Abstract
The development of single-cell and spatial transcriptomics methods was instrumental in the conception of the Human Cell Atlas initiative, which aims to generate an integrated map of all cells across the human body. These technology advances are bringing increasing depth and resolution to maps of human organs and tissues, as well as our understanding of individual human cell types. Commonalities as well as tissue-specific features of primary and supportive cell types across human organs are beginning to emerge from these human tissue maps. In this Review, we highlight key biological insights obtained from cross-tissue studies into epithelial, fibroblast, vascular and immune cells based on single-cell gene expression data in humans and contrast it with mechanisms reported in mice.
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References
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Acknowledgements
The authors thank A. Maartens for providing feedback on writing; V. Kedlian, V. Kleshchevnikov, A. Oliver, E. Madissoon, K. Kanemaru, N. Kumasaka, B. Stewart and R. Bartolome-Casado for proofreading gene markers and cell types listed in Supplementary Table 2.
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The authors contributed equally to all aspects of the article.
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S.A.T. has consulted or been a member of scientific advisory boards at Roche, Genentech, Biogen, GlaxoSmithKline, Qiagen and ForeSite Labs and is an equity holder of Transition Bio. The other authors declare no competing interests.
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Related links
Broad Single-Cell Portal: https://singlecell.broadinstitute.org/single_cell
Cambridge Cell Atlas: https://www.cambridgecellatlas.org/
covid19cellatlas: https://www.covid19cellatlas.org/
HCA Data Coordination Platform: https://data.humancellatlas.org/
Human Protein atlas: https://www.proteinatlas.org/
Tabula Sapiens: https://tabula-sapiens-portal.ds.czbiohub.org/
UCSC Cell Browser: https://cells.ucsc.edu/
Supplementary information
Glossary
- Cell state
-
Intermediate, hybrid or transitional state acquired by the cell types in various contexts that is reflected in the transcriptional profile and function of the cell.
- Primary cells
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A category of cell types that perform the main functions of the tissue (for example, epithelial cells in barrier organs such as lung or gut, myocytes in skeletal or cardiac muscle, neurons in brain).
- Supportive cells
-
A category of cells that provide functional and structural support for primary cells (for example, vascular cells, fibroblasts and immune cells).
- V(D)J gene enrichment and sequencing
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The process whereby immune receptor V, D and J, or V and J gene segments are selectively amplified from the single-cell RNA-sequencing data.
- Clonal expansion
-
In the adaptive immune context, the process by which daughter B or T cells with unique antigen receptor specificity arise from a parent cell.
- Cell ontologies
-
Structured and controlled ways of classifying cell types that aim to capture the full diversity of cell types and states present in an organism.
- Zonation
-
Gradual transcriptional or phenotypic change of cells along a spatial axis.
- Somatic hypermutation
-
A cellular mechanism by which B cells accumulate point mutations in both the heavy and light chains of antibody V regions.
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Elmentaite, R., Domínguez Conde, C., Yang, L. et al. Single-cell atlases: shared and tissue-specific cell types across human organs. Nat Rev Genet 23, 395–410 (2022). https://doi.org/10.1038/s41576-022-00449-w
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DOI: https://doi.org/10.1038/s41576-022-00449-w
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