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

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. TienIgho Ofotokun, Sonya L. Heath, Avishai Shemesh, Coleen A. McNamara, Lewis L. Lanier, Catherine C. Hedrick, Robert C. Kaplan, Klaus Ley

Research output: Contribution to journalArticlepeer-review

14 Scopus citations


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 languageEnglish (US)
Article number193
JournalBMC Biology
Issue number1
StatePublished - Dec 2022
Externally publishedYes


  • Antibodies
  • CVD
  • HIV
  • Human
  • scRNA-seq
  • Transcriptomes

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


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