Reply to Walter and Reyfman: Transcriptomic Analysis of Alveolar Immune Cells in Acute Respiratory Distress Syndrome: To Lump or to Split?
Reply to Walter and Reyfman: Transcriptomic Analysis of Alveolar Immune Cells in Acute Respiratory Distress Syndrome: To Lump or to Split?
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回复沃尔特和雷夫曼：急性呼吸窘迫综合征中肺泡免疫细胞的转录组学分析：结块还是分裂？
DOI：
10.1164/rccm.201907-1309le
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发表时间：
2019
影响因子：
24.7
通讯作者：
Gharib,SinaA
中科院分区：
文献类型：
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作者：
Morrell,EricD;Bhatraju,PavanK;Mikacenic,Carmen;Radella2nd,Frank;Manicone,AnneM;Stapleton,ReneeD;Wurfel,MarkW;Gharib,SinaA
我们感谢博士。沃尔特和雷夫曼关于我们研究的信件 (1)。我们一致认为，免疫细胞异质性，尤其是肺泡巨噬细胞 (AM) 多样性，可能在急性呼吸窘迫综合征 (ARDS) 的发病机制中发挥着关键作用。我们小组 (2) 和其他小组 (3, 4) 最近的研究使用单细胞方法来更好地表征 ARDS 和急性肺损伤动物模型中的肺泡免疫亚型。然而，我们警告不要仅仅依靠单细胞 RNA 测序等“分裂”方法来了解复杂人类综合征的病理学。对有限数量的受试者进行的高度精细的方法可能无法捕获危重疾病中存在的临床表型的多样性，并且单细胞方法仍然存在显着的技术和计算限制 (5)。危重护理转化研究依赖于分析来自相对较大的患者队列的数据来克服外部混杂因素，这些混杂因素可能会导致结果出现偏差，例如临床干预的变化、危险因素发作的时间和基线遗传多样性。单细胞方法的复杂性和成本目前限制了可实际分析的样本数量。此外，由于测序覆盖深度有限和扩增偏差，许多重要基因无法用常用的单细胞 RNA 测序平台捕获 (6)。例如，Myd88（骨髓分化初级反应 88）和 Tlr9（Toll 样受体 9）是两个重要的巨噬细胞效应基因，在最近鉴定急性肺损伤动物模型中 AM 亚型的单细胞 RNA 测序实验中未检测到这两个基因 (3)。
We appreciate Drs. Walter and Reyfman’s correspondence regarding our study (1). We agree that immune cell heterogeneity—particularly alveolar macrophage (AM) diversity—likely plays a key role in the disease pathogenesis of acute respiratory distress syndrome (ARDS). Recent studies by our group (2) and others (3, 4) have used single-cell approaches to better characterize alveolar immune subtypes in ARDS and animal models of acute lung injury. However, we caution against solely relying on “splitting” approaches such as single-cell RNA sequencing to understand the pathobiology of complex human syndromes. Highly granular approaches performed on limited numbers of subjects may not capture the diversity of clinical phenotypes that exist in critical illness, and there remain significant technical and computational limitations (5) regarding single-cell approaches.Critical care translational studies rely on analyzing data from relatively large patient cohorts to overcome external confounders that can bias results such as variation in clinical interventions, timing in the onset of risk factors, and baseline genetic diversity. The complexity and cost of single-cell approaches currently limit the number of samples that can be practically analyzed. In addition, many important genes are not captured with commonly used singlecell RNA sequencing platforms because of the limited depth of sequencing coverage and amplification bias (6). For example, Myd88 (myeloid differentiation primary response 88) and Tlr9 (toll-like receptor 9) are two important macrophage effector genes that were not detected in a recent single-cell RNA sequencing experiment identifying AM subtypes in an animal model of acute lung injury (3).