3种EMT打分算法
看到一个预印本文章对3种EMT打分算法进行了测评，挺有意思的，标题是：《Comparative study of transcriptomics-based scoring metrics for the epithelial-hybrid-mesenchymal spectrum》，链接在 https://www.biorxiv.org/content/10.1101/2020.01.02.892604v1.full
这3种方法的示意图如下所示：
加权线性加和（76-gene EMT signature）
这个算法对CDH1 (E-cadherin)的权重很高，所以epithelial的EMT scores是比mesenchymal高。
参考文献：An epithelial-mesenchymal transition gene signature predicts resistance to EGFR and PI3K inhibitors and identifies Axl as a therapeutic target for overcoming EGFR inhibitor resistance. Clin. Cancer Res.
two-sample Kolmogorov-Smirnov test
This score varies on a scale of −1 to 1, with the higher scores corresponding to more mesenchymal samples (Tan et al., 2014).
参考文献：Epithelial-mesenchymal transition spectrum quantification and its efficacy in deciphering survival and drug responses of cancer patients. EMBO Mol. Med.
multinomial logistic regression
它的值集中于0到2之间， This method particularly focuses on characterizing a hybrid E/M phenotype using the expression levels of 23 genes – 3 predictors and 20 normalizers – identified through NCI-60 gene expression data.
会把样品判断为3种状态：epithelial, mesenchymal, or hybrid E/M categories
参考文献是：2017). Survival outcomes in cancer patients predicted by a partial EMT gene expression scoring metric. Cancer Res. 77, 6415–6428. doi:10.1158/0008-5472.CAN-16-3521.
为什么没有gsva的打分呢？
GSVA生存分析教学视频 https://www.bilibili.com/video/av81874183 https://mp.weixin.qq.com/s/LJjsdf3X66nJ1KmpvvkHOA
每个文章都有自己的EMT打分算法
比如发表于2020年1月的文章；《Gene signatures of tumor inflammation and epithelial-to-mesenchymal transition (EMT) predict responses to immune checkpoint blockade in lung cancer with high accuracy》，链接是：https://www.sciencedirect.com/science/article/pii/S0169500219306932
There is not yet a validated lung cancer EMT signature, so we prospectively generated a gene list based on previous publications describing “classic” EMT genes in cancer [23,24] with the addition of some genes specifically mentioned in studies evaluating EMT in NSCLC [27–29]. Selected genes had levels of expression that were clearly above baseline (using a cutoff of 10 reads in our data set). Supplemental Table 2 shows the list of genes included along with their average expression level. Although the genes SNAI1, TWIST1, TWIST2, CDH2, and ZEB1 are classic mesenchymal markers, their expression levels were very low in our dataset and thus not included. Based on these criteria, we generated the EMT signature by adding the sum of the log2 Z scores of 6 established mesenchymal genes (AGER, FN1, MMP2, SNAI2, VIM, ZEB2) and subtracting the sum of the log2 Z scores of 6 established epithelial genes (CDH1, CDH3, CLDN4, EPCAM, MAL2, and ST14) (Supplemental Table 2). In this signature, the most mesenchymal tumors have the most positive EMT scores and the most epithelial tumors have the most negative scores.
总结起来，其实超级简单，就是选取高表达量的EMT基因，然后6个mesenchymal基因 的log2 Z scores 值的和，减去6个epithelial 基因 的log2 Z scores 值的和，所以这个EMT 打分越高就说明它是mesenchymal 的。
EMT 背景知识
EMT，全称epithelial–mesenchymal transition，又称翻译为上皮间质转换，指的是上皮细胞在一些因素的作用下,失去极性及细胞间紧密连接和黏附连接, 获得了浸润性和游走迁移能力, 变成具备间质细胞形态和特性的细胞的改变。这种行为是可逆的。
EMT的概念最早是1982年由Green-berg和Hay提出。然而，长久以来，科学界对于EMT在肿瘤转移过程中的作用一直存在争议，主要是因为无法在体内观察EMT过程 。
胚胎发育与癌症发展中的细胞可塑性变化有着惊人的相似性，**而这种可塑性变化受到上皮间质转化epithelial-mesenchymal transition （EMT）过程的调节。**胚胎发育时期，上皮状态和间充质状态的细胞能够自由转化。
上皮间质转化（EMT）使得细胞具备转移和浸润特性。 其反向过程，间质上皮转化mesenchymal-epithelialtransition （MET）赋予了细胞极性变化并失去移动能力。
EMT会促发癌细胞从病灶分离，转移到其它部位，而MET导致癌细胞停留，并在停留处引起新的肿瘤。
在很长一段时间内，许多科学家都认为EMT过程对于肿瘤转移是一个必须条件，EMT过程能够剥夺细胞与邻近细胞紧密结合的能力，使细胞能够在全身范围内迁移。科学家们认为是EMT给了癌细胞“双腿”让它们能够脱离原位肿瘤，转移到其他部位形成肿瘤转移灶。
一、 首先介绍下，EMT发生常见的标志分子。
1.表达减少：E- cadherin，Cytokeratin，ZO-1。
2.表达增多：N- cadherin，Vinmentin，Snail1，Snail2，Twi st，MMP-2，MMP-3，MMP-9。
3.活性增加：ILK，Rho。
二．参与EMT过程控制的常见信号通路有：
1.TGF-β信号通路。
2.Wnt信号通路。
3.Notch信号通路。
4.SMAD信号通路。
5.PI3K-AKT-MTOR信号通路。
三. EMT过程有着复杂的调节网络：
表观遗传的调节
转录调节
选择性剪接
蛋白质的稳定
亚细胞定位
这些调节方式多样性使得EMT的调节往往不是线性的。此前，EMT调节过程中关于E-cadherin的转录，EMT转录因子SNAI1，SNAI2， ZEB1，ZEB1和 TWIST1等研究较多。
上皮细胞黏附分子（EpCAM）
与普通血细胞相比,CTCs具有某些特殊的生物标志物,包括CTCs表面的上皮细胞粘附分子(Epithelial cell adhesion molecule,EpCAM)
不同文献报道不一致：
在咽癌中Ep-CAM高表达与淋巴结转移密切相关，Ep-CAM表达越高，淋巴结转移发生频率越高 在头颈部鳞状细胞癌中，Ep-CAM在转移灶中表达比原发灶更高 在胃癌骨髓转移灶中的播散性肿瘤细胞Ep-CAM的表达较原发灶降低
免疫组织化学中的细胞角蛋白(Cytokeratin, CK) :
EMT基因集
简单搜索了一下， 确实是热点：
早在2010的PANS文章https://doi.org/10.1073/pnas.1004900107 就定义过 EMT Core Signature 基因集合We identified an EMT core signature consisting of 159 genes that were down-regulated and 87 genes that were up-regulated at least 2-fold by all of these EMT-inducing signals (Table S1). 数据在 GSE9691 和 GSE9691 然后是 2012 的 Meta-Analysis of Gene Expression https://doi.org/10.1371/journal.pone.0051136 也发布了基因集，包括 EMT-core gene list of 130 up- or downregulated genes shared between at least 10 GES datasets.和 List of 365 genes significantly regulated in at least 10 GES datasets. 也可以在 Pan‐cancer genomic datasets from The Cancer Genome Atlas (TCGA), representing over 10,000 patients and 32 distinct cancer types, provide a rich resource for examining correlative patterns involving EMT mediators in the setting of human cancers.验证：https://onlinelibrary.wiley.com/doi/pdf/10.1002/dvdy.24485 2015 数据库 dbEMT 但是引用率不高， - 被引用次数：28 其整理的 All the 377 human Epithelial-Mesenchymal Transition genes with cancer types 数据是可以下载的：http://dbemt.bioinfo-minzhao.org/download.cgi 最后是 2020的这个最新了，The web-based EMTome portal is a resource for primary and metastatic tumour research publicly available at www.emtome.org. 文章链接是：https://www.nature.com/articles/s41416-020-01178-9