Reconstruction of complex single-cell trajectories using CellRouter
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s41467-018-03214-y.pdf
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3.6 MB
Format
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Checksum (MD5)
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Author(s)
Lummertz da Rocha, Edroaldo
Rowe, R. Grant
Lundin, Vanessa
Malleshaiah, Mohan
Jha, Deepak Kumar
Rambo, Carlos R.
Li, Hu
North, Trista E.
Collins, James J.
Daley, George Q.
Date Issued
March 2018
Journal
Nature Communications
Publisher
Nature Publishing Group
Citation
Lummertz da Rocha, Edroaldo, et al. “Reconstruction of Complex Single-Cell Trajectories Using CellRouter.” Nature Communications 9, 1 (March 2018): 892 © 2018 The Author(s)
Version
Final published version
Abstract
A better understanding of the cell-fate transitions that occur in complex cellular ecosystems in normal development and disease could inform cell engineering efforts and lead to improved therapies. However, a major challenge is to simultaneously identify new cell states, and their transitions, to elucidate the gene expression dynamics governing cell-type diversification. Here, we present CellRouter, a multifaceted single-cell analysis platform that identifies complex cell-state transition trajectories by using flow networks to explore the subpopulation structure of multi-dimensional, single-cell omics data. We demonstrate its versatility by applying CellRouter to single-cell RNA sequencing data sets to reconstruct cell-state transition trajectories during hematopoietic stem and progenitor cell (HSPC) differentiation to the erythroid, myeloid and lymphoid lineages, as well as during re-specification of cell identity by cellular reprogramming of monocytes and B-cells to HSPCs. CellRouter opens previously undescribed paths for in-depth characterization of complex cellular ecosystems and establishment of enhanced cell engineering approaches.
MIT Department
Massachusetts Institute of Technology. Institute for Medical Engineering & Science
Massachusetts Institute of Technology. Department of Biological Engineering
Massachusetts Institute of Technology. Synthetic Biology Center
Terms of Use
Creative Commons Attribution 4.0 International License
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DOI of Published Version
https://doi.org/10.1038/S41467-018-03214-Y
