Computational prediction of protein interactions on single cells by proximity sequencing.
Computational prediction of protein interactions on single cells by proximity sequencing.
复制标题
通过邻近测序计算预测单细胞上的蛋白质相互作用。
DOI：
10.1101/2023.07.27.550388
复制
发表时间：
2023
期刊：
影响因子：
--
通讯作者：
Tay,Savaş
中科院分区：
文献类型：
--
作者：
Xia,Junjie;VanPhan,Hoang;Vistain,Luke;Chen,Mengjie;Khan,AlyA;Tay,Savaş
邻近测序（Prox-seq）同时测量单细胞上的基因表达、蛋白质表达和蛋白质复合物。使用来自双抗体结合事件的信息，Prox-seq在单细胞水平上推断表面蛋白二聚体。Prox-seq提供了高通量的单细胞多维表型分析，最近被用于跟踪细胞信号传导过程中受体复合物的形成，并发现了幼稚T细胞中CD 9和CD 8之间的新型相互作用。蛋白质丰度的分布可以以复杂的方式影响蛋白质复合物在双结合测定（如Prox-seq）中的鉴定。这些影响很难用实验来探索，但对于蛋白质复合物的准确定量很重要。在这里，我们介绍了Prox-seq的物理模型，并在计算上评估了几种不同的方法，用于在定量蛋白质复合物时减少背景噪声。此外，我们开发了一种改进的方法来分析Prox-seq数据，这导致了蛋白质复合物的更准确和更强大的定量。最后，我们的Prox-seq模型提供了一种简单的方法来研究Prox-seq数据在各种生物条件下的行为，并指导用户为其数据选择最佳分析方法。
Proximity sequencing (Prox-seq) simultaneously measures gene expression, protein expression and protein complexes on single cells. Using information from dual-antibody binding events, Prox-seq infers surface protein dimers at the single-cell level. Prox-seq provides multi-dimensional phenotyping of single cells in high throughput, and was recently used to track the formation of receptor complexes during cell signaling and discovered a novel interaction between CD9 and CD8 in naïve T cells. The distribution of protein abundance can affect identification of protein complexes in a complicated manner in dual-binding assays like Prox-seq. These effects are difficult to explore with experiments, yet important for accurate quantification of protein complexes. Here, we introduce a physical model of Prox-seq and computationally evaluate several different methods for reducing background noise when quantifying protein complexes. Furthermore, we developed an improved method for analysis of Prox-seq data, which resulted in more accurate and robust quantification of protein complexes. Finally, our Prox-seq model offers a simple way to investigate the behavior of Prox-seq data under various biological conditions and guide users toward selecting the best analysis method for their data.