Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors
Open accessAbstract
What's in a drop of blood? Blood contains many types of cells, including many immune system components. Immune cells used to be characterized by marker-based assays, but now classification relies on the genes that cells express. Villani et al. used deep sequencing at the single-cell level and unbiased clustering to define six dendritic cell and four monocyte populations. This refined analysis has identified, among others, a previously unknown dendritic cell population that potently activates T cells. Further cell culture revealed possible differentiation progenitors within the different cell populations. Science , this issue p. eaah4573
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Myeloid subsets include CD1C DCs, CLEC9A cells, Langerhans cells, AS DCs, plasmacytoid DCs, and migrating DCs.
“The remaining subsets were re-clustered into CD1C DCs (CD1C, CLEC10A), CLEC9A cells (CLEC9A, CADM1, XCR1), Langerhans cells (CD207, CD1A, S100B), AS DCs (AXL, IGFBP5, PPP1R14A), plasmacytoid DCs (CLEC4C, IL3RA), and migrating DCs (CCR7, CCL19) (Bronte et al., 2016, Kiss et al., 2018, Villani et al., 2017).”
From Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma (2020) · cites this paper as Villani et al., 2017
The sections on unbiased classification and monocyte subsets identify CD1C+ DCs, CLEC9A+ DCs and plasmacytoid DCs with several of the cited markers; the AXL+SIGLEC6+ section identifies AS DCs. Our copy does not identify Langerhans cells or migrating DCs as subsets in this classification, and it does not establish IGFBP5 or PPP1R14A as AS DC markers. Page numbers are not available in the indexed passages. (LLM, conf=0.88)
Experimental — accuracy not yet measuredMyeloid subsets include macrophages (CD163, CD68) and MDSCs (S100A8, S100A9, TREM1).
“clusters high in the monocyte marker CD14, which were further re-clustered into macrophages (CD163, CD68) and MDSCs (S100A8, S100A9, TREM1).”
From Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma (2020) · cites this paper as Villani et al., 2017
In “Two subpopulations within CD1C+ DCs” (page unavailable), the paper reports CD163 as a marker of a dendritic-cell subset and CD14, S100A8, and S100A9 in that subset. In “Discovering monocyte subsets” (page unavailable), it identifies CD14-positive monocytes. It does not support identifying CD163/CD68-positive clusters as macrophages or S100A8/S100A9/TREM1-positive clusters as MDSCs. (LLM, conf=0.82)
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Neutrophilic Inflammation in Asthma and Association with Disease Severity
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Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics
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Single-cell multiomics: technologies and data analysis methods
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- Authors
- Villani, A.-C., Satija, R., Reynolds, G., Sarkizova, S., Shekhar, K., Fletcher, J., Griesbeck, M., Butler, A., Zheng, S., Lazo, S., Jardine, L., Dixon, D., Stephenson, E., Nilsson, E., Grundberg, I., McDonald, D., Filby, A., Li, W., De Jager, P. L., Rozenblatt-Rosen, O., Lane, A. A., Haniffa, M., Regev, A., & Hacohen, N.
- Affiliations
- Broad Institute (US)
- Newcastle University (GB)
- Ragon Institute of MGH, MIT and Harvard (US)
- New York Genome Center (US)
- Harvard University (US)
- Olink (United States) (US)
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Royal Victoria Infirmary (GB)
- Corresponding author
- Villani, Alexandra-Chloé
- Satija, Rahul
- Haniffa, Muzlifah
- Regev, Aviv
- Hacohen, Nir
- ORCID
- Villani, Alexandra-Chloé
- Satija, Rahul
- Reynolds, Gary
- Sarkizova, Siranush
- Shekhar, Karthik
- Fletcher, James
- Griesbeck, Morgane
- Butler, Andrew
- Zheng, Shiwei
- Lazo, Suzan
- Jardine, Laura
- Dixon, David
- Stephenson, Emily
- Nilsson, Emil
- Grundberg, Ida
- McDonald, David
- Filby, Andrew
- Lane, Andrew A.
- Haniffa, Muzlifah
- Regev, Aviv
- Hacohen, Nir
- Venue
- Science
- Published
- 2017-04-21
- Volume
- 356
- Issue
- 6335
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC5775029
- OpenAlex
- W2605810679
- Cited by
- 2,413
- References
- 76
- Citations by year
- 2026: 162 · 2025: 249 · 2024: 243 · 2023: 259 · 2022: 275 · 2021: 360 · 2020: 299 · 2019: 262 · 2018: 220 · 2017: 81 · 2013: 1
- FWCI
- 96.55
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Newcastle University ePrints (Newcastle Univesity)
- Funders
- National Human Genome Research Institute Centers of Excellence in Genomics Science (P50 HG006193)
- Manton Foundation
- Howard Hughes Medical Institute
- NIH BRAIN
- Klarman Family Foundation
- NIH Director’s New Innovator Award (DP2-HG-009623)
- American Society of Hematology Scholar
- Wellcome Trust (WT088555, WT107931/Z/15/Z)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Immunology and Microbiology › Immunology › Immunotherapy and Immune Responses
- Life Sciences › Immunology and Microbiology › Immunology › T-cell and B-cell Immunology
- Keywords
- dendritic cells, monocytes, blood immune cells, T cell activation, dendritic cell differentiation, cell type classification, single-cell transcriptomics, gene expression signatures
- MeSH terms
- Adult, Classification, Dendritic Cells, Female, Humans, Lymphocyte Activation, Male, Monocytes, Neoplasms, T-Lymphocytes, Monitoring, Immunologic, Sequence Analysis, RNA, Antigen Presentation, Gene Expression Profiling, Young Adult, Single-Cell Analysis, Transcriptome
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