SMAD2/3-SMYD2 and developmental transcription factors cooperate with cell-cycle inhibitors to guide tissue formation

Stefania Militi, Reshma Nibhani, Martin Pook, Siim Pauklin

PDF(26211 KB)
PDF(26211 KB)
Protein Cell ›› DOI: 10.1093/procel/pwae031
RESEARCH ARTICLE

SMAD2/3-SMYD2 and developmental transcription factors cooperate with cell-cycle inhibitors to guide tissue formation

Author information +
History +

Abstract

Tissue formation and organ homeostasis are achieved by precise coordination of proliferation and differentiation of stem cells and progenitors. While deregulation of these processes can result in degenerative disease or cancer, their molecular interplays remain unclear. Here we show that the switch of human pluripotent stem cell (hPSC) self-renewal to differentiation is associated with the induction of distinct cyclin-dependent kinase inhibitors (CDKIs). In hPSCs, Activin/Nodal/TGFβ signaling maintains CDKIs in a poised state via SMAD2/3-NANOG-OCT4-EZH2-SNON transcriptional complex. Upon gradual differentiation, CDKIs are induced by successive transcriptional complexes between SMAD2/3-SMYD2 and developmental regulators such as EOMES, thereby lengthening the G1 phase. This, in turn, induces SMAD2/3 transcriptional activity by blocking its linker phosphorylation. Such SMAD2/3-CDKI positive feedback loops drive the exit from pluripotency and stepwise cell-fate specification that could be harnessed for producing cells for therapeutic applications. Our study uncovers fundamental mechanisms of how cell-fate specification is interconnected to cell-cycle dynamics and provides insight into autonomous circuitries governing tissue self-formation.

Keywords

human pluripotent stem cells / epigenetics / TGFβ/ACTIVIN-SMAD2/3 / differentiation / cell cycle / EZH2 / SMYD2

Cite this article

Download citation ▾
Stefania Militi, Reshma Nibhani, Martin Pook, Siim Pauklin. SMAD2/3-SMYD2 and developmental transcription factors cooperate with cell-cycle inhibitors to guide tissue formation. Protein Cell, https://doi.org/10.1093/procel/pwae031

References

[1]
Abu-Farha M, Lambert JP, Al-Madhoun AS et al. The tale of two domains: proteomics and genomics analysis of SMYD2, a new histone methyltransferase. Mol Cell Proteomics 2008;7:560–572.
CrossRef Google scholar
[2]
Awad MM, Sanders JA, Gruppuso PA. A potential role for p15(Ink4b) and p57(Kip2) in liver development. FEBS Lett 2000;483:160–164.
CrossRef Google scholar
[3]
Bertero A, Madrigal P, Galli A et al. Activin/nodal signaling and NANOG orchestrate human embryonic stem cell fate decisions by controlling the H3K4me3 chromatin mark. Genes & Development 2015;29:702–717.
CrossRef Google scholar
[4]
Besson A, Hwang HC, Cicero S et al. Discovery of an oncogenic activity in p27Kip1 that causes stem cell expansion and a multiple tumor phenotype. Genes Dev 2007;21:1731–1746.
CrossRef Google scholar
[5]
Blanco E, Gonzalez-Ramirez M, Alcaine-Colet A et al. The bivalent genome: characterization, structure, and regulation. Trends Genet 2020;36:118–131.
CrossRef Google scholar
[6]
Boyer LA, Plath K, Zeitlinger J et al. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 2006;441:349–353.
CrossRef Google scholar
[7]
Brown MA, Sims RJ 3RD, Gottlieb PD et al. Identification and characterization of Smyd2: a split SET/MYND domain-containing histone H3 lysine 36-specific methyltransferase that interacts with the SiN3 histone deacetylase complex. Mol Cancer 2006;5:26.
CrossRef Google scholar
[8]
Brown S, Teo A, Pauklin S et al. Activin/Nodal signaling controls divergent transcriptional networks in human embryonic stem cells and in endoderm progenitors. Stem Cells 2011;29:1176–1185.
CrossRef Google scholar
[9]
Buchold GM, Magyar PL, Arumugam R et al. p19Ink4d and p18Ink4c cyclin-dependent kinase inhibitors in the male reproductive axis. Mol Reprod Dev 2007;74:997–1007.
CrossRef Google scholar
[10]
Calder A, Roth-Albin I, Bhatia S et al. Lengthened G1 Phase Indicates Differentiation Status in Human Embryonic Stem Cells. Stem Cells Dev 2012;22:279–295.
CrossRef Google scholar
[11]
Cao R, Wang L, Wang H et al. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 2002;298:1039–1043.
CrossRef Google scholar
[12]
Chang SF, Chang TK, Peng HH et al. BMP-4 induction of arrest and differentiation of osteoblast-like cells via p21 CIP1 and p27 KIP1 regulation. Mol Endocrinol 2009;23:1827–1838.
CrossRef Google scholar
[13]
Cho HS, Hayami S, Toyokawa G et al. RB1 methylation by SMYD2 enhances cell cycle progression through an increase of RB1 phosphorylation. Neoplasia 2012;14:476–486.
CrossRef Google scholar
[14]
Collado M, Blasco MA, Serrano M. Cellular senescence in cancer and aging. Cell 2007;130:223–233.
CrossRef Google scholar
[15]
Coronado D, Godet M, Bourillot PY et al. A short G1 phase is an intrinsic determinant of naive embryonic stem cell pluripotency. Stem Cell Res 2013;10:118–131.
CrossRef Google scholar
[16]
Cunningham JJ, Levine EM, Zindy F et al. The cyclin-dependent kinase inhibitors p19(Ink4d) and p27(Kip1) are coexpressed in select retinal cells and act cooperatively to control cell cycle exit. Mol Cell Neurosci 2002;19:359–374.
CrossRef Google scholar
[17]
Delavaine L, La Thangue NB. Control of E2F activity by p21Waf1/Cip1. Oncogene 1999;18:5381–5392.
CrossRef Google scholar
[18]
Deng C, Zhang P, Harper JW et al. Mice lacking p21CIP1/WAF1 undergo normal development, but are defective in G1 checkpoint control. Cell 1995;82:675–684.
CrossRef Google scholar
[19]
Dyer MA, Cepko CL. p27Kip1 and p57Kip2 regulate proliferation in distinct retinal progenitor cell populations. J Neurosci 2001;21:4259–4271.
CrossRef Google scholar
[20]
Edmiston JS, Yeudall WA, Chung TD et al. Inability of transforming growth factor-beta to cause SnoN degradation leads to resistance to transforming growth factor-beta-induced growth arrest in esophageal cancer cells. Cancer Res 2005;65:4782–4788.
CrossRef Google scholar
[21]
Estaras C, Benner C, Jones KA. SMADs and YAP compete to control elongation of beta-catenin:LEF-1-recruited RNAPII during hESC differentiation. Mol Cell 2015;58:780–793.
CrossRef Google scholar
[22]
Franklin DS, Godfrey VL, Lee H et al. CDK inhibitors p18(INK4c) and p27(Kip1) mediate two separate pathways to collaboratively suppress pituitary tumorigenesis. Genes Dev 1998;12:2899–2911.
CrossRef Google scholar
[23]
Fuchs E. The tortoise and the hair: slow-cycling cells in the stem cell race. Cell 2009;137:811–819.
CrossRef Google scholar
[24]
Godin JD, Thomas N, Laguesse S et al. p27(Kip1) is a microtubule-associated protein that promotes microtubule polymerization during neuron migration. Dev Cell 2012;23:729–744.
CrossRef Google scholar
[25]
Gonzales KA, Liang H, Lim YS et al. Deterministic restriction on pluripotent state dissolution by cell-cycle pathways. Cell 2015;162:564–579.
CrossRef Google scholar
[26]
He J, Tegen SB, Krawitz AR et al. The transforming activity of Ski and SnoN is dependent on their ability to repress the activity of Smad proteins. J Biol Chem 2003;278:30540–30547.
CrossRef Google scholar
[27]
Hsu PD, Lander ES, Zhang F. Development and applications of CRISPR-Cas9 for genome engineering. Cell 2014;157:1262–1278.
CrossRef Google scholar
[28]
Huang J, Perez-Burgos L, Placek BJ et al. Repression of p53 activity by Smyd2-mediated methylation. Nature 2006;444:629–632.
CrossRef Google scholar
[29]
Hyun K, Jeon J, Park K et al. Writing, erasing and reading histone lysine methylations. Exp Mol Med 2017;49:e324.
CrossRef Google scholar
[30]
Ibrahim EE, Babaei-Jadidi R, Saadeddin A et al. Embryonic NANOG activity defines colorectal cancer stem cells and modulates through AP1-and TCF-dependent mechanisms. Stem Cells 2012;30:2076–2087.
CrossRef Google scholar
[31]
Jeter CR, Badeaux M, Choy G et al. Functional evidence that the self-renewal gene NANOG regulates human tumor development. Stem Cells 2009;27:993–1005.
CrossRef Google scholar
[32]
Jeter CR, Liu B, Liu X et al. NANOG promotes cancer stem cell characteristics and prostate cancer resistance to androgen deprivation. Oncogene 2011;30:3833–3845.
CrossRef Google scholar
[33]
Kamijo T, Zindy F, Roussel MF et al. Tumor suppression at the mouse INK4a locus mediated by the alternative reading frame product p19ARF. Cell 1997;91:649–659.
CrossRef Google scholar
[34]
Kim WY, Sharpless NE. The regulation of INK4/ARF in cancer and aging. Cell 2006;127:265–275.
CrossRef Google scholar
[35]
Krakowski AR, Laboureau J, Mauviel A et al. Cytoplasmic SnoN in normal tissues and nonmalignant cells antagonizes TGF-beta signaling by sequestration of the Smad proteins. Proc Natl Acad Sci U S A 2005;102:12437–12442.
CrossRef Google scholar
[36]
Kretzschmar M, Doody J, Timokhina I et al. A mechanism of repression of TGFbeta/Smad signaling by oncogenic Ras. Genes Dev 1999;13:804–816.
CrossRef Google scholar
[37]
Ladewig J, Koch P, Brustle O. Leveling Waddington: the emergence of direct programming and the loss of cell fate hierarchies. Nat Rev Mol Cell Biol 2013;14:225–236.
CrossRef Google scholar
[38]
Lange C, Calegari F. Cdks and cyclins link G1 length and differentiation of embryonic, neural and hematopoietic stem cells. Cell Cycle 2010;9:1893–1900.
CrossRef Google scholar
[39]
Li L, Clevers H. Coexistence of quiescent and active adult stem cells in mammals. Science 2010;327:542–545.
CrossRef Google scholar
[40]
Li H, Collado M, Villasante A et al. p27(Kip1) directly represses Sox2 during embryonic stem cell differentiation. Cell Stem Cell 2012;11:845–852.
CrossRef Google scholar
[41]
Lim S, Kaldis P. Cdks, cyclins and CKIs: roles beyond cell cycle regulation. Development 2013;140:3079–3093.
CrossRef Google scholar
[42]
Luedde T, Rodriguez ME, Tacke F et al. p18(INK4c) collaborates with other CDK-inhibitory proteins in the regenerating liver. Hepatology 2003;37:833–841.
CrossRef Google scholar
[43]
Madrigal P, Deng S, Feng Y et al. Epigenetic and transcriptional regulations prime cell fate before division during human pluripotent stem cell differentiation. Nat Commun 2023;14:405.
CrossRef Google scholar
[44]
Marques-Torrejon MA, Porlan E, Banito A et al. Cyclindependent kinase inhibitor p21 controls adult neural stem cell expansion by regulating Sox2 gene expression. Cell Stem Cell 2013;12:88–100.
CrossRef Google scholar
[45]
Mullen AC, Orlando DA, Newman JJ et al. Master transcription factors determine cell-type-specific responses to TGF-beta signaling. Cell 2011;147:565–576.
CrossRef Google scholar
[46]
Nguyen L, Besson A, Heng JI et al. p27kip1 independently promotes neuronal differentiation and migration in the cerebral cortex. Genes Dev 2006;20:1511–1524.
CrossRef Google scholar
[47]
Oh J, Lee YD, Wagers AJ. Stem cell aging: mechanisms, regulators and therapeutic opportunities. Nat Med 2014;20:870–880.
CrossRef Google scholar
[48]
Palazuelos J, Klingener M, Aguirre A. TGFbeta signaling regulates the timing of CNS myelination by modulating oligodendrocyte progenitor cell cycle exit through SMAD3/4/FoxO1/Sp1. J Neurosci 2014;34:7917–7930.
CrossRef Google scholar
[49]
Pauklin S, Vallier L. The cell-cycle state of stem cells determines cell fate propensity. Cell 2013;155:135–147.
CrossRef Google scholar
[50]
Pauklin S, Vallier L. Activin/Nodal signalling in stem cells. Development 2015;142:607–619.
CrossRef Google scholar
[51]
Pauklin S, Madrigal P, Bertero A et al. Initiation of stem cell differentiation involves cell cycle-dependent regulation of developmental genes by Cyclin D. Genes Dev 2016;30:421–433.
CrossRef Google scholar
[52]
Pippa R, Espinosa L, Gundem G et al. p27Kip1 represses transcription by direct interaction with p130/E2F4 at the promoters of target genes. Oncogene 2012;31:4207–4220.
CrossRef Google scholar
[53]
Podkowa M, Christova T, Zhao X et al. p21-Activated kinase (PAK) is required for Bone Morphogenetic Protein (BMP)-induced dendritogenesis in cortical neurons. Mol Cell Neurosci 2013;57:83–92.
CrossRef Google scholar
[54]
Polyak K, Kato JY, Solomon MJ et al. p27Kip1, a cyclin-Cdk inhibitor, links transforming growth factor-beta and contact inhibition to cell cycle arrest. Genes Dev 1994;8:9–22.
CrossRef Google scholar
[55]
Pope BD, Ryba T, Dileep V et al. Topologically associating domains are stable units of replication-timing regulation. Nature 2014;515:402–405.
CrossRef Google scholar
[56]
Reynaud EG, Leibovitch MP, Tintignac LA et al. Stabilization of MyoD by direct binding to p57(Kip2). J Biol Chem 2000;275:18767–18776.
CrossRef Google scholar
[57]
Rivera CM, Ren B. Mapping human epigenomes. Cell 2013;155:39–55.
CrossRef Google scholar
[58]
Sakaue-Sawano A, Kurokawa H, Morimura T et al. Visualizing spatiotemporal dynamics of multicellular cell-cycle progression. Cell. 2008;132:487–498.
CrossRef Google scholar
[59]
Sasai Y. Next-generation regenerative medicine: organogenesis from stem cells in 3D culture. Cell Stem Cell 2013;12:520–530.
CrossRef Google scholar
[60]
Savatier P, Lapillonne H, Van Grunsven LA et al. Withdrawal of differentiation inhibitory activity/leukemia inhibitory factor up-regulates D-type cyclins and cyclin-dependent kinase inhibitors in mouse embryonic stem cells. Oncogene 1996;12:309–322.
[61]
Scandura JM, Boccuni P, Massague J et al. Transforming growth factor beta-induced cell cycle arrest of human hematopoietic cells requires p57KIP2 up-regulation. Proc Natl Acad Sci U S A 2004;101:15231–15236.
CrossRef Google scholar
[62]
Serrano M, Lee H, Chin L et al. Role of the INK4a locus in tumor suppression and cell mortality. Cell 1996;85:27–37.
CrossRef Google scholar
[63]
Sherr CJ, Roberts JM. CDK inhibitors: positive and negative regulators of G1-phase progression. Genes Dev 1999;13:1501–1512.
CrossRef Google scholar
[64]
Singh AM, Chappell J, Trost R et al. Cell-cycle control of developmentally regulated transcription factors accounts for heterogeneity in human pluripotent cells. Stem Cell Rep 2013;1:532–544.
CrossRef Google scholar
[65]
Sterneckert JL, Reinhardt P, Scholer HR. Investigating human disease using stem cell models. Nat Rev Genet 2014;15:625–639.
CrossRef Google scholar
[66]
Tabar V, Studer L. Pluripotent stem cells in regenerative medicine: challenges and recent progress. Nat Rev Genet 2014;15:82–92.
CrossRef Google scholar
[67]
Teo AK, Arnold SJ, Trotter MW et al. Pluripotency factors regulate definitive endoderm specification through eomesodermin. Genes Dev 2011;25:238–250.
CrossRef Google scholar
[68]
Toyoshima H, Hunter T. p27, a novel inhibitor of G1 cyclin-Cdk protein kinase activity, is related to p21. Cell 1994;78:67–74.
CrossRef Google scholar
[69]
Tsankov AM, Gu H, Akopian V et al. Transcription factor binding dynamics during human ES cell differentiation. Nature 2015;518:344–349.
CrossRef Google scholar
[70]
Tsuneyoshi N, Tan EK, Sadasivam A et al. The SMAD2/3 core-pressor SNON maintains pluripotency through selective repression of mesendodermal genes in human ES cells. Genes Dev 2012;26:2471–2476.
CrossRef Google scholar
[71]
Vallier L, Mendjan S, Brown S et al. Activin/Nodal signalling maintains pluripotency by controlling Nanog expression. Development 2009a;136:1339–1349.
CrossRef Google scholar
[72]
Vallier L, Touboul T, Chng Z et al. Early cell fate decisions of human embryonic stem cells and mouse epiblast stem cells are controlled by the same signalling pathways. PLoS One 2009b;4:e6082.
CrossRef Google scholar
[73]
Vallier L, Touboul T, Brown S et al. Signaling pathways controlling pluripotency and early cell fate decisions of human induced pluripotent stem cells. Stem Cells 2009c;27:2655–2666.
CrossRef Google scholar
[74]
Yan Y, Frisen J, Lee MH et al. Ablation of the CDK inhibitor p57Kip2 results in increased apoptosis and delayed differentiation during mouse development. Genes Dev 1997;11:973–983.
CrossRef Google scholar
[75]
Zhang P, Liegeois NJ, Wong C et al. Altered cell differentiation and proliferation in mice lacking p57KIP2 indicates a role in Beckwith-Wiedemann syndrome. Nature 1997;387:151–158.
CrossRef Google scholar
[76]
Zhang J, Espinoza LA, Kinders RJ et al. NANOG modulates stemness in human colorectal cancer. Oncogene 2013;32:4397–4405.
CrossRef Google scholar
[77]
Zhu Q, Pearson-White S, Luo K. Requirement for the SnoN oncoprotein in transforming growth factor beta-induced oncogenic transformation of fibroblast cells. Mol Cell Biol 2005;25:10731–10744.
CrossRef Google scholar
[78]
Zindy F, Quelle DE, Roussel MF et al. Expression of the p16INK4a tumor suppressor versus other INK4 family members during mouse development and aging. Oncogene 1997;15:203–211.
CrossRef Google scholar
[79]
Zindy F, Den Besten W, Chen B et al. Control of spermatogenesis in mice by the cyclin D-dependent kinase inhibitors p18(Ink4c) and p19(Ink4d). Mol Cell Biol 2001;21:3244–3255.
CrossRef Google scholar
[80]
Zwijsen RM, Wientjens E, Klompmaker R et al. CDK-independent activation of estrogen receptor by cyclin D1. Cell 1997;88:405–415.
CrossRef Google scholar

RIGHTS & PERMISSIONS

2024 The Author(s) 2024. Published by Oxford University Press on behalf of Higher Education Press.
AI Summary AI Mindmap
PDF(26211 KB)

Accesses

Citations

Detail

Sections
Recommended

/