Anatomical structures, cell types and biomarkers of the Human Reference Atlas

Börner, Katy; Teichmann, Sarah A.; Quardokus, Ellen M.; Gee, James C.; Browne, Kristen; Osumi-Sutherland, David; Herr, Bruce W.; Bueckle, Andreas; Paul, Hrishikesh; Haniffa, Muzlifah; Jardine, Laura; Bernard, Amy; Ding, Shilei; Miller, Jeremy A.; Lin, Shin; Halushka, Marc K.; Boppana, Avinash; Longacre, Teri A.; Hickey, John W.; Lin, Yiing; Valerius, M. Todd; He, Yongqun; Pryhuber, Gloria S.; Sun, Xin; Jorgensen, Marda; Radtke, Andrea J.; Wasserfall, Clive; Ginty, Fiona; Ho, Jonhan; Sunshine, Joel C.; Beuschel, Rebecca T.; Brusko, Todd M.; Lee, Sujin; Malhotra, Rajeev; Jain, Sanjay; Weber, Griffin M

doi:10.1038/s41556-021-00788-6

Cited by 87 publications

(91 citation statements)

References 155 publications

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“…The CCF reference organs is a constantly growing collection. Using other tools developed by HuBMAP, such as Anatomical Structures and Cell Types Plus Biomarkers (ASCT+B) Tables [2], they are a fundamental building block of generating the HRA by allowing to register data from incredibly diverse donors into one spatial and semantic framework. While HuBMAP as a funded research endeavor will one day be completed, part of its legacy could be educating the general audience about single-cell biology and the relationship between cells, tissue, organs, and disease.…”

Section: Discussionmentioning

confidence: 99%

The Common Coordinate Framework (CCF) Organ VR Gallery

Bueckle¹,

Browne²,

Herr³

et al. 2022

Preprint

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The CCF Organ VR Gallery lets the user explore 21 human organs, journeying from the Whole Body, to the Organ, to the Cell stage and back, presented in real-world size and 3D. The user discovers hidden regions by exploding and collapsing organs into their individual anatomical structures. We show cell type populations for a kidney using a data-driven dot density visualization. The organ models were developed to map trillions of cells for the Human BioMolecular Atlas Program (HuBMAP).

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Section: Discussionmentioning

confidence: 99%

The Common Coordinate Framework (CCF) Organ VR Gallery

Bueckle¹,

Browne²,

Herr³

et al. 2022

Preprint

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“…Mammalian tissues are comprised of hundreds of diverse cell types and anatomical structures that express thousands of unique gene and protein biomarkers 62 . Advances in single‐cell flow cytometry and genomic methods have greatly expanded our understanding of the cellular composition of normal and diseased tissues.…”

Section: Highly Multiplexed Antibody‐based 2d Imagingmentioning

confidence: 99%

Understanding immunity in a tissue‐centric context: Combining novel imaging methods and mathematics to extract new insights into function and dysfunction*

Germain

Radtke

Thakur

et al. 2021

Immunological Reviews

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A central question in immunology is what features allow the immune system to respond in a timely manner to a variety of pathogens encountered at unanticipated times and diverse body sites. Two decades of advanced and static dynamic imaging methods have now revealed several major principles facilitating host defense. Suborgan spatial prepositioning of distinct cells promotes time‐efficient interactions upon pathogen sensing. Such pre‐organization also provides an effective barrier to movement of pathogens from parenchymal tissues into the blood circulation. Various molecular mechanisms maintain effective intercellular communication among otherwise rapidly moving cells. These and related discoveries have benefited from recent increases in the number of parameters that can be measured simultaneously in a single tissue section and the extension of such multiplex analyses to 3D tissue volumes. The application of new computational methods to such imaging data has provided a quantitative, in vivo context for cell trafficking and signaling pathways traditionally explored in vitro or with dissociated cell preparations. Here, we summarize our efforts to devise and employ diverse imaging tools to probe immune system organization and function, concluding with a commentary on future developments, which we believe will reveal even more about how the immune system operates in health and disease.

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“…A standard vocabulary system for fine-grained cell identity annotation is still lacking. A unified informatics framework is needed to tackle these challenges ( Börner et al., 2021 ; S. Chen et al., 2022b ; Osumi-Sutherland et al., 2021 ).…”

Section: Introductionmentioning

confidence: 99%