Tools and Concepts for Interrogating and Defining Cellular Identity.
cell competition
cell type
microscopy
organoid
plasticity
scRNA-seq
smFISH
stem cell
Journal
Cell stem cell
ISSN: 1875-9777
Titre abrégé: Cell Stem Cell
Pays: United States
ID NLM: 101311472
Informations de publication
Date de publication:
07 05 2020
07 05 2020
Historique:
entrez:
11
5
2020
pubmed:
11
5
2020
medline:
28
4
2021
Statut:
ppublish
Résumé
Defining the mechanisms that generate specialized cell types and coordinate their functions is critical for understanding organ development and renewal. New tools and discoveries are challenging and refining our definitions of a cell type. A rapidly growing toolkit for single-cell analyses has expanded the number of markers that can be assigned to a cell simultaneously, revealing heterogeneity within cell types that were previously regarded as homogeneous populations. Additionally, cell types defined by specific molecular markers can exhibit distinct, context-dependent functions; for example, between tissues in homeostasis and those responding to damage. Here we review the current technologies used to identify and characterize cells, and we discuss how experimental and pathological perturbations are adding increasing complexity to our definitions of cell identity.
Identifiants
pubmed: 32386555
pii: S1934-5909(20)30137-5
doi: 10.1016/j.stem.2020.03.015
pmc: PMC7250495
mid: NIHMS1581440
pii:
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
632-656Subventions
Organisme : NICHD NIH HHS
ID : K99 HD101021
Pays : United States
Organisme : NIDCR NIH HHS
ID : R35 DE026602
Pays : United States
Informations de copyright
Copyright © 2020 Elsevier Inc. All rights reserved.
Références
Cell. 2018 Oct 18;175(3):859-876.e33
pubmed: 30318151
Neuron. 2000 Oct;28(1):69-80
pubmed: 11086984
Nat Genet. 2019 Jun;51(6):1060-1066
pubmed: 31152164
Nat Methods. 2008 Dec;5(12):1019-21
pubmed: 18997781
Development. 1998 Aug;125(16):3143-52
pubmed: 9671587
Dev Biol. 1981 Oct 30;87(2):286-300
pubmed: 7286433
Dev Biol. 1980 Aug;78(2):577-97
pubmed: 7190941
Nat Rev Mol Cell Biol. 2019 Dec;20(12):753-765
pubmed: 31690888
Cell. 2019 Aug 8;178(4):901-918.e16
pubmed: 31398343
Nature. 2007 Nov 1;450(7166):56-62
pubmed: 17972876
Nat Med. 2001 Jul;7(7):864-8
pubmed: 11433354
Elife. 2018 Jun 13;7:
pubmed: 29897330
Nat Biotechnol. 2020 Jan;38(1):66-75
pubmed: 31740838
Science. 2015 Apr 24;348(6233):aaa6090
pubmed: 25858977
Adv Biochem Eng Biotechnol. 2005;95:245-65
pubmed: 16080271
Nat Metab. 2019 Feb;1(2):177-188
pubmed: 31245788
Elife. 2017 Jul 14;6:
pubmed: 28708059
Cell Stem Cell. 2017 Jan 5;20(1):120-134
pubmed: 28094016
Science. 2017 Dec 22;358(6370):1622-1626
pubmed: 29217582
Nat Commun. 2015 Sep 24;6:8390
pubmed: 26399630
Nat Methods. 2020 Jan;17(1):11-14
pubmed: 31907462
Intravital. 2016 Jan 13;5(1):e1125562
pubmed: 28243517
Nat Biotechnol. 2020 May;38(5):629-637
pubmed: 32152598
Cell. 2012 Jan 20;148(1-2):33-45
pubmed: 22265400
Nature. 2005 Jun 16;435(7044):969-73
pubmed: 15959517
Cell Syst. 2017 Mar 22;4(3):255-259
pubmed: 28334573
J Cell Biol. 2018 Jan 2;217(1):79-92
pubmed: 29070608
Nature. 2013 Aug 1;500(7460):39-44
pubmed: 23842495
Cell. 2019 Oct 3;179(2):355-372.e23
pubmed: 31564455
Cell. 2010 Oct 1;143(1):134-44
pubmed: 20887898
Nature. 2019 Jun;570(7759):77-82
pubmed: 31086336
Nat Cell Biol. 2012 Oct;14(10):1099-1104
pubmed: 23000963
Nat Methods. 2014 Apr;11(4):417-22
pubmed: 24584193
Nat Methods. 2017 Sep;14(9):865-868
pubmed: 28759029
Nature. 2012 Jul 26;487(7408):496-9
pubmed: 22763436
Nat Immunol. 2001 Jan;2(1):75-82
pubmed: 11135582
Nat Methods. 2014 Sep;11(9):951-8
pubmed: 25042785
Science. 2018 Apr 13;360(6385):176-182
pubmed: 29545511
Science. 2013 Mar 22;339(6126):1445-8
pubmed: 23520113
Cell. 2018 Nov 1;175(4):1156-1167.e15
pubmed: 30270040
Cell Stem Cell. 2019 Nov 7;25(5):713-727.e10
pubmed: 31631012
Nat Biotechnol. 2020 Jan;38(1):35-38
pubmed: 31873215
Nat Genet. 2019 Jan;51(1):19-25
pubmed: 30559489
Nat Commun. 2018 Dec 17;9(1):5345
pubmed: 30559361
Nature. 2014 Oct 16;514(7522):322-7
pubmed: 25296256
Science. 2009 Jul 10;325(5937):217-8
pubmed: 19590005
Nature. 2014 Mar 20;507(7492):362-365
pubmed: 24531760
Nature. 2017 Aug 17;548(7667):334-337
pubmed: 28783732
Nature. 2019 Jul;571(7765):419-423
pubmed: 31292545
Cell. 2018 Aug 9;174(4):968-981.e15
pubmed: 30078711
Proc Natl Acad Sci U S A. 1996 Mar 19;93(6):2414-9
pubmed: 8637888
Nature. 2017 Mar 29;543(7647):676-680
pubmed: 28358093
Methods. 2018 Jan 15;133:81-90
pubmed: 29050826
Nat Biotechnol. 2011 Oct 02;29(10):928-33
pubmed: 21964413
Stem Cell Reports. 2015 Oct 13;5(4):609-20
pubmed: 26344906
Sci Rep. 2013 Nov 15;3:3224
pubmed: 24232854
Proc Natl Acad Sci U S A. 2006 Feb 21;103(8):2707-12
pubmed: 16477039
Cell Stem Cell. 2010 Apr 2;6(4):309-22
pubmed: 20362536
Science. 2016 Jun 24;352(6293):1586-90
pubmed: 27339989
Dev Cell. 2016 Nov 21;39(4):411-423
pubmed: 27840105
Proc Natl Acad Sci U S A. 2013 Dec 3;110(49):19802-7
pubmed: 24248345
Cold Spring Harb Protoc. 2011 Feb 01;2011(2):pdb.prot5562
pubmed: 21285262
Nat Methods. 2019 Jun;16(6):533-544
pubmed: 31110282
Cell. 2018 May 31;173(6):1535-1548.e16
pubmed: 29706549
EMBO J. 2019 Feb 15;38(4):
pubmed: 30635334
Science. 2013 Aug 23;341(6148):1233151
pubmed: 23845947
Nat Biotechnol. 2016 Aug;34(8):852-6
pubmed: 27347753
Neuron. 2017 Oct 11;96(2):313-329.e6
pubmed: 29024657
Cell Stem Cell. 2014 Mar 6;14(3):292-305
pubmed: 24607404
Nat Biotechnol. 2018 Jun;36(5):469-473
pubmed: 29644996
Nat Methods. 2018 Jul;15(7):547-553
pubmed: 29786092
Nature. 2016 Feb 18;530(7590):344-8
pubmed: 26887495
Cell. 2018 Aug 23;174(5):1309-1324.e18
pubmed: 30078704
Cell. 2018 Nov 29;175(6):1620-1633.e13
pubmed: 30415836
Cell Stem Cell. 2020 Apr 2;26(4):569-578.e7
pubmed: 32169167
Blood. 2018 Mar 15;131(11):1195-1205
pubmed: 29295845
Genome Biol. 2014 May 30;15(5):R75
pubmed: 24886633
J Exp Med. 1998 Aug 3;188(3):465-74
pubmed: 9687524
Genome Biol. 2014;15(10):486
pubmed: 25344199
Nature. 2017 Oct 26;550(7677):475-480
pubmed: 29045388
Nat Biotechnol. 2019 Sep;37(9):1080-1090
pubmed: 31427819
Science. 2016 Aug 26;353(6302):925-8
pubmed: 27471252
Cancer Res. 2011 Jul 1;71(13):4608-16
pubmed: 21712408
Nature. 2017 Feb 16;542(7641):313-317
pubmed: 28135720
Cell. 2019 Jun 13;177(7):1873-1887.e17
pubmed: 31178122
Nat Immunol. 2006 Nov;7(11):1225-33
pubmed: 17013390
Cell Stem Cell. 2008 Dec 4;3(6):670-80
pubmed: 19041783
Proc Natl Acad Sci U S A. 2019 Dec 16;:
pubmed: 31843916
Nat Commun. 2016 Feb 25;7:8674
pubmed: 26912388
Science. 2013 Aug 23;341(6148):1233158
pubmed: 23845948
Nat Biotechnol. 2015 Nov;33(11):1165-72
pubmed: 26458175
G3 (Bethesda). 2013 May 20;3(5):851-63
pubmed: 23550142
J Exp Med. 2008 Sep 29;205(10):2309-18
pubmed: 18809713
Dev Cell. 2017 Sep 25;42(6):585-599.e4
pubmed: 28919206
Science. 2017 Aug 18;357(6352):661-667
pubmed: 28818938
Science. 2018 Jun 1;360(6392):981-987
pubmed: 29700229
Nat Biotechnol. 2018 Nov;36(10):962-970
pubmed: 30222169
EMBO J. 2012 May 30;31(11):2473-85
pubmed: 22522699
J Exp Med. 2013 Aug 26;210(9):1657-64
pubmed: 23940255
Science. 2008 Dec 19;322(5909):1861-5
pubmed: 19095944
J Cell Biol. 2019 Oct 7;218(10):3212-3222
pubmed: 31488583
Nature. 2013 Oct 24;502(7472):513-8
pubmed: 24097351
Development. 2019 Jun 27;146(12):
pubmed: 31249006
Cell. 2020 Jun 11;181(6):1410-1422.e27
pubmed: 32413320
Nature. 2019 May;569(7757):497-502
pubmed: 31092920
Blood. 2002 Oct 15;100(8):2737-43
pubmed: 12351380
Science. 2020 Feb 14;367(6479):
pubmed: 31974159
Curr Opin Biotechnol. 2020 Jun;63:70-78
pubmed: 31918114
Nat Methods. 2019 Jul;16(7):619-626
pubmed: 31209384
Nature. 2018 Apr 5;556(7699):108-112
pubmed: 29590089
Science. 2012 Aug 10;337(6095):730-5
pubmed: 22855427
Development. 2011 Mar;138(6):1057-68
pubmed: 21343361
Intravital. 2014 Aug 11;3(2):e29917
pubmed: 28243510
Development. 2013 Jul;140(13):2835-46
pubmed: 23757414
Curr Opin Immunol. 2020 Feb;62:45-53
pubmed: 31874430
Cell. 2000 Jan 7;100(1):41-55
pubmed: 10647930
Nat Methods. 2017 Dec;14(12):1141-1152
pubmed: 29083403
Nature. 2018 Mar 22;555(7697):538-542
pubmed: 29539636
Proc Natl Acad Sci U S A. 1969 Jun;63(2):378-83
pubmed: 4895535
J Histochem Cytochem. 2009 Jun;57(6):567-75
pubmed: 19223296
Science. 2010 Nov 5;330(6005):822-5
pubmed: 20929733
Cell Stem Cell. 2013 Mar 7;12(3):298-303
pubmed: 23415913
Cell Stem Cell. 2018 Nov 1;23(5):677-686.e4
pubmed: 30269903
Nat Biotechnol. 2018 Jun;36(5):428-431
pubmed: 29644997
Nature. 2018 Dec;564(7735):219-224
pubmed: 30518857
Cell Stem Cell. 2010 Aug 6;7(2):214-24
pubmed: 20682447
Nat Biotechnol. 2018 Jan;36(1):89-94
pubmed: 29227470
J Natl Cancer Inst. 1949 Oct;10(2):225-53, incl 8 pl
pubmed: 15393709
Science. 2020 Mar 6;367(6482):1151-1156
pubmed: 32139547
Genome Biol. 2018 Dec 19;19(1):224
pubmed: 30567574
Proc Natl Acad Sci U S A. 2014 Nov 18;111(46):16401-6
pubmed: 25368147
Nature. 2009 May 7;459(7243):103-7
pubmed: 19322176
Cell. 2019 Jun 13;177(7):1888-1902.e21
pubmed: 31178118
Immunity. 2008 Feb;28(2):271-84
pubmed: 18261937
J Exp Med. 1968 Mar 1;127(3):455-64
pubmed: 5636553
Science. 2016 Jun 17;352(6292):1471-4
pubmed: 27229141
Proc Natl Acad Sci U S A. 2013 Jul 16;110(29):11982-7
pubmed: 23818604
Cell. 2005 May 6;121(3):479-92
pubmed: 15882628
Cell Rep. 2017 Oct 10;21(2):301-307
pubmed: 29020617
Cell. 2014 Jan 16;156(1-2):359-72
pubmed: 24439388
Cell. 2019 Oct 17;179(3):772-786.e19
pubmed: 31626774
Nature. 2020 Feb;578(7794):278-283
pubmed: 32025033
Nat Commun. 2019 Apr 29;10(1):1930
pubmed: 31036827
Nature. 1985 Nov 14-20;318(6042):149-54
pubmed: 3903518
Cell. 1985 Aug;42(1):71-9
pubmed: 4016956
Science. 2009 Jul 31;325(5940):612-6
pubmed: 19644120
Nature. 2018 Jan 11;553(7687):212-216
pubmed: 29323290
Nature. 2019 May;569(7754):66-72
pubmed: 31019299
Nature. 2017 Jun 1;546(7656):162-167
pubmed: 28538724
Nature. 2011 Aug 24;476(7361):409-13
pubmed: 21866153
Proc Natl Acad Sci U S A. 2019 Sep 24;116(39):19490-19499
pubmed: 31501331
Dev Cell. 2013 Jul 15;26(1):19-30
pubmed: 23867226
Nat Commun. 2019 Jul 17;10(1):3138
pubmed: 31316066
Nature. 1956 Mar 10;177(4506):452-4
pubmed: 13309336
Nat Biotechnol. 2018 Jun;36(5):442-450
pubmed: 29608178
Stem Cells. 2015 Nov;33(11):3197-204
pubmed: 26284340
Elife. 2018 Mar 29;7:
pubmed: 29595475
Sci Transl Med. 2012 Oct 31;4(158):158ra145
pubmed: 23115354
Development. 2011 Aug;138(16):3367-76
pubmed: 21752931
Nature. 2018 Oct;562(7726):281-285
pubmed: 30258225
Nature. 2009 Jan 1;457(7225):92-6
pubmed: 19052546
Nature. 2009 Feb 12;457(7231):896-900
pubmed: 19212410
Science. 2017 Aug 11;357(6351):600-604
pubmed: 28798132
Nat Cell Biol. 2020 Jan;22(1):38-48
pubmed: 31871321