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. Tien; Igho Ofotokun; Sonya L. Heath; Avishai Shemesh; Coleen A. McNamara; Lewis L. Lanier; Catherine C. Hedrick; Robert C. Kaplan; Klaus Ley

doi:10.1186/s12915-022-01382-4

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 journal › Article › peer-review

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 (US)
Article number	193
Journal	BMC Biology
Volume	20
Issue number	1
DOIs	https://doi.org/10.1186/s12915-022-01382-4
State	Published - 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

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10.1186/s12915-022-01382-4

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Vallejo, J., Saigusa, R., Gulati, R., Armstrong Suthahar, S. S., Suryawanshi, V., Alimadadi, A., Durant, C. P., Ghosheh, Y., Roy, P., Ehinger, E., Pattarabanjird, T., Hanna, D. B., Landay, A. L., Tracy, R. P., Lazar, J. M., Mack, W. J., Weber, K. M., Adimora, A. A., Hodis, H. N., ... Ley, K. (2022). Combined protein and transcript single-cell RNA sequencing in human peripheral blood mononuclear cells. BMC Biology, 20(1), Article 193. https://doi.org/10.1186/s12915-022-01382-4

Vallejo, J, Saigusa, R, Gulati, R, Armstrong Suthahar, SS, Suryawanshi, V, Alimadadi, A, Durant, CP, Ghosheh, Y, Roy, P, Ehinger, E, Pattarabanjird, T, Hanna, DB, Landay, AL, Tracy, RP, Lazar, JM, Mack, WJ, Weber, KM, Adimora, AA, Hodis, HN, Tien, PC, Ofotokun, I, Heath, SL, Shemesh, A, McNamara, CA, Lanier, LL, Hedrick, CC, Kaplan, RC & Ley, K 2022, 'Combined protein and transcript single-cell RNA sequencing in human peripheral blood mononuclear cells', BMC Biology, vol. 20, no. 1, 193. https://doi.org/10.1186/s12915-022-01382-4

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title = "Combined protein and transcript single-cell RNA sequencing in human peripheral blood mononuclear cells",

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{\textquoteright}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",

author = "Jenifer Vallejo and Ryosuke Saigusa and Rishab Gulati and {Armstrong Suthahar}, {Sujit Silas} and Vasantika Suryawanshi and Ahmad Alimadadi and Durant, {Christopher P.} and Yanal Ghosheh and Payel Roy and Erik Ehinger and Tanyaporn Pattarabanjird and Hanna, {David B.} and Landay, {Alan L.} and Tracy, {Russell P.} and Lazar, {Jason M.} and Mack, {Wendy J.} and Weber, {Kathleen M.} and Adimora, {Adaora A.} and Hodis, {Howard N.} and Tien, {Phyllis C.} and Igho Ofotokun and Heath, {Sonya L.} and Avishai Shemesh and McNamara, {Coleen A.} and Lanier, {Lewis L.} and Hedrick, {Catherine C.} and Kaplan, {Robert C.} and Klaus Ley",

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year = "2022",

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doi = "10.1186/s12915-022-01382-4",

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T1 - Combined protein and transcript single-cell RNA sequencing in human peripheral blood mononuclear cells

AU - Vallejo, Jenifer

AU - Saigusa, Ryosuke

AU - Gulati, Rishab

AU - Armstrong Suthahar, Sujit Silas

AU - Suryawanshi, Vasantika

AU - Alimadadi, Ahmad

AU - Durant, Christopher P.

AU - Ghosheh, Yanal

AU - Roy, Payel

AU - Ehinger, Erik

AU - Pattarabanjird, Tanyaporn

AU - Hanna, David B.

AU - Landay, Alan L.

AU - Tracy, Russell P.

AU - Lazar, Jason M.

AU - Mack, Wendy J.

AU - Weber, Kathleen M.

AU - Adimora, Adaora A.

AU - Hodis, Howard N.

AU - Tien, Phyllis C.

AU - Ofotokun, Igho

AU - Heath, Sonya L.

AU - Shemesh, Avishai

AU - McNamara, Coleen A.

AU - Lanier, Lewis L.

AU - Hedrick, Catherine C.

AU - Kaplan, Robert C.

AU - Ley, Klaus

PY - 2022/12

Y1 - 2022/12

N2 - 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.

AB - 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.

KW - Antibodies

KW - CVD

KW - HIV

KW - Human

KW - Transcriptomes

KW - scRNA-seq

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SN - 1741-7007

VL - 20

JO - BMC Biology

JF - BMC Biology

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ER -

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

Abstract

Keywords

ASJC Scopus subject areas

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