Characterizing Nsd3 Amplification In Lung Cancer

<strong>SGC Open Notebook Project to Characterize the HMTase NSD3</strong> <strong>Exp020 Objective: </strong>NSD3 (WHSC1L1) is amplified in ~5% of Non-Small Cell Lung Cancer patients( cBioPortal : Cerami et<br> al. Cancer Discov. 2012 and Gao et al. Sci. Signal. 2013). However, the implications of this event on the<br> formation and progression of the disease are unclear. While NSD3 may be a driver of lung cancer, it is also<br> plausible that this locus is simply amplified at a higher frequency in the context of cancer-associated genomic<br> instability. To dive deeper into this question I will use The Cancer Genome Atlas (TCGA) lung cancer<br> data-sets to look for associations between NSD3 amplification and mutational status as well as gene expression<br> profiles. This data has been generated by the TCGA Research Network: http://cancergenome.nih.gov/. I<br> hypothesize that if NSD3 amplification is a driving force in a subset of lung tumors, these samples will share<br> similar gene expression profiles and exhibit higher expression levels of NSD3. Here, I am using FirebrowserR<br> (Deng M., et al. Database. 2017 - PMID:28062517), an R client for Broad Institute’s Firehose Web API,<br> which allows TCGA data processed by the Firehose Pipeline to be directly imported into R for analysis.SGC开放笔记本项目：组蛋白甲基转移酶（Histone Methyltransferase, HMTase）NSD3的表征 **实验020 研究目标：** NSD3（WHSC1L1）在约5%的非小细胞肺癌（Non-Small Cell Lung Cancer, NSCLC）患者中存在扩增，相关数据引自cBioPortal数据库：Cerami等发表于《Cancer Discov.》2012年的研究，以及Gao等发表于《Sci. Signal.》2013年的研究。然而，该扩增事件对疾病发生与进展的潜在影响尚不明确。尽管NSD3可能作为肺癌的驱动基因，但亦存在另一种合理推测：该基因座仅在癌症相关基因组不稳定的背景下，以更高频率发生扩增。为深入解析这一问题，本研究将借助癌症基因组图谱（The Cancer Genome Atlas, TCGA）肺癌数据集，探究NSD3扩增与突变状态及基因表达谱之间的关联。本研究使用的数据集由TCGA研究网络生成，访问地址为http://cancergenome.nih.gov/。本研究提出如下假说：若NSD3扩增是部分肺肿瘤的驱动因素，则此类样本将呈现高度相似的基因表达谱，且NSD3的表达水平显著升高。本研究采用FirebrowserR工具（Deng M.等，《Database》2017年，PMID:28062517）——一款面向博德研究所（Broad Institute）Firehose Web API的R语言客户端，可将经Firehose分析流程处理的TCGA数据直接导入R环境开展分析。