School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan.
Commun Biol. 2024 May 28;7(1):652. doi: 10.1038/s42003-024-06363-7.
Epitope binning, an approach for grouping antibodies based on epitope similarities, is a critical step in antibody drug discovery. However, conventional methods are complex, involving individual antibody production. Here, we established Epitope Binning-seq, an epitope binning platform for simultaneously analyzing multiple antibodies. In this system, epitope similarity between the query antibodies (qAbs) displayed on antigen-expressing cells and a fluorescently labeled reference antibody (rAb) targeting a desired epitope is analyzed by flow cytometry. The qAbs with epitope similar to the rAb can be identified by next-generation sequencing analysis of fluorescence-negative cells. Sensitivity and reliability of this system are confirmed using rAbs, pertuzumab and trastuzumab, which target human epidermal growth factor receptor 2. Epitope Binning-seq enables simultaneous epitope evaluation of 14 qAbs at various abundances in libraries, grouping them into respective epitope bins. This versatile platform is applicable to diverse antibodies and antigens, potentially expediting the identification of clinically useful antibodies.
表位聚类是一种基于表位相似性对抗体进行分组的方法，是抗体药物发现的关键步骤。然而，传统方法复杂，涉及单个抗体的生产。在这里，我们建立了 Epitope Binning-seq，这是一个用于同时分析多个抗体的表位聚类平台。在该系统中，通过流式细胞术分析表达抗原的细胞上展示的查询抗体 (qAb) 与针对所需表位的荧光标记参考抗体 (rAb) 之间的表位相似性。通过对荧光阴性细胞的下一代测序分析，可以鉴定出与 rAb 表位相似的 qAb。我们使用针对人表皮生长因子受体 2 的 pertuzumab 和 trastuzumab 这两种 rAb 来验证该系统的灵敏度和可靠性。Epitope Binning-seq 能够同时对文库中不同丰度的 14 个 qAb 进行表位评估，并将它们分组到各自的表位 bin 中。这个多功能平台适用于各种不同的抗体和抗原，有可能加快识别具有临床应用价值的抗体。
