Liu Junwei, Liu Lulu, Qu Saisi, Zhang Tongtong, Wang Danyang, Ji Qinghua, Wang Tian, Shi Hongyu, Song Kaichen, Fang Weijia, Chen Wei, Yin Weiwei
Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, School of Basic Medical Science and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China.
Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310000, China.
Bioinformatics. 2021 Dec 11;37(24):4787-4792. doi: 10.1093/bioinformatics/btab537.
Mass cytometry (Cytometry by Time-Of-Flight, CyTOF) is a single-cell technology that is able to quantify multiplex biomarker expressions and is commonly used in basic life science and translational research. However, the widely used Gadolinium (Gd)-based contrast agents (GBCAs) in magnetic resonance imaging (MRI) scanning in clinical practice can lead to signal contamination on the Gd channels in the CyTOF analysis. This Gd contamination greatly affects the characterization of the real signal from Gd-isotope-conjugated antibodies, severely impairing the CyTOF data quality and ruining downstream single-cell data interpretation.
We first in-depth characterized the signals of Gd isotopes from a control sample that was not stained with Gd-labeled antibodies but was contaminated by Gd isotopes from GBCAs, and revealed the collinear intensity relationship across Gd contamination signals. We also found that the intensity ratios of detected Gd contamination signals to the reference Gd signal were highly correlated with the natural abundance ratios of corresponding Gd isotopes. We then developed a computational method named by GdClean to remove the Gd contamination signal at the single-cell level in the CyTOF data. We further demonstrated that the GdClean effectively cleaned up the Gd contamination signal while preserving the real Gd-labeled antibodies signal in Gd channels. All of these shed lights on the promising applications of the GdClean method in preprocessing CyTOF datasets for revealing the true single-cell information.
The R package GdClean is available on GitHub at https://github.com/JunweiLiu0208/GdClean.
Supplementary data are available at Bioinformatics online.
质谱流式细胞术（飞行时间质谱细胞术，CyTOF）是一种单细胞技术，能够对多种生物标志物的表达进行定量，常用于基础生命科学和转化研究。然而，临床实践中磁共振成像（MRI）扫描广泛使用的基于钆（Gd）的造影剂（GBCAs）会导致CyTOF分析中Gd通道出现信号污染。这种Gd污染极大地影响了来自Gd同位素偶联抗体的真实信号的表征，严重损害了CyTOF数据质量并破坏了下游单细胞数据的解读。
我们首先深入表征了一个未用Gd标记抗体染色但被来自GBCAs的Gd同位素污染的对照样本中Gd同位素的信号，并揭示了Gd污染信号之间的共线强度关系。我们还发现，检测到的Gd污染信号与参考Gd信号的强度比与相应Gd同位素的自然丰度比高度相关。然后，我们开发了一种名为GdClean的计算方法，用于在CyTOF数据的单细胞水平上去除Gd污染信号。我们进一步证明，GdClean有效地清除了Gd污染信号，同时保留了Gd通道中真实的Gd标记抗体信号。所有这些都为GdClean方法在预处理CyTOF数据集以揭示真实单细胞信息方面的应用前景提供了启示。
R包GdClean可在GitHub上获取，网址为https://github.com/JunweiLiu0208/GdClean。
补充数据可在《生物信息学》在线获取。
