Epigenetic regulation of dental pulp stem cells and its potential in regenerative endodontics

Table 1 Enzymes related to epigenetic modifications of dental pulp stem cells activities

Proteins and their function	Epigenetic Targets	Gene manipulation of each epigenetic marker	Downstream targets	Biological process implicated	Reference
DNA methylation
TET1, demethylation		Gene activation	FAM20C	(↑) proliferation, (↑) odontoblast differentiation	[41-43]
Histone methylation
EHMT1, methylation	H3K9me2	Gene repression	Runx2	(↓) odontoblast differentiation	[51]
KMT2A, methylation	H3K4me3	Gene activation	WNT5A, RUNX2, MSX2, DLX5	(↑) odontoblast differentiation	[12,52]
EZH2, demethylation	H3K27me2/me3	Gene repression	Wnt/β-Catenin pathway, IL-6, IL-8, CCL2	(↑) Inflammation, (↓) odontoblast differentiation	[54-56]
KDM6B/JMJD3, demethylation	H3K27me3	Gene repression	WNT5A, BMP2	(↑) odontoblast differentiation	[52,58]
KDM5A, demethylation	H3K4me3/me2	Gene activation	DMP1, DSPP, OSX, OCN	(↓) odontoblast differentiation	[60]
Histone acetylation
p300, acetylation	H3K9ac		OCN, NANOG, SOX2, DSPP, Dmp1, Osx	(↑) pluripotency, (↑) proliferation, (↑) odontoblast differentiation	[14,64]
HDAC3, deacetylation	H3K27ac		Dmp1, Osx	(↓) odontoblast differentiation	[13,66]
HDAC6, deacetylation				(↓) odontoblast differentiation	[15]

TET1: Ten-eleven translocation 1; EHMT1: Euchromatic histone lysine methyltransferase 1; KMT2A: Lysine methyltransferase 2A; KDM6B: Lysine demethylase 6B; KDM5A: Lysine demethylase 5A; p300: E1A binding protein p300; HDAC3: Histone deacetylase 3; HDAC6: Histone deacetylase 6; H3K9me2: Dimethylated histone H3 lysine 9; H3K4me3/me2: Tri-/di-methylated histone H3 lysine 4; H3K27me2/me3: Di-/tri-methylated histone H3 lysine 27; H3K9ac: Acetylated histone H3 lysine 9; H3K27ac: Acetylated histone H3 lysine 27; FAM20C: FAM20C golgi associated secretory pathway kinase; Runx2: RUNX family transcription factor 2; WNT5A: Wnt family member 5A; MSX2: Msh homeobox 2; DLX5: Distal-less homeobox 5; CCL2: C-C motif chemokine ligand 2; IL-6/-8: Interleukin 6/8; BMP2: Bone morphogenetic protein 2; DMP1: Dentin matrix acidic phosphoprotein 1; DSPP: Dentin sialophosphoprotein; OSX: Osterix; OCN: Osteocalcin; NANOG: Nanog homeobox; SOX2: SRY-box transcription factor 2.

Table 2 Epigenetic molecules promoting odontogenic differentiation of dental pulp stem cells

	Targets	Cell population	Medium	Upregulated odontogenic genes	Downregulated odontogenic genes	Reference
HDACis
TSA	HDAC 1, 2, 3 (Class I); HDAC 4, 5, 6 (Class II)	pDPSCs	MM	DMP1, DSPP, BSP	OCN	[124]
		Murine MDPC23	MM	Dmp1		[119]
		Rodent primary dental pulp cells	MM	Bmp4, Dspp, Bmp2, Opn		[116]
		Rodent MDPC23	GM	Bmp4, Ocn, Dmp1, Runx2		[16]
SAHA	classes I and II	Murine MDPC23	MM	Nfic, Dspp, Alp, Dmp1, nestin		[122]
VPA	HDAC 1, 2, 3 (class I)	pDPSCs	GM, MM	BSP, OPN	OCN	[117]
		Murine MDPC23	MM	Dmp1, Bmp4, Tgfβ1		[119]
		rodent MDPC23	GM	Bmp2/4, Ocn, Runx2		[16]
		Rodent primary DPSCs	MM	Dmp1, Bmp2, Bmp4, Dspp, Opn		[116]
MS-275	HDAC 1, 3 (class I)	pDPSCs	GM	RUNX2, DMP1, ALP, DSPP		[126]
		rodent MDPC23	GM	Bmp2/4, Col1α1, Ocn, Dmp1, Dspp, Runx2, Klf5, Msx1		[16]
LMK-235	HDAC 4, 5 (class II)	pDPSCs	GM	ALP, DSPP		[127]
			MM	ALP, DSPP, RUNX2		[127]
DNMTis
5-Aza-CdR		pDPSCs	MM	DSPP, DMP1, OSX, DLX5, RUNX2		[38]
RG-108		Murine mDPC6T	MM	Klf4, Dspp, Dmp1		[40]

HDACis: Histone deacetylase inhibitors; TSA: Trichostatin A; SAHA: Suberoylanilide hydroxamic acid; VPA: Valproic acid; MS-275: Entinostat; DNMTis: DNA methyltransferases inhibitors; 5-Aza-CdR: 5-Aza-2’-deoxycytidine; HDAC: Histone deacetylase; pDPSCs: Dental pulp stem cells from permanent teeth; MDPC23: Murine odontoblast-like cell line; mDPC6T: Murine preodontoblast cell line; MM: Mineralized medium; GM: Growth medium; DMP1: Dentin matrix acidic phosphoprotein 1; DSPP: Dentin sialophosphoprotein; BSP: Bone sialoprotein; BMP4: Bone morphogenetic protein 4; BMP2: Bone morphogenetic protein 2; OPN: Osteopontin; Runx2: RUNX Family transcription factor 2; Nfic: Nuclear factor I C; ALP: Alkaline phosphatase; Tgfβ1: Transforming growth factor beta 1; OCN: Osteocalcin; Col1α1: Collagen type I alpha 1; Klf5: Kruppel like factor 5; MSX1: Msh homeobox 1.