Advances and Prospects for the Human BioMolecular Atlas Program (HuBMAP)

Overview

Journal Nat Cell Biol

Specialty Cell Biology

Date 2023 Jul 19

PMID 37468756

Authors

Sanjay Jain

Liming Pei

Jeffrey M Spraggins

Michael Angelo

James P Carson

Nils Gehlenborg

Fiona Ginty

Joana P Goncalves

James S Hagood

John W Hickey

Neil L Kelleher

Louise C Laurent

Shin Lin

Yiing Lin

Huiping Liu

Alexandra Naba

Ernesto S Nakayasu

Wei-Jun Qian

Andrea Radtke

Paul Robson

Brent R Stockwell

Raf Van de Plas

Ioannis S Vlachos

Mowei Zhou

Katy Borner

Michael P Snyder

Affiliations

Soon will be listed here.

Abstract

The Human BioMolecular Atlas Program (HuBMAP) aims to create a multi-scale spatial atlas of the healthy human body at single-cell resolution by applying advanced technologies and disseminating resources to the community. As the HuBMAP moves past its first phase, creating ontologies, protocols and pipelines, this Perspective introduces the production phase: the generation of reference spatial maps of functional tissue units across many organs from diverse populations and the creation of mapping tools and infrastructure to advance biomedical research.

Citing Articles

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References

Borner K, Bueckle A, Herr 2nd B, Cross L, Quardokus E, Record E . Tissue registration and exploration user interfaces in support of a human reference atlas. Commun Biol. 2022; 5(1):1369. PMC: 9747802. DOI: 10.1038/s42003-022-03644-x. View

Borner K, Teichmann S, Quardokus E, Gee J, Browne K, Osumi-Sutherland D . Anatomical structures, cell types and biomarkers of the Human Reference Atlas. Nat Cell Biol. 2021; 23(11):1117-1128. PMC: 10079270. DOI: 10.1038/s41556-021-00788-6. View

Stelzer E . Light-sheet fluorescence microscopy for quantitative biology. Nat Methods. 2014; 12(1):23-6. DOI: 10.1038/nmeth.3219. View

. The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nature. 2019; 574(7777):187-192. PMC: 6800388. DOI: 10.1038/s41586-019-1629-x. View

de Boer I, Alpers C, Azeloglu E, Balis U, Barasch J, Barisoni L . Rationale and design of the Kidney Precision Medicine Project. Kidney Int. 2021; 99(3):498-510. PMC: 8330551. DOI: 10.1016/j.kint.2020.08.039. View

Guilliams M, Bonnardel J, Haest B, Vanderborght B, Wagner C, Remmerie A . Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022; 185(2):379-396.e38. PMC: 8809252. DOI: 10.1016/j.cell.2021.12.018. View

Mungall C, Torniai C, Gkoutos G, Lewis S, Haendel M . Uberon, an integrative multi-species anatomy ontology. Genome Biol. 2012; 13(1):R5. PMC: 3334586. DOI: 10.1186/gb-2012-13-1-r5. View

Meehan T, Masci A, Abdulla A, Cowell L, Blake J, Mungall C . Logical development of the cell ontology. BMC Bioinformatics. 2011; 12:6. PMC: 3024222. DOI: 10.1186/1471-2105-12-6. View

Wallace D . Mitochondrial DNA variation in human radiation and disease. Cell. 2015; 163(1):33-8. PMC: 4743751. DOI: 10.1016/j.cell.2015.08.067. View

10.

Zhang W, Li Y, Fung A, Li Z, Jang H, Zha H . Multi-molecular hyperspectral PRM-SRS microscopy. Nat Commun. 2024; 15(1):1599. PMC: 10881988. DOI: 10.1038/s41467-024-45576-6. View

11.

Eng C, Lawson M, Zhu Q, Dries R, Koulena N, Takei Y . Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH. Nature. 2019; 568(7751):235-239. PMC: 6544023. DOI: 10.1038/s41586-019-1049-y. View

12.

Melani R, Gerbasi V, Anderson L, Sikora J, Toby T, Hutton J . The Blood Proteoform Atlas: A reference map of proteoforms in human hematopoietic cells. Science. 2022; 375(6579):411-418. PMC: 9097315. DOI: 10.1126/science.aaz5284. View

13.

Rozenblatt-Rosen O, Stubbington M, Regev A, Teichmann S . The Human Cell Atlas: from vision to reality. Nature. 2017; 550(7677):451-453. DOI: 10.1038/550451a. View

14.

He S, Bhatt R, Brown C, Brown E, Buhr D, Chantranuvatana K . High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging. Nat Biotechnol. 2022; 40(12):1794-1806. DOI: 10.1038/s41587-022-01483-z. View

15.

Ardini-Poleske M, Clark R, Ansong C, Carson J, Corley R, Deutsch G . LungMAP: The Molecular Atlas of Lung Development Program. Am J Physiol Lung Cell Mol Physiol. 2017; 313(5):L733-L740. PMC: 5792185. DOI: 10.1152/ajplung.00139.2017. View

16.

Black S, Phillips D, Hickey J, Kennedy-Darling J, Venkataraaman V, Samusik N . CODEX multiplexed tissue imaging with DNA-conjugated antibodies. Nat Protoc. 2021; 16(8):3802-3835. PMC: 8647621. DOI: 10.1038/s41596-021-00556-8. View

17.

Uhlen M, Fagerberg L, Hallstrom B, Lindskog C, Oksvold P, Mardinoglu A . Proteomics. Tissue-based map of the human proteome. Science. 2015; 347(6220):1260419. DOI: 10.1126/science.1260419. View

18.

Canela V, Bowen W, Ferreira R, Syed F, Lingeman J, Sabo A . A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease. Nat Commun. 2023; 14(1):4140. PMC: 10356953. DOI: 10.1038/s41467-023-38975-8. View

19.

Rodriques S, Stickels R, Goeva A, Martin C, Murray E, Vanderburg C . Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science. 2019; 363(6434):1463-1467. PMC: 6927209. DOI: 10.1126/science.aaw1219. View

20.

Lake B, Menon R, Winfree S, Hu Q, Ferreira R, Kalhor K . An atlas of healthy and injured cell states and niches in the human kidney. Nature. 2023; 619(7970):585-594. PMC: 10356613. DOI: 10.1038/s41586-023-05769-3. View