空间蛋白质组学和蛋白质共定位的进展是理解细胞机制及其对生物过程影响的驱动力。空间蛋白质组学领域的新方法呼唤算法的发展并开辟新的研究途径。新引入的分子像素化 (MPX) 提供了单细胞中表面蛋白及其相互关系的空间信息。这允许在计算机中将膜蛋白的邻域表示为图表。为了分析这种新的数据模式，我们在 MPX 单细胞图网络中采用了局部分类性，并创建了一种能够捕获蛋白质空间关系详细信息的方法。所引入的方法可以评估蛋白质的成对共定位并获得高阶相似性以同时研究多个蛋白质的共定位。我们使用公开的 MPX 数据集评估了该方法，其中 T 细胞用趋化因子处理来研究尾足动物的形成。我们证明，调整后的局部分类性可以在单标记和多标记水平上检测刺激的影响，这增强了我们对尾足类形成的理解。我们还应用我们的方法使用治疗性抗体来治疗癌性 B 细胞系。通过调整局部配型，我们概括了利妥昔单抗对 CD20 极性的影响。我们的计算方法与 MPX 一起不仅提高了我们对刺激下细胞极性形成和蛋白质共定位的理解，而且提高了对免疫反应和细胞表面蛋白质重组的整体了解，从而可以设计新的疗法。当表示为无向图时，我们预见到它对其他类型的生物空间数据的适用性。版权所有 © 2024 Rhomberg-Kauert、Karlsson、Thiagarajan、Kallas、Karlsson、Fredriksson、Dahlberg 和 Martinez Barrio。

Advances in spatial proteomics and protein colocalization are a driving force in the understanding of cellular mechanisms and their influence on biological processes. New methods in the field of spatial proteomics call for the development of algorithms and open up new avenues of research. The newly introduced Molecular Pixelation (MPX) provides spatial information on surface proteins and their relationship with each other in single cells. This allows for in silico representation of neighborhoods of membrane proteins as graphs. In order to analyze this new data modality, we adapted local assortativity in networks of MPX single-cell graphs and created a method that is able to capture detailed information on the spatial relationships of proteins. The introduced method can evaluate the pairwise colocalization of proteins and access higher-order similarity to investigate the colocalization of multiple proteins at the same time. We evaluated the method using publicly available MPX datasets where T cells were treated with a chemokine to study uropod formation. We demonstrate that adjusted local assortativity detects the effects of the stimuli at both single- and multiple-marker levels, which enhances our understanding of the uropod formation. We also applied our method to treating cancerous B-cell lines using a therapeutic antibody. With the adjusted local assortativity, we recapitulated the effect of rituximab on the polarity of CD20. Our computational method together with MPX improves our understanding of not only the formation of cell polarity and protein colocalization under stimuli but also advancing the overall insight into immune reaction and reorganization of cell surface proteins, which in turn allows the design of novel therapies. We foresee its applicability to other types of biological spatial data when represented as undirected graphs.Copyright © 2024 Rhomberg-Kauert, Karlsson, Thiagarajan, Kallas, Karlsson, Fredriksson, Dahlberg and Martinez Barrio.