Biological Validation of RNA Sequencing Data From Formalin-Fixed Paraffin-Embedded Primary Melanomas
Biological Validation of RNA Sequencing Data From Formalin-Fixed Paraffin-Embedded Primary Melanomas
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DOI：
10.1200/po.17.00259
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发表时间：
2018-06-14
影响因子：
4.6
通讯作者：
Gershenwald, Jeffrey E.
中科院分区：
文献类型：
--
作者：
Kwong, Lawrence N.;De Macedo, Mariana Petaccia;Gershenwald, Jeffrey E.
癌症基因组图谱和国际癌症基因组联盟等倡议已经从数千个冷冻肿瘤样本中产生了高质量的多平台分子数据。尽管这些举措为癌症生物学提供了宝贵的见解，但在福尔马林固定，材料和方法我们从FFPE原发性黑色素瘤中提取RNA，并评估两种基因表达平台--基因组--广泛的RNA测序和靶向NanoString，因为它们能够产生连贯的生物信号。为此，我们提出了一种改进的方法来量化基因表达途径。我们通过相关性指导的基因子集细化途径分数。我们还比较了癌症基因组图谱和其他公开的黑色素瘤dataset.Results基因表达模式的比较，以建立生物模块，临床和免疫组化数据证实了保真度的生物信号从两个平台使用FFPE样本已知的生物学。此外，与患者的结果数据的相关性与以前的冷冻组织为基础的study.Conclusion FFPE样本从以前难以访问的癌症类型，如小原发性黑色素瘤，代表了一个有价值的和以前未开发的来源的分析物RNA测序和NanoString平台。这项工作为使用此类平台解锁新的分子基础并为未来生物驱动的临床决策提供信息迈出了重要一步。(C)2018年美国临床肿瘤学会
Purpose Initiatives such as The Cancer Genome Atlas and International Cancer Genome Consortium have generated high-quality, multiplatform molecular data from thousands of frozen tumor samples. Although these initiatives have provided invaluable insight into cancer biology, a tremendous potential resource remains largely untapped in formalin-fixed, paraffin-embedded (FFPE) samples that are more readily available but which can present technical challenges because of crosslinking of fragile molecules such as RNA.Materials and Methods We extracted RNA from FFPE primary melanomas and assessed two gene expression platforms-genome-wide RNA sequencing and targeted NanoString for their ability to generate coherent biologic signals. To do so, we generated an improved approach to quantifying gene expression pathways. We refined pathway scores through correlation-guided gene subsetting. We also make comparisons to The Cancer Genome Atlas and other publicly available melanoma datasets.Results The comparison of the gene expression patterns to each other, to established biologic modules, and to clinical and immunohistochemical data confirmed the fidelity of biologic signals from both platforms using FFPE samples to known biology. Moreover, correlations with patient outcome data were consistent with previous frozen-tissue-based studies.Conclusion FFPE samples from previously difficult-to-access cancer types, such as small primary melanomas, represent a valuable and previously unexploited source of analyte for RNA sequencing and NanoString platforms. This work provides an important step toward the use of such platforms to unlock novel molecular underpinnings and inform future biologically driven clinical decisions. (C) 2018 by American Society of Clinical Oncology