Exploration of Cell Development Pathways through High-Dimensional Single Cell Analysis in Trajectory Space.
Developmental Biology
In Silico Biology
Systems Biology
Journal
iScience
ISSN: 2589-0042
Titre abrégé: iScience
Pays: United States
ID NLM: 101724038
Informations de publication
Date de publication:
21 Feb 2020
21 Feb 2020
Historique:
received:
10
07
2019
revised:
17
12
2019
accepted:
10
01
2020
pubmed:
15
2
2020
medline:
15
2
2020
entrez:
15
2
2020
Statut:
ppublish
Résumé
High-dimensional single cell profiling coupled with computational modeling is emerging as a powerful tool to elucidate developmental programs directing cell lineages. We introduce tSpace, an algorithm based on the concept of "trajectory space", in which cells are defined by their distance along nearest neighbor pathways to every other cell in a population. Graphical mapping of cells in trajectory space allows unsupervised reconstruction and exploration of complex developmental sequences. Applied to flow and mass cytometry data, the method faithfully reconstructs thymic T cell development and reveals development and trafficking regulation of tonsillar B cells. Applied to the single cell transcriptome of mouse intestine and C. elegans, the method recapitulates development from intestinal stem cells to specialized epithelial phenotypes more faithfully than existing algorithms and orders C. elegans cells concordantly to the associated embryonic time. tSpace profiling of complex populations is well suited for hypothesis generation in developing cell systems.
Identifiants
pubmed: 32058956
pii: S2589-0042(20)30025-0
doi: 10.1016/j.isci.2020.100842
pmc: PMC6997593
pii:
doi:
Types de publication
Journal Article
Langues
eng
Pagination
100842Subventions
Organisme : NIAID NIH HHS
ID : R37 AI047822
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA228019
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI109452
Pays : United States
Organisme : NIH HHS
ID : S10 OD016318
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI130471
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI047822
Pays : United States
Organisme : BLRD VA
ID : I01 BX002919
Pays : United States
Organisme : NCI NIH HHS
ID : U54 CA209971
Pays : United States
Informations de copyright
Copyright © 2020 The Author(s). Published by Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of Interests The authors have declared no conflict of interest.
Références
Cell. 2009 Mar 6;136(5):903-12
pubmed: 19269367
Biochem Biophys Res Commun. 1997 Jul 18;236(2):313-22
pubmed: 9240432
Gastroenterology. 2009 Jul;137(1):15-7
pubmed: 19450592
Nature. 2009 Jan 29;457(7229):603-7
pubmed: 19092805
Nature. 1982 Jul 22;298(5872):377-9
pubmed: 6806671
Nat Rev Immunol. 2015 Mar;15(3):137-48
pubmed: 25656706
J Lipid Res. 2015 Jul;56(7):1262-70
pubmed: 25070952
EMBO J. 2002 Dec 2;21(23):6338-47
pubmed: 12456641
Cell Mol Life Sci. 2012 Sep;69(17):2907-17
pubmed: 22527717
Cell Stem Cell. 2016 Feb 4;18(2):203-13
pubmed: 26831517
Science. 2019 Sep 20;365(6459):
pubmed: 31488706
Cell Syst. 2018 Jan 24;6(1):37-51.e9
pubmed: 29153838
Int Immunol. 2009 Dec;21(12):1317-27
pubmed: 19819936
J Immunol. 2014 May 1;192(9):4017-23
pubmed: 24748636
BMC Genomics. 2018 Jun 19;19(1):477
pubmed: 29914354
J Immunol. 2014 Dec 1;193(11):5370-8
pubmed: 25411432
Gastroenterology. 2018 Nov;155(5):1508-1523.e10
pubmed: 30055169
Cell Stem Cell. 2012 Oct 5;11(4):452-60
pubmed: 23040474
Cell. 2014 Apr 24;157(3):714-25
pubmed: 24766814
Science. 2000 Dec 22;290(5500):2319-23
pubmed: 11125149
Nat Cell Biol. 2012 Oct;14(10):1099-1104
pubmed: 23000963
Proteins. 2010 Feb 1;78(2):223-35
pubmed: 19731366
Eur J Immunol. 2006 Jan;36(1):73-81
pubmed: 16342233
EMBO Rep. 2011 Jun;12(6):558-64
pubmed: 21508962
Cell. 2013 Jul 18;154(2):274-84
pubmed: 23870119
Cell Stem Cell. 2017 Jul 6;21(1):78-90.e6
pubmed: 28686870
JCI Insight. 2017 Mar 23;2(6):e90233
pubmed: 28352656
Nat Immunol. 2014 Oct;15(10):982-95
pubmed: 25173345
Nat Biotechnol. 2011 Oct 02;29(10):886-91
pubmed: 21964415
Dev Biol. 2004 Jun 15;270(2):443-54
pubmed: 15183725
J Immunol. 1996 May 15;156(10):3727-36
pubmed: 8621908
Curr Opin Immunol. 2017 Apr;45:112-118
pubmed: 28319730
Cell Mol Gastroenterol Hepatol. 2018 Jan 12;5(4):499-522
pubmed: 29930976
Nat Cell Biol. 2011 Nov 27;14(1):106-14
pubmed: 22119784
J Lipid Res. 2015 Mar;56(3):489-501
pubmed: 25231105
Eur J Immunol. 2016 Nov;46(11):2496-2506
pubmed: 27682842
J Exp Med. 1983 Mar 1;157(3):813-27
pubmed: 6339668
Nature. 2018 Oct;562(7727):367-372
pubmed: 30283141