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2.2.10 研究| 2021-单细胞转录组分析COVID-19重症患者肺泡巨噬细胞亚型

刘小泽写于2021.10.18

前言

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

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

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

重症样本注释

包括了:basal cells, vascular cells, dendritic cells, ionocytes, monocyte-derived alveolar macrophages, plasma cells, and 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
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FCGR3BCCL3L1TNFAIP6 (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