensive genomics workflows. To the best of our knowledge, these preliminary experiments are among the earliest to combine both mutational and gene expression profiles using Ion Torrent and NanoString technologies. This reports serves as a proof of principle methodology in OPSCC.
分子方法在头颈部癌诊断中的作用正在迅速演变，对于改善所有罹患这类多样恶性肿瘤的患者的治疗结果具有巨大潜力。然而，关于最佳临床方法，尤其是针对下一代测序（NGS），存在相当大的争议。诸如全外显子组、全基因组、全转录组（RNA测序）或多个基因重测序面板等NGS方法的选择，基于数据质量、数据大小、数据分析周转时间和临床可操作性，各有优缺点。也有从微阵列研究建立的多种与复发和治疗反应相关的基因表达特征，但这些方法均未作为口咽鳞状细胞癌（OPSCC）的护理标准实施。由于许多基因组方法仍远超出大多数临床实验室的能力范围，我们选择探索使用现成的靶向突变分析和基因表达分析方法的组合，以补充标准解剖病理学方法。具体而言，我们将Ion Torrent AmpliSeq癌症检测板与NanoString nCounter人类癌症参考试剂盒联合应用于8例福尔马林固定石蜡包埋（FFPE）的OPSCC肿瘤标本，其中4例HPV阳性，4例HPV阴性。HPV阳性和阴性组之间的差异表达分析表明，几个基因的表达极有可能与HPV状态相关。例如，WNT1、PDGFA和OGG1在阳性组中均过度表达。我们的结果显示了这些方法在常规FFPE临床标本中的实用性，以识别潜在的治疗靶点，这些靶点可在临床试验环境中轻松应用于缺乏支持全面基因组学工作流程的仪器或生物信息学基础设施的临床实验室。据我们所知，这些初步实验是最早使用Ion Torrent和NanoString技术结合突变和基因表达谱的实验之一。本报告作为OPSCC的原理验证方法。
