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
