一篇单细胞和WGCNA结合的文献解读-1

文章题目

Single Cell Gene Co-Expression Network Reveals FECH/CROT Signature as a Prognostic Marker

背景知识

AR（Androgen receptor，雄激素受体）活性的增加驱动晚期前列腺癌的治疗耐药，深入剖析AR调控网络的机制至关重要。GCN（co-expression network）有助于成功识别AR变量驱动的基因模块，但是由于GCN的高度稀疏性和维数高，为所有被检测基因构建的GCN太大而无法解释。而加权相关网络分析(WGCNA)利用层次聚类方法识别基因簇，并能提取潜在表型的有意义的生物信息。近期研究表明LNCaP细胞对雄激素剥夺治疗反应不一。现已发现雄激素剥夺治疗的耐药亚群，其特征是细胞周期活动增强。因此，本研究旨在从单细胞的角度找出AR调控的关键生物学过程及其雄激素调控基因。

==androgen（R1881）==，也被称为甲基三烯醇，是一种合成的雄激素。它是AR激动剂。

biomodal：双峰性表达，描述如下图

image-20200601113642215

BI value:BI index,用来代表 biomodal expression的extent，The bimodality index (BI) is used to distribution of marker genes (AR, KLK3, and TMPRSS2) in single cells; Genes with BI > 1.2 are regarded as bimodally expressed genes

材料方法

数据：We downloaded the processed expression (RPKM) profiles of LNCaP cells generated by single cell RNA-seq from GEO (accession ID: GSE99795). The dataset contains 144 LNCaP cells from 0 h untreated, 12 h untreated and 12 h R1881 treated conditions. There are 48 cells under each condition.

Bimodality expression was performed using the ==R package, SIBER== . First, a normal mixture model (‘NL’) was specified on the log2 transformed RPKM expression values to fit the gene expression distribution into a two component mixture model (component 1 and 2). Next the average values (mu1 and mu2) were calculated. Other parameters were also obtained including variance values (sigma1, sigma2) and corresponding proportion of the component 1 and 2 (pi1 and pi2).

结果

结果1.我们尝试用双峰表达模式来表征细胞的异质性。

• 作者研究了已知的ARGs，如KLK3和TMPRSS2的表达

image-20200601112841618 image-20200601114836790

结果2.WGCNA

• he gene expression profiles, comprising of 10,445 genes in 144 samples, were log2 transformed and subjected to WGCNA.

image-20200601113020409

结果3.确定由AR调控的模块

• 已有研究表明由AR调控的DEGS-共272个，现在看哪些模块与这272个DEGs 重叠性最高。黄色和红色模块中的基因与来自单细胞RNA-seq数据集的ARGs明显重叠

image-20200601113404534

结果4. 由AR受体调控的 Biological Functions of Modules

• Because the bimodal gene expression commonly existed of function enrichment is shown in Figure 4A. Because the bimodal gene expression commonly among single cells (Figure 1), we aimed to find the function terms that showed most expressed pattern. The average_BI value (Figure 4A) for a function term is the average BI of module bimodally express.主要是generation of precursor metabolites and energy这个通路

==应用的包是RobustRankaAggreg==

image-20200601114617483

• Jiang et al. developed the androgen responsive gene database (ARGDB) to provide integrated knowledge on androgen-controlled genes .Among these 11 genes, FECH and CROT are novel androgen regulated genes according to ARGDB.

• 两种基因FECH是非双峰性基因，BI值小于1.2，而CHOT是双峰性基因，BI值大于1.2

• image-20200601115759420

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结果5.FECH and CROT在病人中的表达

• 两个数据：TCGA/MSKCC ，其中FECH和CROT在MSKCC和TCGA中的表达在正常、tumor、转移组中均无差异，但CROT在TCGA数据库中的表达在normol和tumor中的表达有差异

image-20200601121303350 image-20200601121310723

结果6.FECH/CROT 可以作为由AR调控的预后因子 image-20200601121913343

image-20200601121943767

• 加了==androgen（R1881）==AR激动剂以后，FECH/CROT的表达量下降

image-20200601122352176

• 同时高表达FECH/CROT在两个数据集中都是预后差，所以FECH/CROT可作为预后因子

image-20200601122434810