A Methodology for Utilization of Predictive Genomic Signatures in FFPE Samples. Homo sapiens

Purpose: Gene expression signatures developed to measure the activity of oncogenic signaling pathways have been used to dissect the heterogeneity of tumor samples and to predict sensitivity to various cancer drugs that target components of the relevant pathways, thus potentially identifying therapeutic options for subgroups of patients. To facilitate broad use, including in a clinical setting, the ability to generate data from formalin-fixed, paraffin-embedded (FFPE) tissues is essential. Experimental Design: Patterns of pathway activity in matched fresh-frozen and FFPE xenograft tumor samples were generated using the MessageAmp Premier methodology in combination with assays using Affymetrix arrays. Results generated were compared with those obtained from fresh-frozen samples using a standard Affymetrix assay. In addition, gene expression data from patient matched fresh-frozen and FFPE melanomas were also utilized to evaluate the consistency of predictions of oncogenic signaling pathway status. Results: Significant correlation of pathway activity predictions was observed between paired fresh-frozen and FFPE xenograft tumor samples. In addition, significant concordance of pathway activity predictions was also observed between patient matched fresh-frozen and FFPE melanomas. Conclusion: Reliable and consistent predictions of oncogenic pathway activities can be obtained from FFPE tumor tissue samples. The ability to reliably utilize FFPE patient tumor tissue samples for genomic analyses will lead to a better understanding of the biology of disease progression and, in the clinical setting, will provide tools to guide the choice of therapeutics to those most likely to be effective in treating a patient’s disease. Overall design: 8 replicates of HMECs infected with adenovirus expressing GFP, 8 replicates of HMECs infected with adenovirus expressing RAS, 6 replicates of HMECs infected with adenovirus expressing MYC, 25 fresh-frozen melanoma xenografts, 25 FFPE melanoma xenografts, 6 FFPE human melanoma研究目的：用于衡量致癌信号通路活性的基因表达特征，已被用于解析肿瘤样本的异质性，并可预测靶向相关通路组分的各类抗癌药物的敏感性，从而有望为患者亚群确定个性化治疗方案。为推动其广泛应用（包括临床场景），从福尔马林固定石蜡包埋（Formalin-Fixed Paraffin-Embedded, FFPE）组织中获取有效数据的能力至关重要。实验设计：采用MessageAmp Premier技术结合Affymetrix芯片检测，获取配对新鲜冷冻与FFPE异种移植肿瘤样本的通路活性特征数据。将所得结果与采用标准Affymetrix检测方法获得的新鲜冷冻样本结果进行比对。此外，还利用患者配对的新鲜冷冻与FFPE黑色素瘤样本的基因表达数据，评估致癌信号通路状态预测的一致性。研究结果：配对的新鲜冷冻与FFPE异种移植肿瘤样本的通路活性预测结果呈现显著相关性。此外，患者配对的新鲜冷冻与FFPE黑色素瘤样本的通路活性预测结果也呈现显著一致性。研究结论：可从FFPE肿瘤组织样本中获得可靠且一致的致癌通路活性预测结果。能够可靠地将FFPE患者肿瘤组织样本用于基因组分析，将有助于更深入地理解疾病进展的生物学机制，并在临床场景中为患者筛选最有可能起效的治疗方案提供科学指导工具。整体实验设计：感染表达绿色荧光蛋白（Green Fluorescent Protein, GFP）腺病毒的HMECs生物学重复8例、感染表达RAS腺病毒的HMECs生物学重复8例、感染表达MYC腺病毒的HMECs生物学重复6例、新鲜冷冻黑色素瘤异种移植样本25例、FFPE黑色素瘤异种移植样本25例，以及FFPE人黑色素瘤样本6例。