1. Combined protein and transcript single-cell RNA sequencing in human peripheral blood mononuclear cells
- Author
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Jenifer Vallejo, Ryosuke Saigusa, Rishab Gulati, Sujit Silas Armstrong Suthahar, Vasantika Suryawanshi, Ahmad Alimadadi, Christopher P. Durant, Yanal Ghosheh, Payel Roy, Erik Ehinger, Tanyaporn Pattarabanjird, David B. Hanna, Alan L. Landay, Russell P. Tracy, Jason M. Lazar, Wendy J. Mack, Kathleen M. Weber, Adaora A. Adimora, Howard N. Hodis, Phyllis C. Tien, Igho Ofotokun, Sonya L. Heath, Avishai Shemesh, Coleen A. McNamara, Lewis L. Lanier, Catherine C. Hedrick, Robert C. Kaplan, and Klaus Ley
- Subjects
CVD ,HIV ,scRNA-seq ,Transcriptomes ,Antibodies ,Human ,Biology (General) ,QH301-705.5 - Abstract
Abstract 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.
- Published
- 2022
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