人外周血单核细胞的蛋白和转录组联合单细胞 RNA 测序。
Combined protein and transcript single-cell RNA sequencing in human peripheral blood mononuclear cells.
机构信息
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.
出版信息
BMC Biol. 2022 Sep 1;20(1):193. doi: 10.1186/s12915-022-01382-4.
BACKGROUND
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.
RESULTS
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.
CONCLUSIONS
In conclusion, combined protein and transcript scRNA sequencing is a suitable and powerful method for clinical investigations using PBMCs.
背景
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）。
结果
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。
结论
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。
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