La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.
Carter Immunology Center, Cardiovascular Division, Department of Medicine, University of Virginia, Charlottesville, VA, USA.
BMC Biol. 2022 Sep 1;20(1):193. doi: 10.1186/s12915-022-01382-4.
Cryopreserved peripheral blood mononuclear cells (PBMCs) are frequently collected and provide disease- and treatment-relevant data in clinical studies. Here, we developed combined protein (40 antibodies) and transcript single-cell (sc)RNA sequencing (scRNA-seq) in PBMCs.
Among 31 participants in the Women's Interagency HIV Study (WIHS), we sequenced 41,611 cells. Using Boolean gating followed by Seurat UMAPs (tool for visualizing high-dimensional data) and Louvain clustering, we identified 50 subsets among CD4+ T, CD8+ T, B, NK cells, and monocytes. This resolution was superior to flow cytometry, mass cytometry, or scRNA-seq without antibodies. Combined protein and transcript scRNA-seq allowed for the assessment of disease-related changes in transcriptomes and cell type proportions. As a proof-of-concept, we showed such differences between healthy and matched individuals living with HIV with and without cardiovascular disease.
In conclusion, combined protein and transcript scRNA sequencing is a suitable and powerful method for clinical investigations using PBMCs.
冷冻保存的外周血单核细胞（PBMCs）经常被采集，并在临床研究中提供与疾病和治疗相关的数据。在这里，我们开发了 PBMCs 中联合蛋白质（40 种抗体）和转录单细胞（sc）RNA 测序（scRNA-seq）。
在妇女艾滋病研究机构间（WIHS）的 31 名参与者中，我们对 41611 个细胞进行了测序。使用布尔门控（Boolean gating），然后使用 Seurat UMAPs（用于可视化高维数据的工具）和 Louvain 聚类，我们在 CD4+T、CD8+T、B、NK 细胞和单核细胞中鉴定出 50 个亚群。这种分辨率优于流式细胞术、质谱流式细胞术或没有抗体的 scRNA-seq。联合蛋白质和转录 scRNA-seq 可以评估转录组和细胞类型比例与疾病相关的变化。作为一个概念验证，我们展示了健康个体与 HIV 匹配个体之间、以及有或没有心血管疾病个体之间的差异。
总之，联合蛋白质和转录 scRNA 测序是使用 PBMCs 进行临床研究的一种合适且强大的方法。
