Lineage-specific differences and regulatory networks governing human chondrocyte development.
articular cartilage
developmental biology
embryonic stem cells
epigenetics
growth plate cartilage
human
mouse
regenerative medicine
stem cells
transcription factors
Journal
eLife
ISSN: 2050-084X
Titre abrégé: Elife
Pays: England
ID NLM: 101579614
Informations de publication
Date de publication:
15 03 2023
15 03 2023
Historique:
received:
03
05
2022
accepted:
14
03
2023
medline:
4
4
2023
pubmed:
16
3
2023
entrez:
15
3
2023
Statut:
epublish
Résumé
To address large gaps in our understanding of the molecular regulation of articular and growth plate cartilage development in humans, we used our directed differentiation approach to generate these distinct cartilage tissues from human embryonic stem cells. The resulting transcriptomic profiles of hESC-derived articular and growth plate chondrocytes were similar to fetal epiphyseal and growth plate chondrocytes, with respect to genes both known and previously unknown to cartilage biology. With the goal to characterize the regulatory landscapes accompanying these respective transcriptomes, we mapped chromatin accessibility in hESC-derived chondrocyte lineages, and mouse embryonic chondrocytes, using ATAC-sequencing. Integration of the expression dataset with the differentially accessible genomic regions revealed lineage-specific gene regulatory networks. We validated functional interactions of two transcription factors (TFs) (RUNX2 in growth plate chondrocytes and RELA in articular chondrocytes) with their predicted genomic targets. The maps we provide thus represent a framework for probing regulatory interactions governing chondrocyte differentiation. This work constitutes a substantial step towards comprehensive and comparative molecular characterizations of distinct chondrogenic lineages and sheds new light on human cartilage development and biology.
Identifiants
pubmed: 36920035
doi: 10.7554/eLife.79925
pii: 79925
pmc: PMC10069868
doi:
pii:
Substances chimiques
Transcription Factors
0
Banques de données
GEO
['GSE195688', 'GSE122877']
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : NIAMS NIH HHS
ID : R01-AR073821
Pays : United States
Organisme : NIAMS NIH HHS
ID : R01-AR070139
Pays : United States
Informations de copyright
© 2023, Richard, Pregizer et al.
Déclaration de conflit d'intérêts
DR, SP, DV, RR, PM, ZL, TC, AC No competing interests declared
Références
Dev Biol. 2008 Apr 1;316(1):62-73
pubmed: 18295755
Nat Genet. 1999 May;22(1):85-9
pubmed: 10319868
Cell Rep. 2019 Jun 11;27(11):3228-3240.e7
pubmed: 31189107
Cell Tissue Res. 2008 Apr;332(1):111-22
pubmed: 18239943
Proc Natl Acad Sci U S A. 2013 Dec 3;110(49):19914-9
pubmed: 24248346
Cell Calcium. 2016 May;59(5):262-70
pubmed: 26975899
Mol Cancer Res. 2013 Dec;11(12):1481-6
pubmed: 24043668
J Biol Chem. 2001 Sep 7;276(36):33995-4005
pubmed: 11404353
Commun Biol. 2021 Mar 12;4(1):332
pubmed: 33712729
J Biol Chem. 2013 Oct 4;288(40):28620-9
pubmed: 23963448
Clin Pediatr Endocrinol. 2017;26(3):119-125
pubmed: 28804204
Cell. 1997 May 30;89(5):765-71
pubmed: 9182764
Cell. 1997 May 30;89(5):747-54
pubmed: 9182762
Front Cell Dev Biol. 2021 Jan 18;8:628222
pubmed: 33537316
Arthritis Res Ther. 2017 Aug 2;19(1):179
pubmed: 28764769
Bone. 2007 May;40(5):1361-9
pubmed: 17337262
PLoS One. 2010 Apr 09;5(4):e10113
pubmed: 20404928
Osteoarthritis Cartilage. 2009 Aug;17(8):1065-75
pubmed: 19254740
Mol Biol Cell. 2005 Nov;16(11):5316-33
pubmed: 16135533
OMICS. 2012 May;16(5):284-7
pubmed: 22455463
Nat Med. 2010 Jun;16(6):678-86
pubmed: 20495570
Genome Biol. 2014;15(12):550
pubmed: 25516281
J Biol Chem. 2005 May 27;280(21):20509-15
pubmed: 15781473
Genes Dev. 2002 Nov 1;16(21):2813-28
pubmed: 12414734
J Histochem Cytochem. 2002 Mar;50(3):333-40
pubmed: 11850436
Dev Biol. 2009 Aug 15;332(2):383-95
pubmed: 19520072
Dev Biol. 2002 Dec 15;252(2):257-70
pubmed: 12482714
Cell Rep. 2015 Jul 14;12(2):229-43
pubmed: 26146088
Dev Dyn. 1999 Apr;214(4):279-90
pubmed: 10213384
PLoS One. 2010 Jan 13;5(1):e8693
pubmed: 20084171
Proc Natl Acad Sci U S A. 1993 Jul 15;90(14):6859-63
pubmed: 8341710
Sci Rep. 2017 Nov 1;7(1):14833
pubmed: 29093466
Osteoarthritis Cartilage. 2020 Apr;28(4):516-527
pubmed: 31945456
Dev Cell. 2015 Nov 9;35(3):322-32
pubmed: 26555052
Birth Defects Res C Embryo Today. 2014 Mar;102(1):37-51
pubmed: 24677722
Matrix Biol. 2002 Jan;21(1):89-102
pubmed: 11827796
FASEB J. 2020 Apr;34(4):5317-5331
pubmed: 32058623
Dev Cell. 2012 May 15;22(5):927-39
pubmed: 22595668
Dev Dyn. 2001 May;221(1):72-80
pubmed: 11357195
RMD Open. 2015 Aug 15;1(Suppl 1):e000061
pubmed: 26557379
Nucleic Acids Res. 2015 Sep 30;43(17):8183-203
pubmed: 26150426
EMBO Rep. 2018 Dec;19(12):
pubmed: 30413482
Cell. 2019 Feb 7;176(4):897-912.e20
pubmed: 30686579
Cell Div. 2019 Nov 25;14:13
pubmed: 31788020
Tissue Eng Part A. 2009 Oct;15(10):2807-16
pubmed: 19231914
Genome Biol. 2014 Mar 21;15(3):R52
pubmed: 24655370
Genes Dev. 2001 Nov 1;15(21):2865-76
pubmed: 11691837
Cell Rep. 2022 Sep 6;40(10):111315
pubmed: 36070691
Curr Protoc Mol Biol. 2015 Jan 05;109:21.29.1-21.29.9
pubmed: 25559105
Acta Orthop. 2013 Dec;84(6):585-92
pubmed: 24237425
Nucleic Acids Res. 2016 Jan 4;44(D1):D110-5
pubmed: 26531826
J Biol Chem. 2010 Jun 11;285(24):18948-58
pubmed: 20404334
Bioinformatics. 2016 Sep 15;32(18):2847-9
pubmed: 27207943
Cell Death Dis. 2014 Oct 16;5:e1469
pubmed: 25321476
Elife. 2023 Mar 15;12:
pubmed: 36920035
F1000Res. 2015 Dec 30;4:1521
pubmed: 26925227
Arthritis Res Ther. 2013;15(6):R197
pubmed: 24257415
Nat Methods. 2013 Dec;10(12):1213-8
pubmed: 24097267
J Cell Biochem. 2013 Apr;114(4):735-42
pubmed: 23060229
J Orthop Translat. 2019 Dec 23;23:132-139
pubmed: 32913706
Development. 2001 Dec;128(24):5099-108
pubmed: 11748145
Genes Dev. 1994 Feb 1;8(3):277-89
pubmed: 8314082
Osteoarthritis Cartilage. 2016 May;24(5):883-91
pubmed: 26687825
BMC Genomics. 2017 Dec 20;18(1):983
pubmed: 29262782
Genome Biol. 2008;9(9):R137
pubmed: 18798982
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Tissue Eng. 2007 Sep;13(9):2163-73
pubmed: 17518732
Mol Cell. 2010 May 28;38(4):576-89
pubmed: 20513432
PLoS Genet. 2018 Apr 16;14(4):e1007346
pubmed: 29659575
Ann Rheum Dis. 2003 Oct;62(10):995-8
pubmed: 12972480
Nat Biotechnol. 2015 Jun;33(6):638-45
pubmed: 25961409
J Cell Physiol. 2009 Aug;220(2):401-9
pubmed: 19365806
BMC Dev Biol. 2009 Mar 10;9:20
pubmed: 19272164
Elife. 2017 Dec 05;6:
pubmed: 29205154
Dev Dyn. 2019 Sep;248(9):882-893
pubmed: 31290205
FEBS Lett. 2020 May;594(9):1368-1378
pubmed: 31981416
Immunity. 2007 Jun;26(6):715-25
pubmed: 17582344
Nat Biotechnol. 2010 May;28(5):495-501
pubmed: 20436461
Genes Dev. 1999 Aug 15;13(16):2072-86
pubmed: 10465785
Biomater Res. 2018 Mar 16;22:9
pubmed: 29568558
Mol Cell Biol. 2005 Jan;25(2):699-705
pubmed: 15632070
Development. 2016 Aug 15;143(16):3012-23
pubmed: 27471255
Osteoarthritis Cartilage. 2012 Mar;20(3):223-32
pubmed: 22178514
Nat Protoc. 2013 Dec;8(12):2502-15
pubmed: 24263090
Dev Biol. 2007 May 1;305(1):40-51
pubmed: 17336282
Sci Rep. 2017 May 24;7(1):2371
pubmed: 28539595
Cell. 1997 May 30;89(5):755-64
pubmed: 9182763
Mech Dev. 1999 Feb;80(2):159-70
pubmed: 10072783
Pediatr Res. 2015 Mar;77(3):406-15
pubmed: 25521919
PLoS One. 2014 Jul 28;9(7):e103061
pubmed: 25068449
Exp Ther Med. 2020 Jun;19(6):3620-3626
pubmed: 32346426
Endocrinology. 2003 Oct;144(10):4659-68
pubmed: 12960068
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Nat Commun. 2016 Nov 10;7:13336
pubmed: 27830706
Dev Cell. 2007 Mar;12(3):377-89
pubmed: 17336904
Nat Methods. 2017 Apr;14(4):417-419
pubmed: 28263959
PLoS One. 2014 Sep 17;9(9):e107577
pubmed: 25229425
Proc Natl Acad Sci U S A. 2005 Mar 1;102(9):3324-9
pubmed: 15728361
J Tissue Eng Regen Med. 2020 Jan;14(1):29-44
pubmed: 31503387
Adv Cancer Res. 2013;119:1-61
pubmed: 23870508
Dev Biol. 2014 Dec 15;396(2):224-36
pubmed: 25446537
J Mol Diagn. 2012 Jan;14(1):22-9
pubmed: 22166544
Cancer Res. 2011 Nov 15;71(22):6940-7
pubmed: 21940749
Cell. 2020 Apr 16;181(2):362-381.e28
pubmed: 32220312
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Development. 2009 Apr;136(8):1351-61
pubmed: 19304887
Nucleic Acids Res. 2014 Jan;42(Database issue):D764-70
pubmed: 24270787
Physiol Rev. 2016 Jul;96(3):831-71
pubmed: 27142453
PLoS One. 2019 Aug 26;14(8):e0218230
pubmed: 31449527
Sci Rep. 2018 Jan 17;8(1):950
pubmed: 29343853
J Bone Miner Res. 2013 Oct;28(10):2081-93
pubmed: 23553928
Cell. 2018 Feb 8;172(4):650-665
pubmed: 29425488
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W202-8
pubmed: 19458158
J Bone Miner Res. 2019 Sep;34(9):1676-1689
pubmed: 31189030
Biochem J. 2004 Jun 15;380(Pt 3):651-9
pubmed: 15015934
Genes Dev. 2004 Apr 15;18(8):952-63
pubmed: 15107406
J Biol Chem. 2002 Nov 1;277(44):42214-8
pubmed: 12239209
Science. 1996 Aug 2;273(5275):663-6
pubmed: 8662561