做了上百个单细胞转录组项目,发现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!
参考前面的例子:人人都能学会的单细胞聚类分群注释 ,第一次分群就非常漂亮!但是如果细分这个CAFs,就没那么简单了。