Molecular signatures of melanoma histology and progression: A Population Based A

描述（由申请人提供）：原发性黑色素瘤分子和基因组分类的关键障碍是需要提供福尔马林固定石蜡包埋（FFPE）生物标本的预后测量（即Breslow厚度）和相关组织学参数，与冷冻材料不同，未掺假的mRNA和DNA很难或不可能提取和研究。与我们的合作者一起，我们成功地应用了Fan等人在2004年首次开发的一项新技术，用于黑色素瘤FFPE生物标本的全球基因表达谱分析。该平台命名为DASL （dna介导的退火、选择、延伸和连接），使福尔马林固定的生物标本以石蜡块的形式嵌入和存档，可用于基因表达分析。我们发现了两个截然不同的亚类，它们具有两个强大的特征：一个是由一组小眼症和黑素细胞分化基因（“MITF”类）广泛定义的亚类，另一个是由炎症、先天免疫和生长相关基因（“IIG”类）组成的异质性更强的亚类。我们的初步数据表明，DASL可以成功地描述和恢复FFPE原发性黑色素瘤的2级结构。布莱根妇女医院的钱宁实验室是大型队列研究的所在地，即护士健康研究1 (NHS1)，护士健康研究2 （NHS2）和卫生专业人员随访研究（HPFS）。这些队列的进一步优势在于疾病随访，每两年更新一次新病例和死亡率，以及队列中黑色素瘤病例原发肿瘤部位组织阻滞的可用性。我们假设黑色素瘤的侵袭性是由MITF/IIG类别决定的，我们建议评估这两类结构是否与已知的组织学参数（如Breslow厚度）和黑色素瘤复发/死亡率有关。通过与我们的合作者一起获得独特的基于人群的国家队列和开发新技术，本提案的具体目标如下：具体目标1：使用包含超过6000个基因的Illumina表达阵列平台和Sequonome平台开发NHS、NHS2和HPFS黑色素瘤FFPE样本的分子特征，对BRAF和NRAS的MC1R和基因型特异性位点进行测序，以便：a.为每个黑色素瘤样本分配MITF或IIG类别，并评估其与BRAF/NRAS/MC1R状态和黑色素瘤组织学决定因素（例如Breslow厚度、Clark's水平、垂直生长期）的关联。b.评估每个黑色素瘤样本的全基因组（6,000个基因）类别发现，并评估其与BRAF/NRAS/MC1R状态和黑色素瘤组织学决定因素（例如Breslow、Clark's水平、垂直生长期）的关联。利用Aim 1的转录和基因组特征：a.确定MITF或IIG类与BRAF/NRAS/MC1R状态和黑色素瘤复发和死亡率的关联；b.评估全基因组（6000个基因）与BRAF/NRAS/MC1R状态和黑色素瘤复发和死亡率的关联

DESCRIPTION (provided by applicant): critical obstacle to molecular and genomic classification of primary melanoma has been the requirement to provide prognostic measures (i.e. Breslow thickness) and related histologic parameters in formalin-fixed, paraffin-embedded (FFPE) biospecimens, where unlike frozen material, unadulterated mRNA and DNA have been difficult or impossible to extract and study. With our collaborators, we have successfully applied a novel technology first developed by Fan et al in 2004 for global gene expression profiling of melanoma FFPE biospecimens. This platform, designated DASL for DNA-mediated Annealing, Selection, extension, and Ligation) renders formalin-fixed biospecimens embedded and archived in the form of paraffin blocks usable for gene expression analysis. We found two distinct subclasses characterized by two robust signatures: one broadly defined by a cluster of microphthalmia and melanocyte differentiation genes ("MITF" class) and a more heterogeneous group of inflammation, innate immune, and growth-related genes ("IIG" class). Our preliminary data indicate that DASL can successfully profile and recover the 2-class structure from FFPE primary melanomas in the Nurses Health Study 1. The Channing Laboratory at Brigham and Women's Hospital is home to large cohort studies, i.e. the Nurses' Health Study 1 (NHS1), Nurses' Health Study-2 (NHS2) and the Health Professionals Follow-up Study (HPFS). The further strength of these cohorts lies in disease follow-up with bi-annual updates on new cases and mortality and availability of tissue blocks from the primary tumor site for melanoma cases in the cohorts. We hypothesize that melanoma aggressiveness is determined by MITF/IIG classes and we propose to evaluate whether this 2-class structure is associated with known histological parameters (e.g. Breslow thickness), and melanoma recurrence/mortality. With access to unique population-based national cohorts and development of new technologies with our collaborators, the specific aims of this proposal are as follows: Specific Aim 1: Develop molecular signatures of NHS, NHS2 and HPFS melanoma FFPE samples using an Illumina expression array platform with over 6000 genes and a Sequonome platform to sequence MC1R and genotype specific loci for BRAF and NRAS to: a. Assign MITF or IIG class for each melanoma sample and evaluate their association with BRAF/NRAS/MC1R status and determinants of melanoma histology (e.g. Breslow thickness, Clark's level, vertical growth phase) b. Evaluate genome-wide (6,000 genes) class discovery for each melanoma sample and evaluate their association with BRAF/ NRAS/MC1R status and determinants of melanoma histology (e.g. Breslow, Clark's level, vertical growth phase) Specific Aim 2: Using the transcriptional and genomic signatures from Aim 1 to: a. Assign MITF or IIG class association with BRAF/NRAS/MC1R status and melanoma recurrence and mortality due to melanoma b. Evaluate genome-wide (6,000 genes) association with BRAF/NRAS/MC1R status and melanoma recurrence and mortality due to melanoma