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 dat...
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2025-04-01
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| Series: | BioTechniques |
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| Online Access: | https://www.tandfonline.com/doi/10.1080/07366205.2025.2505347 |
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| author | Elizabeth Guinto Sameeksha Chopra I-Chih Kuo Samuel B. Shin Melina Messing Chung Y. Cheung Julia SW. Yang Firoozeh V. Gerayeli William Yip Stephen Milne Rachel L. Eddy Janice M. Leung Kelly M. McNagny Don D. Sin |
| author_facet | Elizabeth Guinto Sameeksha Chopra I-Chih Kuo Samuel B. Shin Melina Messing Chung Y. Cheung Julia SW. Yang Firoozeh V. Gerayeli William Yip Stephen Milne Rachel L. Eddy Janice M. Leung Kelly M. McNagny Don D. Sin |
| author_sort | Elizabeth Guinto |
| collection | DOAJ |
| description | 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 (p < .01). Overall, we recommend CyTOF as a tool to validate sc-RNA-seq data for select proteins and cell populations in BAL samples. |
| format | Article |
| id | doaj-art-1f5238c9ba8847d3969e75fb2ff29c48 |
| institution | Kabale University |
| issn | 0736-6205 1940-9818 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | BioTechniques |
| spelling | doaj-art-1f5238c9ba8847d3969e75fb2ff29c482025-08-20T03:44:17ZengTaylor & Francis GroupBioTechniques0736-62051940-98182025-04-0177417919010.1080/07366205.2025.2505347Integration of mass cytometry and single-cell RNA-sequencing of cells in bronchoalveolar lavageElizabeth Guinto0Sameeksha Chopra1I-Chih Kuo2Samuel B. Shin3Melina Messing4Chung Y. Cheung5Julia SW. Yang6Firoozeh V. Gerayeli7William Yip8Stephen Milne9Rachel L. Eddy10Janice M. Leung11Kelly M. McNagny12Don D. Sin13Centre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, Vancouver, CanadaSchool of Biomedical Engineering, University of British Columbia, Vancouver, CanadaSchool of Biomedical Engineering, University of British Columbia, Vancouver, CanadaSchool of Biomedical Engineering, University of British Columbia, Vancouver, CanadaSchool of Biomedical Engineering, University of British Columbia, Vancouver, CanadaCentre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, Vancouver, CanadaCentre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, Vancouver, CanadaCentre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, Vancouver, CanadaCentre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, Vancouver, CanadaSydney Medical School, The University of Sydney, Sydney, AustraliaCentre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, Vancouver, CanadaCentre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, Vancouver, CanadaCentre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, Vancouver, CanadaCentre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, Vancouver, CanadaSingle-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 (p < .01). Overall, we recommend CyTOF as a tool to validate sc-RNA-seq data for select proteins and cell populations in BAL samples.https://www.tandfonline.com/doi/10.1080/07366205.2025.2505347Bronchoalveolar lavagemass cytometryproteinrNAsingle-cell RNA sequencing |
| spellingShingle | Elizabeth Guinto Sameeksha Chopra I-Chih Kuo Samuel B. Shin Melina Messing Chung Y. Cheung Julia SW. Yang Firoozeh V. Gerayeli William Yip Stephen Milne Rachel L. Eddy Janice M. Leung Kelly M. McNagny Don D. Sin Integration of mass cytometry and single-cell RNA-sequencing of cells in bronchoalveolar lavage BioTechniques Bronchoalveolar lavage mass cytometry protein rNA single-cell RNA sequencing |
| title | Integration of mass cytometry and single-cell RNA-sequencing of cells in bronchoalveolar lavage |
| title_full | Integration of mass cytometry and single-cell RNA-sequencing of cells in bronchoalveolar lavage |
| title_fullStr | Integration of mass cytometry and single-cell RNA-sequencing of cells in bronchoalveolar lavage |
| title_full_unstemmed | Integration of mass cytometry and single-cell RNA-sequencing of cells in bronchoalveolar lavage |
| title_short | Integration of mass cytometry and single-cell RNA-sequencing of cells in bronchoalveolar lavage |
| title_sort | integration of mass cytometry and single cell rna sequencing of cells in bronchoalveolar lavage |
| topic | Bronchoalveolar lavage mass cytometry protein rNA single-cell RNA sequencing |
| url | https://www.tandfonline.com/doi/10.1080/07366205.2025.2505347 |
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