本文來源:生信菜鳥團
題目:Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19投稿日期:2020年2月24日接收日期:2020年4月23日發表日期:2020年5月12日雜誌:Nature Medicine文章在:https://www.nature.com/articles/s41591-020-0901-9
讓我想起來了另外一個COVID-19病毒感染病人的單細胞研究,發表在Cell Discov. 2020 May ,標題是:Immune Cell Profiling of COVID-19 Patients in the Recovery Stage by Single-Cell Sequencing,差不多是同一時間發表的哦!
畢竟Cell Discov雜誌和 Nature Medicine差別還是蠻大的,不知道是不是研究者特別想把研究寫在祖國大地上。
文章實驗設計
很清晰的實驗設計,如下:
15個人5個early recovery stage (ERS)5個late recovery stage (LRS)5個heathy controls (HCs)單細胞數量10個COVID-19 病人,共計 (70,858 PBMCs)5個正常人,共計 (57,238 cells)第一次分群
使用 t-distributed stochastic neighbor embedding (t-SNE) 方法降維
全部15個人的 128,096 scRNA-seq profiles36,442 myeloid cells,64,247 NK and T cells,10,177 B cells標記基因是:CD14, CD1C, and FCGR3A for myeloid cells;CD3E, CD4, CD8A, and NCAM1 for NK and T cells;CD19 for B cells第二次分群
使用 Uniform manifold approximation and projection (UMAP) 方法降維
36,442 myeloid cells 分成6群Classical CD14++ monocytes (M1),non-classical CD16++ (FCGR3A) CD14/+ monocytes (M2),intermediate CD14++ CD16+ monocytes (M3),CD1C+ cDC2 (M4),CLEC9A+ cDC1 (M5),pDC (CLEC4C+CD123+) (M6)64,247 NK and T cells 分成10群nave CD8+ T cells (T5), which expressed high levels of CCR7, LEF1, and TCF7, similar to nave CD4+ T cells;effector memory CD8+T cells (T6, CD8 Tm), which expressed high levels of GZMK;cytotoxic CD8+ lymphocytes (CD8+ CTL) (T7), which expressed high levels of GZMB, GNLY, and PRF1. Proliferating T cells (T8, Tprol) were TYMS+MKI67+ cells.nave CD4+ T cells (T1), which expressed high levels ofCCR7, LEF1, and TCF7;central memory CD4+ T cells (T2, CD4 Tcm), which expressed high levels of CCR7, but more AQP3 andCD69 compared to nave CD4+ T cells;effector memory CD4+ T cells (T3, CD4 Tem), which expressed high levels of CCR6, CXCR6, CCL5, and PRDM1;regulatory T cells (T4, Treg), which expressed FOXP3.C56CD16+ NK cells (NK2), which expressed high levels of CD16 and low levels of CD56.CD56+CD16 NK cells (NK1), which expressed high levels of CD56 and low levels of CD16;NK cells highly expressed NCAM1, KLRF1, KLRC1, andKLRD1; then, we sub-divided the NK cells intoCD4+ T cells expressed CD3E and CD4; then, we sub-divided these cells into four clusters:CD8+ T cells expressed CD8A and CD8B and were sub-divided into three clusters:10,177 B cells 分成 4群nave B cells (B1) expressing CD19, CD20 (MS4A1), IGHD, IGHM, IL4R, and TCL1A;memory B cells (B2) expressing CD27, CD38, andIGHG;immature B cells (B3) only expressing CD19 and CD20 (MS4A1);plasma cells (B4) expressing high levels ofXBP1 and MZB1分析層面的細節,都展現在分群以及細胞亞群的定義上面了。
主要分析
文章的圖表很清晰,都是顯而易見的分析,讀起來很友好反正:
3群細胞(myeloid, NK and T, and B cells),在3組人(five HCs, five ERS patients, and five LRS patients.)的比例myeloid的6個亞群,NK和T細胞的10亞群,以及4個B細胞亞群在3組人的比例情況Classical CD14++ monocytes (M1) 的差異分析,全套(火山圖,熱圖,GO/KEGG資料庫注釋)CD4+ T cells 的差異分析,全套(火山圖,熱圖,GO/KEGG資料庫注釋)Memory B cells and plasma cells (MPB) 的差異分析,全套(火山圖,熱圖,GO/KEGG資料庫注釋)也有一點點高級分析,包括sc-BCR, and sc-TCR 數據分析
主要是 (IgA+IgG+IgE) to (IgD+IgM) 比例情況以及 Cell-to-cell communication
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