单细胞转录组分析COVID-19重症患者肺泡巨噬细胞亚型

文章信息

文章题目：Single-cell transcriptome identifies FCGR3B upregulated subtype of alveolar macrophages in patients with critical COVID-19 日期：2021-09-24 期刊：iScience DOI：https://doi.org/10.1016/j.isci.2021.103030

一句话概括

数据分析文章：scRNA分析重症COVID-19患者多个样本，得到一种单核细胞衍生的肺泡巨噬细胞 (MoAMs) 亚型，并且FCGR3B基因在其中特异性表达，提供了一个新的biomarker。

使用的数据

• 对照1：10例健康气管样本（ Deprez et al., 2020）
• 对照2：4例健康肺样本（Madissoon et al., 2019）
• BALF单细胞数据（支气管肺泡灌洗液, broncho-alveolar lavage fluid）：总共14个样本，包括对照、轻度和重症患者样本 (Liao et al., 2020)

BALF单细胞群初步注释

利用Liao文章的marker基因，大致分成macrophages, myeloid dendritic cells, and T-cells，但发现很多cluster的细胞类型不好确定【A) Control. B) Moderate. C) Severe BALF clusters using Liao et al markers】

于是自己又细分亚群，分别得到19, 17, and 18个cluster， 21939, 7316 and 37197 cells

然后又找了一些marker自行细胞注释：https://www.cell.com/cms/10.1016/j.isci.2021.103030/attachment/24e25182-6d40-41fa-a4f5-fc33e365f86f/mmc2

重症样本注释

包括了：

• basal cells,
• vascular cells,
• dendritic cells,
• ionocytes,
• monocyte-derived alveolar macrophages,
• plasma cells,
• alveolar epithelial cells

重症样本的cluster11与COVID-19并发症基因之间的关联

并发症包括了：encoding cytokines and cytokine receptors, or associated with rare infectious diseases, rare syndromes, chronic obstructive pulmonary disease, cardiovascular disease, hypertension, obesity, and diabetes

基因列表：https://www.cell.com/cms/10.1016/j.isci.2021.103030/attachment/0b421468-3a53-48b6-8c28-3eee4d7e06f7/mmc4

发现重症的17个cluster中，cluster11表现非常突出，9个基因列表中表达了8个，并且表达量还主要是上调

因此，这个cluster11就被标记为monocyte-derived alveolar macrophages (MoAMs)，它的marker 基因就是CCl3L1 ，而且这个MoAMs亚型在 moderate or control样本中都没发现

之后也看了一下富集分析，主要集中在：

• host immune response signaling networks related to TNFα
• cytokine and interferon gamma responses
• response to type1 interferon and biotic stimulus
• innate immune and inflammatory responses

MoAM亚型top20基因分析

既然感兴趣的cluster找到，那么接下来就看其中的top基因（这里选择前20）

做了一个气泡图【 A) Control. B) Moderate and C) Severe BALF】，不过感觉没啥必要，既然选择cluster11的前20，那么肯定这些基因（横坐标）就主导啊

然后就定位到了其中一个差异最大的基因：FCGR3B

然后开始研究这个基因了：

• regulate both adaptive and innate immune responses which are crucial for the defense against infection and prevention of chronic inflammation or autoimmune diseases
• FcRs mediate important immune responses such as release of cytokines or phagocytosis (Ben Mkaddem et al., 2019)

并且图C中cluster11表达的FCGR3B，比其他FcR族基因更多

FCGR3B的数据集验证

在bulk PBMC data进行验证 (Arunachalam et al., 2020) ，并且发现在non-classical monocytes中表达更多

在 bulk data set from nasopharyngeal swabs数据集验证（左图），另外之前看cluster11特异性表达CCL3L1，那么同样在重症的CCL3L1高表达细胞中，FCGR3B表达同样高

不过，不同于FCGR3B，CCL3L1和TNFAIP6 (indicator of COVID-19 severity) 在其他数据集中并非一直是重症表达量高于对照组。所以最后的目光又集中于FCGR3B 这一个基因了

FCGR3B的实验验证

qPCR positive COVID-19 patients (n = 31) and qPCR negative controls (n = 11)，发现：

• 左图（单纯covid）：50% had greater than 1.5-fold change of FCGR3B compared with 28.1% in controls
• 右图（covid+并发症）：57.1% of patients with severe COVID-19 with comorbidity had greater than 1.5-fold change of FCGR3B compared with 28.1% in controls

当然，最后还拓展了一下，做了个体外并发症（肥胖）关联实验，发现：FCGR3B as a potential modulator of COVID-19 severity in patients with obesity

文中链接

[1] Deprez et al., 2020: https://www.cell.com/iscience/fulltext/S2589-0042(21)00998-6?rss=yes&utm_source=dlvr.it&utm_medium=twitter#bib14 [2] Madissoon et al., 2019: https://www.cell.com/iscience/fulltext/S2589-0042(21)00998-6?rss=yes&utm_source=dlvr.it&utm_medium=twitter#bib30 [3] Liao et al., 2020: https://www.cell.com/iscience/fulltext/S2589-0042(21)00998-6?rss=yes&utm_source=dlvr.it&utm_medium=twitter#bib29 [4] Ben Mkaddem et al., 2019: https://www.cell.com/iscience/fulltext/S2589-0042(21)00998-6?rss=yes&utm_source=dlvr.it&utm_medium=twitter#bib5 [5] Arunachalam et al., 2020: https://www.cell.com/iscience/fulltext/S2589-0042(21)00998-6?rss=yes&utm_source=dlvr.it&utm_medium=twitter#bib2