【原】肺上皮細(xì)胞單細(xì)胞亞群

健明 2022-04-15

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肺癌單細(xì)胞數(shù)據(jù)集也有好幾十個(gè)了，拿到表達(dá)量矩陣后的第一層次降維聚類分群通常是：

immune (CD45+,PTPRC),
epithelial/cancer (EpCAM+,EPCAM),
stromal (CD10+,MME,fibo or CD31+,PECAM1,endo)

參考我前面介紹過(guò) CNS圖表復(fù)現(xiàn)08—腫瘤單細(xì)胞數(shù)據(jù)第一次分群通用規(guī)則，這3大單細(xì)胞亞群構(gòu)成了腫瘤免疫微環(huán)境的復(fù)雜。比如 Science Advances 27 Jan 2021: 的文章《 Decoding the multicellular ecosystem of lung adenocarcinoma manifested as pulmonary subsolid nodules by single-cell RNA sequencing》，就是如此：

腫瘤免疫微環(huán)境的復(fù)雜

絕大部分文章都是抓住免疫細(xì)胞亞群進(jìn)行細(xì)分，包括淋巴系（T,B,NK細(xì)胞）和髓系（單核，樹(shù)突，巨噬，粒細(xì)胞）的兩大類作為第二次細(xì)分亞群。但是也有不少文章是抓住stromal 里面的fibo 和endo進(jìn)行細(xì)分，并且編造生物學(xué)故事的。

反而是上皮細(xì)胞，大家很少涉及到，但是肺癌既然是來(lái)源于結(jié)直腸這樣的組織，它的上皮細(xì)胞就不可能是一個(gè)純粹的上皮，理論上是可以細(xì)分的。上面的這個(gè)文章其實(shí)也接下來(lái)部分細(xì)分：

正常的肺的上皮細(xì)胞細(xì)分

可以看到來(lái)自于正常的肺的上皮細(xì)胞約2000個(gè)，可以分成如下所示的5個(gè)亞群：

alveolar type I cell (AT1; AGER+)
alveolar type II cell (AT2; SFTPA1)
secretory club cell (Club; SCGB1A1+)
basal airway epithelial cells (Basal; KRT17+)
ciliated airway epithelial cells (Ciliated; TPPP3+)

上皮細(xì)胞的細(xì)分亞群數(shù)量肯定是不止這些，比如文章：《Pre-activated antiviral innate immunity in the upper airways controls early SARS-CoV-2 infection in children》，就列出來(lái)了近十種細(xì)胞亞群：

近十種細(xì)胞亞群

大家也可以去測(cè)試一下這些基因在你的肺部單細(xì)胞數(shù)據(jù)集里面是否好用。

代碼給大家；

library(ggplot2) 
genes_to_check =  c(SPRR3","GDPD3","SPRR1A","SPRR2A","RARRES2","TMPRSS11E",
"ASCL3","CFTR","FOXI2","1SG20","FOXI1",
"SAA4","SAA2","EFHC1","CCDC153","CCDC113","SAA1","CDC20B","FOXJ1",
"MYCL","FOXN4","CCNO",
"PIGR","BP1","MUC5A","VMO1","SCGB3A1","CYP2A13","CYP2B6","SCGB1A1",
"BCAM","KRT1","RT5","P63")