Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro.
Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro.
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使用 DecontPro 对基于液滴的单细胞蛋白质表达数据中的背景噪声进行表征和净化。
DOI：
10.1101/2023.01.27.525964
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
Campbell,JoshuaD
中科院分区：
文献类型：
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作者：
Yin,Yuan;Yajima,Masanao;Campbell,JoshuaD
诸如CITE-seq的测定可以使用抗体衍生标签（ADT）测量单个细胞上的细胞表面蛋白的丰度。然而，许多ADT具有高水平的背景噪声，这可能会混淆下游分析。在PBMC数据集的探索性分析中，我们发现一些最初由于低水平RNA而被称为“空”的液滴含有高水平的ADT，并且可能对应于中性粒细胞。我们在空液滴中鉴定了一种新型的伪影，称为“海绵”，其具有中等水平的ADT表达，并且与环境噪声不同。在几个数据集中，海绵体中的ADT表达水平与真细胞背景峰中的ADT表达水平相关，表明它们可以与周围ADT一起沿着背景噪声。然后，我们开发了DecontPro，这是一种新型的贝叶斯分层模型，可以通过估计和去除这些来源的污染来净化ADT数据。DecontPro在去除异常表达的ADT同时保留天然ADT和提高聚类特异性方面优于其他去污工具。总的来说，这些结果表明，对于RNA和ADT数据，应单独进行空液滴的鉴定，并且可以将DecontPro纳入CITE-seq工作流程，以提高下游分析的质量。
Assays such as CITE-seq can measure the abundance of cell surface proteins on individual cells using antibody derived tags (ADTs). However, many ADTs have high levels of background noise that can obfuscate down-stream analyses. In an exploratory analysis of PBMC datasets, we find that some droplets that were originally called ‘empty’ due to low levels of RNA contained high levels of ADTs and likely corresponded to neutrophils. We identified a novel type of artifact in the empty droplets called a ‘spongelet’ which has medium levels of ADT expression and is distinct from ambient noise. ADT expression levels in the spongelets correlate to ADT expression levels in the background peak of true cells in several datasets suggesting that they can contribute to background noise along with ambient ADTs. We then developed DecontPro, a novel Bayesian hierarchical model that can decontaminate ADT data by estimating and removing contamination from these sources. DecontPro outperforms other decontamination tools in removing aberrantly expressed ADTs while retaining native ADTs and in improving clustering specificity. Overall, these results suggest that identification of empty drops should be performed separately for RNA and ADT data and that DecontPro can be incorporated into CITE-seq workflows to improve the quality of downstream analyses.