作者,Evil Genius
今天我们来汇总一下所有的关于空间邻域通讯的分析方法,供大家参考。
分析方法包括单细胞的改良版cellphoneDB、CellChat、Nichenet、以及专门为空转通讯分析的stlearn、COMMOT,我们来汇总其中的内容并且分享其中的细节。
其中专门分析单细胞的通讯方法cellphoneDB、CellChat、Nichenet全部更新了配套的空间转录组内容,可见配受体共定位已经成为了共识。
关于时空的通讯分析,之前分享过一篇,大家可以看时空通讯分析大盘点
1、cellphoneDB
关于cellphoneDB,大家应该看了很多的推文了,主要是用来做单细胞的通讯分析的,不过从cellphoneDB V3版本开始,cellphoneDB加入了空间通讯分析的内容,这个内容之前分享过,大家可以看考虑空间位置的通讯分析手段---CellphoneDB(V3.0),并且该方法被高分文章Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro(Nature Genetics, IF 30.8)所引用。
其中cellphoneDB分析空间通讯需要一个生态位文件,其中这个文件的示例官网给出的如下,细胞类型所在的生态位(微环境):
并且官网推荐采用cell2location进行生态位的判定,借助生态位的文件,CellphoneDB will use this information to restrict the pairs of interacting cell types (i.e. pairs of clusters sharing/coexisting in a microenvironment).
生态文件的获得在文章Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro的描述是
To investigate how surrounding cells may shape signaling in the surface and glandular compartments, we developed CellPhoneDB v.3.0, an updated version of our cell–cell communication pipeline that takes into account spatial cellular colocalization when map-ping ligand–receptor pairs
define three endometrial microenvironments centered on epithelial cells based on the cellular coordinates provided by cell2location: (1) lumenal—preciliated, ciliated
and SOX9+LGR5+ epithelium (proliferative phase) and ciliated and lumenal (secretory phase); (2) functional—SOX9+ proliferative epithelium, immune and eS (proliferative phase) and immune, glandular and dS (secretory phase); and (3) basal—SOX9+LGR5− and fibroblasts C7其中生态位的判定To account for the distinct temporal and spatial location of cells (that is, microenvironment), we further classified the epithelial interactions based on (1) the phase of the menstrual cycle where cell subsets coexist and (2) their location in the three main endometrial layers (luminal,glandular and basal) according to cell2location