# 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 ## 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 链接： ## 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](https://www.cell.com/iscience/fulltext/S2589-0042\(21\)00998-6?rss=yes\&utm_source=dlvr.it\&utm_medium=twitter#bib14)） * 对照2：4例健康肺样本（[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)） * 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](https://www.cell.com/iscience/fulltext/S2589-0042\(21\)00998-6?rss=yes\&utm_source=dlvr.it\&utm_medium=twitter#bib29)) ## 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】 ![image-20211018212214987](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2021-10-18-132215.png) 于是自己又细分亚群，分别得到19, 17, and 18个cluster， 21939, 7316 and 37197 cells ![image-20211018212407400](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2021-10-18-132407.png) 然后又找了一些marker自行细胞注释： ![image-20211018212524960](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2021-10-18-132525.png) ## 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 ![image-20211018212755234](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2021-10-18-132755.png) ![image-20211018212928624](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2021-10-18-132928.png) ## 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： 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 ![image-20211018213458204](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2021-10-18-133458.png) 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 ![image-20211018213759747](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2021-10-18-133800.png) ## 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 ![image-20211018214139670](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2021-10-18-134140.png) 然后就定位到了其中一个差异最大的基因：*FCGR3B* ![image-20211018214440837](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2021-10-18-134441.png) 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](https://www.cell.com/iscience/fulltext/S2589-0042\(21\)00998-6?rss=yes\&utm_source=dlvr.it\&utm_medium=twitter#bib5)) 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](https://www.cell.com/iscience/fulltext/S2589-0042\(21\)00998-6?rss=yes\&utm_source=dlvr.it\&utm_medium=twitter#bib2)) ，并且发现在non-classical monocytes中表达更多 ![image-20211018214849262](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2021-10-18-134849.png) 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 ![image-20211018215022234](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2021-10-18-135022.png) 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 ![image-20211018215544716](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2021-10-18-135545.png) ## 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 ![image-20211018215754823](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2021-10-18-135754.png) 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 ![image-20211018220058328](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2021-10-18-140058.png)
--- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://jieandze1314.osca.top/02/2.2.10-yan-jiu-2021-dan-xi-bao-zhuan-lu-zu-fen-xi-covid19-zhong-zheng-huan-zhe-fei-pao-ju-shi-xi-bao.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.