Combined protein and transcript single-cell RNA sequencing in human peripheral blood mononuclear cells

• Type of Material: Article
• Authors: Jenifer Vallejo, La Jolla Institute for Immunology; Ryosuke Saigusa, La Jolla Institute for Immunology; Rishab Gulati, La Jolla Institute for Immunology; Sujit Silas A Suthahar, La Jolla Institute for Immunology; Vasantika Suryawanshi, La Jolla Institute for Immunology; Ahmad Alimadadi, La Jolla Institute for Immunology; Christopher P Durant, La Jolla Institute for Immunology; Yanal Ghosheh, La Jolla Institute for Immunology; Payel Roy, La Jolla Institute for Immunology; Erik Ehinger, La Jolla Institute for Immunology; Tanya Pattarabanjird, University of Virginia; David B Hanna, Albert Einstein College of Medicine; Alan L Landay, Rush University; Russell P Tracy, University of Vermont; Jason M Lazar, SUNY Downstate Health Sciences University; Wendy J Mack, University of Southern California; Kathleen M Weber, Cook County Health/Hektoen Institute of Medicine; Adaora A Adimora, University of North Carolina; Howard N Hodis, University of Southern California; Phyllis C Tien, University of California San Francisco; Ighovwerha Ofotokun, Emory University; Sonya L Heath, University of Alabama Birmingham; Avishai Shemesh, University of California San Francisco; Coleen A McNamara, University of Virginia; Lewis L Lanier, University of California San Francisco; Catherine C Hedrick, La Jolla Institute for Immunology; Robert C Kaplan, Albert Einstein College of Medicine; Klaus Ley, La Jolla Institute for Immunology
• Language: English
• Date: 2022-09-01
• Publisher: BMC
• Publication Version: Final Published Version
• Copyright Statement: © The Author(s) 2022
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1186/s12915-022-01382-4
• Title of Journal or Parent Work: BMC BIOLOGY
• Volume: 20
• Issue: 1
• Start Page: 193
• End Page: 193
• Keywords: Life Sciences & Biomedicine; ATHEROSCLEROTIC LESIONS; Antibodies; Human; Transcriptomes; CVD; T-CELLS; QUANTIFICATION; PROGRESSION; Science & Technology; IL-32; scRNA-seq; HIV-INFECTION; MONOCYTE SUBSET; Life Sciences & Biomedicine - Other Topics; EXPRESSION; Biology; HIV; DISEASE; ACTIVATION

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.