iMAC: An interactive atlas to explore phenotypic differences between in vivo, ex vivo and in vitro-derived myeloid cells in the Stemformatics platform

Understanding the myriad of myeloid subsets and identifying specific and discrete phenotypes is challenging in a human setting. Laboratory models of human myeloid biology lack tissue context, but the differences between common models and in vivo phenotypes have not been systematically evaluated. Her...

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Published inbioRxiv
Main Authors Rajab, Nadia, Angel, Paul, Deng, Yidi, Gu, Jennifer, Jameson, Vanta, Kurowska-Stolarska, Mariola, Milling, Simon, Pacheco, Chris, Chris Pacheco Rivera, Rutar, Matt, Laslett, Andrew L, Kim-Anh Le Cao, Choi, Jarny, Wells, Christine A
Format Paper
LanguageEnglish
Published Cold Spring Harbor Cold Spring Harbor Laboratory Press 28.05.2020
Subjects
Biology
Cell culture
Dendritic cells
Gene expression
Homeostasis
Laboratories
Macrophages
Myeloid cells
Pluripotency
Stem cells
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Summary:Understanding the myriad of myeloid subsets and identifying specific and discrete phenotypes is challenging in a human setting. Laboratory models of human myeloid biology lack tissue context, but the differences between common models and in vivo phenotypes have not been systematically evaluated. Here, we assemble a large transcriptional atlas of human myeloid biology representing ~1000 samples, comparing freshly isolated, cultured, and stem-cell derived myeloid cell types. Common myeloid models including pluripotent stem cell-derived macrophages fail to recapitulate developmental or tissue contexts. A shared feature of pluripotent stem cell-derived macrophages is the atypical expression of collagen, in addition to being highly efferocytotic. The resulting iMAC atlas is available at the Stemformatics.org platform, where users can review gene expression as well as upload and benchmark their own samples for comparison against a library of human tissue-resident and laboratory models of macrophage or dendritic cell biology. Competing Interest Statement The authors have declared no competing interest. Footnotes * Use of the atlas as a classification tool for single cell data in Fig 1, Supp Fig 1. Addition of functional validation of the collagen profile in Fig 4. * https://www.stemformatics.org/atlas/imac * https://bitbucket.org/stemformatics/s4m_pyramid/src/master/scripts/atlas.py * https://bitbucket.org/stemformatics
DOI:10.1101/719237