학술논문
Combined protein and transcript single-cell RNA sequencing in human peripheral blood mononuclear cells.
Document Type
Article
Author
Vallejo, Jenifer; Saigusa, Ryosuke; Gulati, Rishab; Armstrong Suthahar, Sujit Silas; Suryawanshi, Vasantika; Alimadadi, Ahmad; Durant, Christopher P.; Ghosheh, Yanal; Roy, Payel; Ehinger, Erik; Pattarabanjird, Tanyaporn; Hanna, David B.; Landay, Alan L.; Tracy, Russell P.; Lazar, Jason M.; Mack, Wendy J.; Weber, Kathleen M.; Adimora, Adaora A.; Hodis, Howard N.; Tien, Phyllis C.
Source
Subject
*MONONUCLEAR leukocytes
*MESSENGER RNA
*RNA sequencing
*KILLER cells
*CRYOPRESERVATION of cells
*CYTOMETRY
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Language
ISSN
1741-7007
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. [ABSTRACT FROM AUTHOR]