细胞亚群的特异性标记基因也许真的很难
做了上百个单细胞转录组项目，绝大部分都是肿瘤研究，在教程 CNS图表复现08—肿瘤单细胞数据第一次分群通用规则，这个第一次分群规则是 ：
immune (CD45+,PTPRC), epithelial/cancer (EpCAM+,EPCAM), stromal (CD10+,MME,fibo or CD31+,PECAM1,endo)
的表达量来划分即可，这就是肿瘤免疫微环境的话题了！
肿瘤微环境这个热点应该不仅仅是集中在免疫细胞，其实还有基质细胞，其中热度最高的基质细胞应该是Cancer-associated fibroblasts (CAFs) ，但是目前呢，学界对CAFs的来源本来就是并不那么清晰，理论上不可能存的单一的标记基因来区分出来CAFs。通常CAFs有4种来源：
The primary source is normal local fibroblasts, which are activated by stimuli from the tumor microenvironment. Mesenchymal stem cells (MSCs) and other mesenchymal precursor cells are other sources. Endothelial cells and epithelial cells do not belong to the fibroblast lineage, but they could transdifferentiate into CAFs-state cells. Finally, a self-renewable CAFs-stem cell population might exist in the hierarchical organization, and these cells share similar characteristics as MSCs.
如果要筛选CAFs，首先要去除4个基因表达量为阳性的细胞亚群 ：
CD31 (an endothelial marker) CD45 (a hematopoietic cell marker), desmin (a smooth muscle cell marker), EPCAM (epithelial cell adhesion molecule, an epithelial cell marker).
然后各种文献整理一下，发现它的阳性标记基因可能是有：α-SMA, Collegen1A1, FAP, FSP1, PDGFRα and PDGFRβ, Podoplanin, and vimentin. 这么多，但是呢，都会有例外：
α-SMA is unable to identify all CAFs in the TME, and it is expressed in smooth muscle in normal gastrointestinal and vascular FAP combined with CD45 is used to label a subgroup of cancer-associated macrophages FSP1 also corresponds to epithelial cells experiencing epithelial-to-mesenchymal transition (EMT; In a liver fibrosis model, FSP1 distinguishes inflammatory macrophage subpopulation
在人类疾病领域，可以区分成为：CAFs pro-tumorigenic function (pCAFs) or CAFs tumor-restain (rCAFs)
以上资料整理来源于新鲜出炉的综述：Front. Cell Dev. Biol., 04 February 2021 | https://doi.org/10.3389/fcell.2021.613534 标题是：《Cancer-Associated Fibroblasts Suppress Cancer Development: The Other Side of the Coin》
在小鼠模型里面，比如胰腺癌的小鼠模型里面，通常是3种不一样的，myofibroblast (myCAF), inflammatory fibroblast (iCAF), and antigen-presenting fibroblast (apCAF). ：
myCAF produces the majority of αSMA and collagen I transcripts S100a4 (Fsp1) expression in apCAFs iCAF 当然也是有自己的标记基因啦！
这3个分群，来源于文章：《Type I collagen deletion in αSMA+ myofibroblasts augments immune suppression and accelerates progression of pancreatic cancer》，于 March 2021发表于 cancer cell杂志，链接是：https://www.sciencedirect.com/science/article/pii/S1535610821001094
最后借用2018的一篇CELL文章《Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease》的 CyTOF panel 表格，信息如下：
可以看到，细胞发育谱系，细胞类型，细胞状态，其实还是水蛮深的！