Reconstruction of complex single-cell trajectories using CellRouter

Edroaldo Lummertz da Rocha, R. Grant Rowe, Vanessa Lundin, Mohan Malleshaiah, Deepak Kumar Jha, Carlos R. Rambo, Hu Li, Trista E. North, James J. Collins () and George Q. Daley ()
Additional contact information
Edroaldo Lummertz da Rocha: Boston Children’s Hospital and Dana-Farber Cancer Institute
R. Grant Rowe: Boston Children’s Hospital and Dana-Farber Cancer Institute
Vanessa Lundin: Boston Children’s Hospital and Dana-Farber Cancer Institute
Mohan Malleshaiah: Harvard Medical School
Deepak Kumar Jha: Boston Children’s Hospital and Dana-Farber Cancer Institute
Carlos R. Rambo: Federal University of Santa Catarina
Hu Li: Mayo Clinic
Trista E. North: Boston Children’s Hospital and Dana-Farber Cancer Institute
James J. Collins: Broad Institute of MIT and Harvard
George Q. Daley: Boston Children’s Hospital and Dana-Farber Cancer Institute

Nature Communications, 2018, vol. 9, issue 1, 1-13

Abstract: 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.

Date: 2018
References: Add references at CitEc
Citations: View citations in EconPapers (3)

Downloads: (external link)
https://www.nature.com/articles/s41467-018-03214-y Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-03214-y

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-018-03214-y

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().