Functional Tissue Units in the Human Reference Atlas

Overview

Journal bioRxiv

Date 2023 Oct 31

PMID 37905079

Authors

Supriya Bidanta

Katy Borner

Bruce W Herr 2nd

Marcell Nagy

Katherine S Gustilo

Rachel Bajema

Libby Maier

Roland Molontay

Griffin Weber

Affiliations

Soon will be listed here.

Abstract

Functional tissue units (FTUs) form the basic building blocks of organs and are important for understanding and modeling the healthy physiological function of the organ and changes during disease states. In this first comprehensive catalog of FTUs, we document the definition, physical dimensions, vasculature, and cellular composition of 22 anatomically correct, nested functional tissue units (FTUs) in 10 healthy human organs. The catalog includes datasets, illustrations, an interactive online FTU explorer, and a large printable poster. All data and code are freely available. This is part of a larger ongoing international effort to construct a Human Reference Atlas (HRA) of all cells in the human body.

References

Ginzberg M, Kafri R, Kirschner M . Cell biology. On being the right (cell) size. Science. 2015; 348(6236):1245075. PMC: 4533982. DOI: 10.1126/science.1245075. View

Fruhstorfer H, Abel U, Garthe C, Knuttel A . Thickness of the stratum corneum of the volar fingertips. Clin Anat. 2000; 13(6):429-33. DOI: 10.1002/1098-2353(2000)13:6<429::AID-CA6>3.0.CO;2-5. View

Osumi-Sutherland D, Xu C, Keays M, Levine A, Kharchenko P, Regev A . Cell type ontologies of the Human Cell Atlas. Nat Cell Biol. 2021; 23(11):1129-1135. DOI: 10.1038/s41556-021-00787-7. View

de Bono B, Grenon P, Baldock R, Hunter P . Functional tissue units and their primary tissue motifs in multi-scale physiology. J Biomed Semantics. 2013; 4(1):22. PMC: 4126067. DOI: 10.1186/2041-1480-4-22. View

Ostedgaard L, Price M, Whitworth K, Abou Alaiwa M, Fischer A, Warrier A . Lack of airway submucosal glands impairs respiratory host defenses. Elife. 2020; 9. PMC: 7541087. DOI: 10.7554/eLife.59653. View

Weber G, Ju Y, Borner K . Considerations for Using the Vasculature as a Coordinate System to Map All the Cells in the Human Body. Front Cardiovasc Med. 2020; 7:29. PMC: 7082726. DOI: 10.3389/fcvm.2020.00029. View

Wang Y, Ahmad A, Shah P, Sims C, Magness S, Allbritton N . Capture and 3D culture of colonic crypts and colonoids in a microarray platform. Lab Chip. 2013; 13(23):4625-34. PMC: 3841105. DOI: 10.1039/c3lc50813g. View

Wang Z, Keogh A, Waldt A, Cuttat R, Neri M, Zhu S . Single-cell and bulk transcriptomics of the liver reveals potential targets of NASH with fibrosis. Sci Rep. 2021; 11(1):19396. PMC: 8481490. DOI: 10.1038/s41598-021-98806-y. View

Elmore S . Enhanced histopathology of the spleen. Toxicol Pathol. 2006; 34(5):648-55. PMC: 1828535. DOI: 10.1080/01926230600865523. View

10.

Jain Y, Godwin L, Ju Y, Sood N, Quardokus E, Bueckle A . Segmentation of human functional tissue units in support of a Human Reference Atlas. Commun Biol. 2023; 6(1):717. PMC: 10356924. DOI: 10.1038/s42003-023-04848-5. View

11.

Moreno P, Fexova S, George N, Manning J, Miao Z, Mohammed S . Expression Atlas update: gene and protein expression in multiple species. Nucleic Acids Res. 2021; 50(D1):D129-D140. PMC: 8728300. DOI: 10.1093/nar/gkab1030. View

12.

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

13.

Himmerkus N, Svendsen S, Quintanova C, Bleich M, von Schwerdtner O, Benzing T . Viewing Cortical Collecting Duct Function Through Phenotype-guided Single-Tubule Proteomics. Function (Oxf). 2022; 1(1):zqaa007. PMC: 8788781. DOI: 10.1093/function/zqaa007. View

14.

Morgan R, Schaeffer B, Longnecker D . Size and number of nuclei differ in normal and neoplastic acinar cells from rat pancreas. Pancreas. 1986; 1(1):37-43. DOI: 10.1097/00006676-198601000-00008. View

15.

Fullwood N, Lawlor A, Martin-Hirsch P, Matanhelia S, Martin F . An analysis of benign human prostate offers insights into the mechanism of apocrine secretion and the origin of prostasomes. Sci Rep. 2019; 9(1):4582. PMC: 6418221. DOI: 10.1038/s41598-019-40820-2. View

16.

Vieira Braga F, Kar G, Berg M, Carpaij O, Polanski K, Simon L . A cellular census of human lungs identifies novel cell states in health and in asthma. Nat Med. 2019; 25(7):1153-1163. DOI: 10.1038/s41591-019-0468-5. View

17.

Lundstrom R, Dahlqvist H, Hagberg M, Nilsson T . Vibrotactile and thermal perception and its relation to finger skin thickness. Clin Neurophysiol Pract. 2018; 3:33-39. PMC: 6133778. DOI: 10.1016/j.cnp.2018.01.001. View

18.

da Silva Xavier G . The Cells of the Islets of Langerhans. J Clin Med. 2018; 7(3). PMC: 5867580. DOI: 10.3390/jcm7030054. View

19.

Jain Y, Godwin L, Joshi S, Mandarapu S, Le T, Lindskog C . Segmenting functional tissue units across human organs using community-driven development of generalizable machine learning algorithms. Nat Commun. 2023; 14(1):4656. PMC: 10400613. DOI: 10.1038/s41467-023-40291-0. View

20.

Hickey J, Becker W, Nevins S, Horning A, Perez A, Zhu C . Organization of the human intestine at single-cell resolution. Nature. 2023; 619(7970):572-584. PMC: 10356619. DOI: 10.1038/s41586-023-05915-x. View