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

BMC Biol. 2022 Sep 1;20(1):193. doi: 10.1186/s12915-022-01382-4.


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.

Keywords: Antibodies; CVD; HIV; Human; Transcriptomes; scRNA-seq.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • Female
  • Flow Cytometry
  • Gene Expression Profiling / methods
  • HIV Infections* / genetics
  • Humans
  • Leukocytes, Mononuclear* / metabolism
  • Sequence Analysis, RNA / methods
  • Single-Cell Analysis / methods
  • Transcriptome