Deciphering cell-cell interactions and communication from gene expression.
Journal
Nature reviews. Genetics
ISSN: 1471-0064
Titre abrégé: Nat Rev Genet
Pays: England
ID NLM: 100962779
Informations de publication
Date de publication:
02 2021
02 2021
Historique:
accepted:
25
09
2020
pubmed:
11
11
2020
medline:
16
3
2021
entrez:
10
11
2020
Statut:
ppublish
Résumé
Cell-cell interactions orchestrate organismal development, homeostasis and single-cell functions. When cells do not properly interact or improperly decode molecular messages, disease ensues. Thus, the identification and quantification of intercellular signalling pathways has become a common analysis performed across diverse disciplines. The expansion of protein-protein interaction databases and recent advances in RNA sequencing technologies have enabled routine analyses of intercellular signalling from gene expression measurements of bulk and single-cell data sets. In particular, ligand-receptor pairs can be used to infer intercellular communication from the coordinated expression of their cognate genes. In this Review, we highlight discoveries enabled by analyses of cell-cell interactions from transcriptomic data and review the methods and tools used in this context.
Identifiants
pubmed: 33168968
doi: 10.1038/s41576-020-00292-x
pii: 10.1038/s41576-020-00292-x
pmc: PMC7649713
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
71-88Subventions
Organisme : NIGMS NIH HHS
ID : R35 GM119850
Pays : United States
Organisme : NLM NIH HHS
ID : T15 LM011271
Pays : United States
Organisme : NCI NIH HHS
ID : U01 CA196406
Pays : United States
Références
Immunity. 2019 Oct 15;51(4):638-654.e9
pubmed: 31561945
Oncoimmunology. 2012 Nov 1;1(8):1223-1225
pubmed: 23243584
Nucleic Acids Res. 2019 Jan 8;47(D1):D759-D765
pubmed: 30364959
Proc Natl Acad Sci U S A. 1997 Jul 22;94(15):8099-103
pubmed: 9223321
Nature. 2019 Oct;574(7778):365-371
pubmed: 31597962
Nat Rev Genet. 2020 Oct;21(10):630-644
pubmed: 32709985
Cell Rep Methods. 2021 Jul 26;1(3):
pubmed: 34761247
Nat Commun. 2015 Jul 22;6:7866
pubmed: 26198319
Cell. 2019 Oct 3;179(2):432-447.e21
pubmed: 31585082
Cell. 2018 Dec 13;175(7):1931-1945.e18
pubmed: 30550790
Elife. 2020 Feb 24;9:
pubmed: 32091393
Science. 2015 Jan 23;347(6220):1260419
pubmed: 25613900
Science. 2016 Jul 1;353(6294):78-82
pubmed: 27365449
Nat Rev Mol Cell Biol. 2019 May;20(5):285-302
pubmed: 30659282
Cell Host Microbe. 2015 Jul 8;18(1):109-21
pubmed: 26118995
Science. 2019 Mar 29;363(6434):1463-1467
pubmed: 30923225
Perspect Clin Res. 2016 Oct-Dec;7(4):187-190
pubmed: 27843795
Nature. 2018 Nov;563(7731):347-353
pubmed: 30429548
Nature. 2017 Nov 23;551(7681):457-463
pubmed: 29088705
Mol Syst Biol. 2014 Jul 15;10:741
pubmed: 25028490
PLoS Comput Biol. 2019 Jul 19;15(7):e1007185
pubmed: 31323017
Nature. 2011 Dec 21;481(7381):365-70
pubmed: 22190034
Cell Res. 2020 Sep;30(9):763-778
pubmed: 32541867
Nature. 2015 Sep 10;525(7568):251-5
pubmed: 26287467
ACS Infect Dis. 2019 Mar 8;5(3):336-344
pubmed: 30702856
Curr Opin Cell Biol. 2011 Aug;23(4):383-92
pubmed: 21616652
Cell Rep. 2019 Feb 12;26(7):1951-1964.e8
pubmed: 30759402
Nat Med. 2019 Jul;25(7):1153-1163
pubmed: 31209336
Nat Biotechnol. 2020 May;38(5):629-637
pubmed: 32152598
Bioinformatics. 2021 May 17;37(7):968-975
pubmed: 32886099
J Hepatol. 2020 Nov;73(5):1118-1130
pubmed: 32505533
Nat Methods. 2020 Feb;17(2):159-162
pubmed: 31819264
Bioinformatics. 2019 Apr 1;35(7):1098-1107
pubmed: 30169744
Nat Commun. 2018 Sep 25;9(1):3894
pubmed: 30254269
Bioinformatics. 2017 Aug 15;33(16):2591-2593
pubmed: 28398467
Commun Biol. 2020 Apr 23;3(1):188
pubmed: 32327715
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W193-200
pubmed: 17478515
Nucleic Acids Res. 2013 Jan;41(Database issue):D358-65
pubmed: 23180791
Nat Rev Genet. 2019 Dec;20(12):724-746
pubmed: 31515541
Cell Rep. 2015 Feb 24;10(7):1187-201
pubmed: 25704820
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D452-5
pubmed: 14681455
Trends Microbiol. 2016 Jun;24(6):425-427
pubmed: 27197692
Cold Spring Harb Perspect Biol. 2012 Jun 01;4(6):
pubmed: 22570373
Nature. 2017 Jun 22;546(7659):533-538
pubmed: 28614297
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D535-9
pubmed: 16381927
PLoS Biol. 2019 Jul 3;17(7):e3000365
pubmed: 31269016
Sci Rep. 2017 Aug 18;7(1):8815
pubmed: 28821810
Cell Rep. 2018 Oct 16;25(3):585-597.e7
pubmed: 30332640
Cell. 2019 Oct 31;179(4):829-845.e20
pubmed: 31675496
Nat Immunol. 2017 May;18(5):583-593
pubmed: 28263321
Cell. 2018 Nov 1;175(4):1031-1044.e18
pubmed: 30318149
Nat Commun. 2020 Aug 20;11(1):4033
pubmed: 32820167
Bioinformatics. 2012 Mar 1;28(5):694-700
pubmed: 22210865
mSystems. 2018 May 15;3(3):
pubmed: 29795809
Protein Cell. 2020 Dec;11(12):866-880
pubmed: 32435978
iScience. 2019 Nov 22;21:273-287
pubmed: 31677479
Nat Genet. 2000 May;25(1):25-9
pubmed: 10802651
Nat Methods. 2020 May;17(5):505-508
pubmed: 32371966
Cell Rep. 2019 Oct 1;29(1):202-211.e6
pubmed: 31577949
Bioinformatics. 2014 Feb 15;30(4):523-30
pubmed: 24336805
Nature. 2020 Jul;583(7815):296-302
pubmed: 32612232
Cell Syst. 2018 May 23;6(5):579-592.e4
pubmed: 29778837
Nat Rev Urol. 2020 Mar;17(3):137-150
pubmed: 32020040
Int J Proteomics. 2014;2014:147648
pubmed: 24693427
Nat Rev Mol Cell Biol. 2019 Nov;20(11):681-697
pubmed: 31417196
Nat Rev Mol Cell Biol. 2014 Dec;15(12):786-801
pubmed: 25415508
Nat Methods. 2018 Jul;15(7):547-553
pubmed: 29786092
Nat Neurosci. 2019 Oct;22(10):1696-1708
pubmed: 31551601
Front Physiol. 2019 Sep 18;10:1170
pubmed: 31620013
Nucleic Acids Res. 2010 Jan;38(Database issue):D463-7
pubmed: 19910365
Front Microbiol. 2015 Feb 24;6:94
pubmed: 25759684
Cell Rep. 2020 Apr 28;31(4):107574
pubmed: 32348757
Front Microbiol. 2015 Feb 06;6:65
pubmed: 25705211
Cell. 2019 Feb 7;176(4):928-943.e22
pubmed: 30712874
Nucleic Acids Res. 2014 Jan;42(Database issue):D1098-106
pubmed: 24234439
Biophys J. 2012 Feb 8;102(3):417-26
pubmed: 22325263
Nat Med. 2019 Oct;25(10):1576-1588
pubmed: 31591603
Front Microbiol. 2015 Apr 09;6:235
pubmed: 25914674
Nature. 2019 Feb;566(7745):553-557
pubmed: 30728496
Cell Syst. 2016 Sep 28;3(3):221-237.e9
pubmed: 27641957
Front Genet. 2019 Dec 23;10:1280
pubmed: 31921315
Nat Commun. 2021 Feb 17;12(1):1088
pubmed: 33597522
Neuron. 2016 Sep 7;91(5):988-1004
pubmed: 27545711
Cell. 2016 Apr 21;165(3):535-50
pubmed: 27104977
Am J Hypertens. 2001 Jun;14(6 Pt 2):44S-54S
pubmed: 11411765
Sci Adv. 2018 Oct 31;4(10):eaau4788
pubmed: 30402542
J Gen Physiol. 2017 Jan;149(1):121-147
pubmed: 27993951
Nucleic Acids Res. 2011 Jan;39(Database issue):D685-90
pubmed: 21071392
Cell Rep. 2018 Jan 16;22(3):600-610
pubmed: 29346760
Nat Biotechnol. 2018 Nov;36(10):962-970
pubmed: 30222169
Trends Microbiol. 2016 Nov;24(11):853-861
pubmed: 27374775
J Chem Inf Model. 2013 Apr 22;53(4):763-72
pubmed: 23480697
BMC Bioinformatics. 2019 Jan 18;20(1):40
pubmed: 30658573
Nat Methods. 2018 Oct;15(10):796-798
pubmed: 30275573
Nat Rev Genet. 2013 Apr;14(4):249-61
pubmed: 23458856
Nat Neurosci. 2018 Jan;21(1):120-129
pubmed: 29230054
Biochem Biophys Res Commun. 2020 May 21;526(1):135-140
pubmed: 32199615
Nat Commun. 2018 May 15;9(1):1911
pubmed: 29765029
Cancer Med. 2019 Jun;8(6):3072-3085
pubmed: 31033233
Am J Pathol. 1999 Jan;154(1):61-6
pubmed: 9916919
Genome Res. 2017 Mar;27(3):349-361
pubmed: 28174237
Science. 2020 Feb 21;367(6480):
pubmed: 32079746
Cell. 2017 Sep 7;170(6):1134-1148.e10
pubmed: 28886382
Sci Rep. 2018 Sep 14;8(1):13866
pubmed: 30217992
PLoS One. 2017 Dec 21;12(12):e0190152
pubmed: 29267363
Nat Biotechnol. 2018 Aug;36(7):651-659
pubmed: 29912209
Biotechnol Adv. 2019 Dec;37(8):107447
pubmed: 31513841
Cell. 2020 Aug 20;182(4):872-885.e19
pubmed: 32783915
Nat Methods. 2019 Sep;16(9):809-812
pubmed: 31406385
Nucleic Acids Res. 2019 Jan 8;47(D1):D607-D613
pubmed: 30476243
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W298-302
pubmed: 16845013
Mol Cell Proteomics. 2016 Oct;15(10):3190-3202
pubmed: 27562671
Proc Natl Acad Sci U S A. 1997 Nov 11;94(23):12258-62
pubmed: 9356436
Nat Biotechnol. 2020 Mar;38(3):333-342
pubmed: 31932730
Sci Adv. 2019 Dec 04;5(12):eaaw3851
pubmed: 31840053
J Natl Cancer Inst. 2019 Mar 1;111(3):272-282
pubmed: 29860390
Curr Opin Cell Biol. 1994 Apr;6(2):174-9
pubmed: 8024807
Immunity. 2020 Jan 14;52(1):183-199.e9
pubmed: 31924475
Nat Methods. 2008 Jul;5(7):621-8
pubmed: 18516045
Science. 2019 Sep 27;365(6460):1461-1466
pubmed: 31604275
PLoS One. 2017 Oct 12;12(10):e0186039
pubmed: 29023571
Protein Cell. 2020 Apr;11(4):299-303
pubmed: 32002793
Nat Cell Biol. 2020 Jan;22(1):108-119
pubmed: 31915373
Diabetes. 2006 Oct;55(10):2713-22
pubmed: 17003335
Nat Genet. 2001 Nov;29(3):295-300
pubmed: 11685206
Nat Commun. 2020 Aug 25;11(1):4239
pubmed: 32843640
Cell Rep. 2019 Apr 30;27(5):1567-1578.e5
pubmed: 31042481
Development. 2019 Jun 14;146(12):
pubmed: 31142541
Cell. 2018 Feb 8;172(4):744-757.e17
pubmed: 29398113
Cell. 2018 Feb 22;172(5):1091-1107.e17
pubmed: 29474909
Nucleic Acids Res. 2015 Jan;43(Database issue):D204-12
pubmed: 25348405
Nucleic Acids Res. 2011 Jan;39(Database issue):D736-43
pubmed: 21036869
Cell. 2017 Dec 14;171(7):1611-1624.e24
pubmed: 29198524
Nat Rev Genet. 2020 Jul;21(7):410-427
pubmed: 32235876
NAR Genom Bioinform. 2019 Oct 30;2(1):lqz010
pubmed: 33575562
Cell. 1992 Dec 11;71(6):1003-14
pubmed: 1333888
Cell Commun Signal. 2019 May 22;17(1):48
pubmed: 31118022
Nat Biotechnol. 2020 Aug;38(8):970-979
pubmed: 32591762
Genome Biol. 2015 Jun 19;16:128
pubmed: 26087699
J Am Soc Nephrol. 2019 Jan;30(1):23-32
pubmed: 30510133
Mol Cell. 2019 Aug 8;75(3):644-660.e5
pubmed: 31398325
Cell. 2019 Sep 5;178(6):1493-1508.e20
pubmed: 31474370
Dis Model Mech. 2020 Jun 26;13(6):
pubmed: 32461220
Genome Biol. 2016 Jan 26;17:13
pubmed: 26813401
Mol Ther Methods Clin Dev. 2018 Aug 02;10:189-196
pubmed: 30094294
Annu Rev Immunol. 2000;18:143-64
pubmed: 10837055
Mol Syst Biol. 2013 Dec 22;9:714
pubmed: 24366814
Cell. 2018 Dec 13;175(7):1917-1930.e13
pubmed: 30550789
Nat Microbiol. 2019 Dec;4(12):2184-2191
pubmed: 31591554
Nucleic Acids Res. 2007 Jan;35(Database issue):D472-5
pubmed: 17099225
J Am Soc Nephrol. 2018 Aug;29(8):2069-2080
pubmed: 29980650
Nucleic Acids Res. 2000 Jan 1;28(1):27-30
pubmed: 10592173
Front Genet. 2019 Mar 01;10:8
pubmed: 30881372
Genome Biol. 2020 Feb 7;21(1):31
pubmed: 32033589
Circ Res. 2018 Aug 3;123(4):443-450
pubmed: 29986945
Nucleic Acids Res. 2019 Jun 20;47(11):e66
pubmed: 30923815
Nat Commun. 2020 Apr 29;11(1):2084
pubmed: 32350282
Mol Syst Biol. 2019 Jun 19;15(6):e8746
pubmed: 31217225
Nat Protoc. 2020 Apr;15(4):1484-1506
pubmed: 32103204
Nature. 2020 Jul;583(7816):459-468
pubmed: 32353859
Nat Methods. 2017 Sep;14(9):873-876
pubmed: 28783155
Nat Methods. 2019 Oct;16(10):987-990
pubmed: 31501547
Nat Methods. 2009 May;6(5):377-82
pubmed: 19349980
Hum Vaccin Immunother. 2020 Oct 2;16(10):2374-2388
pubmed: 32186959
Nucleic Acids Res. 2020 Jun 4;48(10):e55
pubmed: 32196115
Nat Biotechnol. 2015 May;33(5):495-502
pubmed: 25867923
Cell Rep. 2018 Nov 6;25(6):1458-1468.e4
pubmed: 30404002
Mol Syst Biol. 2010 Oct 5;6:417
pubmed: 20924352
Nat Cell Biol. 2020 Jan;22(1):38-48
pubmed: 31871321