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.
Original language | English |
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Article number | 193 |
Journal | BMC Biology |
Volume | 20 |
Issue number | 1 |
DOIs | |
State | Published - 1 Dec 2022 |
Externally published | Yes |
Keywords
- Antibodies
- CVD
- HIV
- Human
- Transcriptomes
- scRNA-seq
ASJC Scopus subject areas
- Biotechnology
- Structural Biology
- Ecology, Evolution, Behavior and Systematics
- Physiology
- General Biochemistry, Genetics and Molecular Biology
- General Agricultural and Biological Sciences
- Plant Science
- Developmental Biology
- Cell Biology