# Wnt3a promotes in situ dentin formation through NKD1-MSX1 axis-mediated odontogenic differentiation of dental pulp stem cells

**Authors:** Haoran Du, Qiong Li, Chenchen Zhou, Junji Xu, Kang Gao, Zixiao Li, Yifan Xu, Ousheng Liu, Bing Li, Jianguang Xu, Jingsong Wang, Hideaki Kagami, Xianqi Li, Su Chen, Jian Zhou

PMC · DOI: 10.1038/s41368-025-00406-3 · International Journal of Oral Science · 2026-01-13

## TL;DR

This study shows how Wnt3a helps form dentin by activating a specific pathway in dental pulp stem cells, offering new insights for tooth regeneration.

## Contribution

The study identifies a conserved Wnt3a-NKD1-MSX1 axis that controls odontoblast differentiation from dental pulp stem cells.

## Key findings

- Wnt3a induces an NKD1+ subpopulation with odontoblast features in dental pulp stem cells.
- The NKD1-MSX1 axis is essential for odontogenic gene activation and dentin formation.
- Wnt3a signaling enhances reparative dentin formation in murine pulp exposure models.

## Abstract

The functional regeneration of the dentin-pulp complex is pivotal for tooth preservation, yet the molecular mechanisms governing odontoblast differentiation remain poorly understood. In the current study, we revealed a distinct NKD1+ subpopulation exhibiting secretory odontoblast characteristics, which was specifically induced in dental pulp stem cells (DPSCs) by Wnt3a, but not by Wnt5a or Wnt10a through single-cell transcriptomic profiling. We then found that the NKD1+ subpopulation was functional conservation, which were consistently identified in the odontoblast layers of developing tooth germs in both murine and miniature pig models, as well as within the apical open area in human molars. This conserved spatial distribution and co-localization with DSPP strongly indicates that NKD1+ cells were active dentin-secreting odontoblasts. Analysis of gene regulatory networks using SCENIC identified MSX1 as a key transcription factor regulating the specification of NKD1+ lineage. Mechanistically, Wnt3a orchestrates a tripartite cascade: upregulating NKD1/MSX1 expression, triggering NKD1 membrane detachment, and facilitating direct NKD1-MSX1 interaction to promote MSX1 nuclear translocation. CUT&Tag analysis demonstrated MSX1 occupancy at promoters of odontogenic regulators, establishing its necessity for odontogenic gene activation. Murine pulp exposure models validated that Wnt3a-activated NKD1-MSX1 signaling significantly enhances reparative dentin formation. This study delineates an evolutionarily conserved Wnt3a-NKD1-MSX1 axis that resolves stem cell heterogeneity into functional odontoblast commitment, providing both mechanistic insights into dentin-pulp regeneration and a foundation for targeted regenerative therapies.

## Linked entities

- **Genes:** NKD1 (NKD inhibitor of Wnt signaling pathway 1) [NCBI Gene 85407], MSX1 (msh homeobox 1) [NCBI Gene 4487], DSPP (dentin sialophosphoprotein) [NCBI Gene 1834]
- **Species:** Homo sapiens (taxon 9606)

## Full-text entities

- **Genes:** Ssu2 (ssu-2 homolog) [NCBI Gene 243612] {aka D630042P16Rik, Fls485, Ssuh2}, P9Ehs1 (protein, Chr 9, NIEHS 1) [NCBI Gene 109957], NKD1 (NKD inhibitor of Wnt signaling pathway 1) [NCBI Gene 85407] {aka Naked1}, Fam20c (FAM20C, golgi associated secretory pathway kinase) [NCBI Gene 80752] {aka DMP-4, DMP4, GEF-CK, mKIAA4081}, Bmp2 (bone morphogenetic protein 2) [NCBI Gene 12156] {aka Bmp2a}, Itpr3 (inositol 1,4,5-triphosphate receptor 3) [NCBI Gene 16440] {aka IP3R 3, IP3R-3, Ip3r3, Itpr-3, tf}, Mki67 (antigen identified by monoclonal antibody Ki 67) [NCBI Gene 17345] {aka D630048A14Rik, Ki-67, Ki67}, Gapdh (glyceraldehyde-3-phosphate dehydrogenase) [NCBI Gene 14433] {aka Gapd}, Wnt3a (wingless-type MMTV integration site family, member 3A) [NCBI Gene 22416] {aka Wnt-3a, vt}, Ctnnb1 (catenin beta 1) [NCBI Gene 12387] {aka Bfc, Catnb, Mesc}, Rhoa (ras homolog family member A) [NCBI Gene 11848] {aka Arha, Arha1, Arha2}, Sfrp2 (secreted frizzled-related protein 2) [NCBI Gene 20319] {aka Sdf5}, Nkd1 (naked cuticle 1) [NCBI Gene 93960] {aka 2810434J10Rik, 9030215G15Rik, Nkd}, WNT5A (Wnt family member 5A) [NCBI Gene 7474] {aka hWNT5A}, Krt14 (keratin 14) [NCBI Gene 16664] {aka CK-14, K14, Krt-1.14, Krt1-14}, Dspp (dentin sialophosphoprotein) [NCBI Gene 666279] {aka Dmp2, Dmp3, Dpp, Dsp}, alp (alopecia, recessive) [NCBI Gene 11691], Lef1 (lymphoid enhancer binding factor 1) [NCBI Gene 16842] {aka 3000002B05, Lef-1}, H3c7 (H3 clustered histone 7) [NCBI Gene 260423] {aka H3.2-221, H3c13, H3c14, H3c15, H3c2, H3c3}, Msx1 (msh homeobox 1) [NCBI Gene 17701] {aka Hox-7, Hox7, Hox7.1, msh}, Wnt10a (wingless-type MMTV integration site family, member 10A) [NCBI Gene 22409], Wif1 (Wnt inhibitory factor 1) [NCBI Gene 24117] {aka WIF-1}, MSX1 (msh homeobox 1) [NCBI Gene 4487] {aka ECTD3, HOX7, HYD1, STHAG1}, Ctsk (cathepsin K) [NCBI Gene 13038] {aka MMS10-Q, Ms10q, catK}, Axin2 (axin 2) [NCBI Gene 12006] {aka Axi1, Axil, Conductin}, Wnt8a (wingless-type MMTV integration site family, member 8A) [NCBI Gene 20890] {aka Stra11, Wnt-8A, Wnt-8D, Wnt8d}, WNT10A (Wnt family member 10A) [NCBI Gene 80326] {aka ECTD16, OODD, SSPS, STHAG4}, Cd24a (CD24a antigen) [NCBI Gene 12484] {aka Cd24, HSA, Ly-52, nectadrin}, Dmp1 (dentin matrix protein 1) [NCBI Gene 13406] {aka AG1, DMP-1, Dmp, PP}, Wnt5a (wingless-type MMTV integration site family, member 5A) [NCBI Gene 22418] {aka 8030457G12Rik, Wnt-5a}, Pax9 (paired box 9) [NCBI Gene 18511] {aka Pax-9}, WNT3A (Wnt family member 3A) [NCBI Gene 89780], DSPP (dentin sialophosphoprotein) [NCBI Gene 1834] {aka DFNA39, DGI1, DMP3, DPP, DSP}, Dkk2 (dickkopf WNT signaling pathway inhibitor 2) [NCBI Gene 56811]
- **Diseases:** pulpitis (MESH:D011671), tooth fractures (MESH:D014082), tooth agenesis (MESH:D000848), jaw hypoplasia (MESH:D007571), inflammatory (MESH:D007249), osteogenesis (MESH:D010013)
- **Chemicals:** HA1004 (MESH:C043204), methanol (MESH:D000432), DAPI (MESH:C007293), nitrogen (MESH:D009584), Alexa Fluor 488 (MESH:C000711379), calcium (MESH:D002118), dexamethasone (MESH:D003907), Puromycin (MESH:D011691), ascorbic acid (MESH:D001205), AZD2858 (MESH:C583189), HA1127 (-), FITC (MESH:D016650), PVDF (MESH:C024865), digitonin (MESH:D004072), alpha-MEM (MESH:C420642), streptomycin (MESH:D013307), ethanol (MESH:D000431), EDTA (MESH:D004492), penicillin (MESH:D010406), Triton X-100 (MESH:D017830), beta-glycerophosphate (MESH:C031463), chloroform (MESH:D002725), PFA (MESH:C003043), ARS (MESH:C004468), LPS (MESH:D008070), H2O2 (MESH:D006861), NaCl (MESH:D012965), Duolink (MESH:C431350), pentobarbital sodium (MESH:D010424), phenol (MESH:D019800), CO2 (MESH:D002245), paraffin (MESH:D010232), PBS (MESH:D007854)
- **Species:** Mycoplasma (genus) [taxon 2093], Adeno-associated virus (species) [taxon 272636], Mus musculus (house mouse, species) [taxon 10090], Sus scrofa (pig, species) [taxon 9823], Homo sapiens (human, species) [taxon 9606]
- **Cell lines:** SaCas9 — Homo sapiens (Human), Blast phase chronic myelogenous leukemia, BCR-ABL1 positive, Cancer cell line (CVCL_RY28), 293T — Homo sapiens (Human), Transformed cell line (CVCL_0063), /6J — Homo sapiens (Human), Cutaneous melanoma, Cancer cell line (CVCL_W797), NM_033119 — Bos taurus (Bovine), Finite cell line (CVCL_3074)

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Source: https://tomesphere.com/paper/PMC12796365