Integration of mass cytometry and single-cell RNA-sequencing of cells in bronchoalveolar lavage

Single-cell RNA sequencing (sc-RNA-seq) is a popular method for characterization of cell populations. However, the relationship between RNA and protein expression in cells is often discordant. Protein-based detection methods, such as cytometry by time-of-flight (CyTOF), can provide complementary data to sc-RNA-seq. We collected bronchoalveolar lavage (BAL) from healthy participants and co-evaluated cell populations and gene/protein expression by applying sc-RNA-seq and CyTOF to the same samples. Cell populations were well correlated between these two platforms, but differences emerged at the sub-population level. Notably, macrophage subtypes did not correlate well; whereas T-lymphocytes did. Gene and protein expression levels were significantly correlated (<i>p</i> < .01). Overall, we recommend CyTOF as a tool to validate sc-RNA-seq data for select proteins and cell populations in BAL samples.

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Publication Details

Journal
BioTechniques
Published
2025-04-03
DOI
https://doi.org/10.1080/07366205.2025.2505347
Citations
2
Primary Topic
Single-cell and spatial transcriptomics
Type
article
Field-Weighted Citation Impact
1.61

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article

Integration of mass cytometry and single-cell RNA-sequencing of cells in bronchoalveolar lavage

Sameeksha Chopra, William Yip, Stephen B Milne, Elizabeth Guinto et al.
2 citations
BioTechniques
Single-cell and spatial transcriptomics
1.61
article

Integration of mass cytometry and single-cell RNA-sequencing of cells in bronchoalveolar lavage

Sameeksha Chopra, William Yip, Stephen B Milne, Elizabeth Guinto, Samuel B. Shin, Rachel L. Eddy, Kelly M. McNagny, Don D. Sin, Melina Messing, Firoozeh V. Gerayeli, Chung Yan Cheung, I-Chih Kuo, Jiong Yang, Janice M. Leung
article en
2 citations

Abstract

Single-cell RNA sequencing (sc-RNA-seq) is a popular method for characterization of cell populations. However, the relationship between RNA and protein expression in cells is often discordant. Protein-based detection methods, such as cytometry by time-of-flight (CyTOF), can provide complementary data to sc-RNA-seq. We collected bronchoalveolar lavage (BAL) from healthy participants and co-evaluated cell populations and gene/protein expression by applying sc-RNA-seq and CyTOF to the same samples. Cell populations were well correlated between these two platforms, but differences emerged at the sub-population level. Notably, macrophage subtypes did not correlate well; whereas T-lymphocytes did. Gene and protein expression levels were significantly correlated (<i>p</i> < .01). Overall, we recommend CyTOF as a tool to validate sc-RNA-seq data for select proteins and cell populations in BAL samples.

BioTechniquesVol. 77(4)
The University of Sydney (AU), University of British Columbia (CA), Westmead Hospital (AU), Sydney Local Health District (AU)
Genome British Columbia, Mitacs, Canadian Institutes of Health Research
Openalex Percentile: Top 17%
Single-cell and spatial transcriptomics
1.61
DOIOpen Access PDFOpenAlex
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