# KDM6B/Pdk1 glycolytic pathway-driven ZEB2 lactylation promotes cellular cementum formation

**Authors:** Zhengkun Yang, Huiyi Wang, Junhong Xiao, Qiudong Yang, Jiahui Sun, Heyu Liu, Zhendong Huang, Li Ma, Xin Huang, Chuan Wang, Xiaoxuan Wang, Zhengguo Cao

PMC · DOI: 10.1038/s41368-025-00420-5 · International Journal of Oral Science · 2026-03-03

## TL;DR

This study reveals a new pathway involving KDM6B, Pdk1, and ZEB2 lactylation that promotes cementum formation, offering insights for periodontal regeneration.

## Contribution

The study identifies a novel KDM6B–Pdk1–ZEB2 lactylation axis crucial for cementogenesis and periodontal regeneration.

## Key findings

- KDM6B promotes cementoblast mineralization through glycometabolic reprogramming.
- PDK1 is a direct target of KDM6B, and its activation increases lactate production.
- ZEB2 lactylation enhances cementoblast mineralization and can be restored with sodium lactate.

## Abstract

Periodontitis is a common chronic inflammatory disease that ultimately results in irreversible tooth loss. Cementum, a bone-like tissue surrounding tooth roots, deteriorates as periodontitis advances, ultimately causing tooth loss. Therefore, cementum regeneration is considered a key factor in periodontal regeneration. Given the shared gene expression patterns and characteristics between cementum and bone, strategies for cementum regeneration may inform approaches for bone regeneration. Cementoblasts are responsible for cementum formation. This study identified lysine demethylase 6B (KDM6B) as a positive regulatory molecule that promotes cementoblast mineralization and formation. The seahorse assay revealed that KDM6B regulates glycometabolic reprogramming during cementoblast mineralization. Chromatin Immunoprecipitation (ChIP) sequencing and bulk RNA sequencing revealed that pyruvate dehydrogenase kinase 1 (PDK1), a crucial enzyme in glycolysis, is a direct target of KDM6B. Activation of the KDM6B-Pdk1 axis enhanced lactate production, driving lactylation of zinc finger E-box binding homeobox 2 (ZEB2). ZEB2 lactylation subsequently promotes cementoblast mineralization. Moreover, both in vitro and in vivo experiments showed that sodium lactate supplementation restores mineralization impaired by KDM6B suppression. In conclusion, our findings identify the KDM6B–Pdk1–ZEB2 lactylation axis as essential for cementogenesis, providing new insights for periodontal regeneration strategies.

## Linked entities

- **Genes:** KDM6B (lysine demethylase 6B) [NCBI Gene 23135], PDK1 (pyruvate dehydrogenase kinase 1) [NCBI Gene 5163], ZEB2 (zinc finger E-box binding homeobox 2) [NCBI Gene 9839]
- **Chemicals:** sodium lactate (PubChem CID 23666456), lactate (PubChem CID 61503)
- **Diseases:** periodontitis (MONDO:0005076)

## Full-text entities

- **Genes:** KDM6A (lysine demethylase 6A) [NCBI Gene 7403] {aka KABUK2, UTX, bA386N14.2}, PDK1 (pyruvate dehydrogenase kinase 1) [NCBI Gene 5163], LDHA (lactate dehydrogenase A) [NCBI Gene 3939] {aka GSD11, HEL-S-133P, LDHM, PIG19}, Nfkb1 (nuclear factor of kappa light polypeptide gene enhancer in B cells 1, p105) [NCBI Gene 18033] {aka NF-KB1, NF-kappaB, NF-kappaB1, p105, p50, p50/p105}, Tff2 (trefoil factor 2 (spasmolytic protein 1)) [NCBI Gene 21785] {aka SP, mSP}, Sp7 (Sp7 transcription factor 7) [NCBI Gene 170574] {aka 6430578P22Rik, C22, Osx}, Sdha (succinate dehydrogenase complex, subunit A, flavoprotein (Fp)) [NCBI Gene 66945] {aka 1500032O14Rik, 2310034D06Rik, 4921513A11, FP, SDH2, SDHF}, Ldha (lactate dehydrogenase A) [NCBI Gene 16828] {aka Ldh1, Ldhm, l7R2}, Kdm6a (lysine (K)-specific demethylase 6A) [NCBI Gene 22289] {aka Utx}, Pkm (pyruvate kinase, muscle) [NCBI Gene 18746] {aka Pk-2, Pk-3, Pk3, Pkm2}, BMP2 (bone morphogenetic protein 2) [NCBI Gene 650] {aka BDA2, BMP2A, SSFSC, SSFSC1}, PRKCD (protein kinase C delta) [NCBI Gene 5580] {aka ALPS3, CVID9, MAY1, PKCD, nPKC-delta}, SP7 (Sp7 transcription factor) [NCBI Gene 121340] {aka OI11, OI12, OSX, osterix}, H3c7 (H3 clustered histone 7) [NCBI Gene 260423] {aka H3.2-221, H3c13, H3c14, H3c15, H3c2, H3c3}, Actb (actin, beta) [NCBI Gene 11461] {aka Actx, E430023M04Rik, beta-actin}, Dock2 (dedicator of cyto-kinesis 2) [NCBI Gene 94176] {aka CED-5, Hch, MBC}, Fgf23 (fibroblast growth factor 23) [NCBI Gene 64654] {aka Fgf8b}, RUNX2 (RUNX family transcription factor 2) [NCBI Gene 860] {aka AML3, CBF-alpha-1, CBFA1, CCD, CCD1, CLCD}, alp (alopecia, recessive) [NCBI Gene 11691], ALPP (alkaline phosphatase, placental) [NCBI Gene 250] {aka ALP, PALP, PLAP, PLAP-1}, Bsp (black spleen) [NCBI Gene 103993], ZEB2 (zinc finger E-box binding homeobox 2) [NCBI Gene 9839] {aka HSPC082, SIP-1, SIP1, SMADIP1, ZFHX1B}, Slurp1 (secreted Ly6/Plaur domain containing 1) [NCBI Gene 57277] {aka 1110021N19Rik, ARS, ArsB, Slurp-1}, Gli1 (GLI-Kruppel family member GLI1) [NCBI Gene 14632] {aka Zfp-5, Zfp5}, Pdk1 (pyruvate dehydrogenase kinase, isoenzyme 1) [NCBI Gene 228026] {aka B830012B01, D530020C15Rik}, KDM6B (lysine demethylase 6B) [NCBI Gene 23135] {aka JMJD3, NEDCFSA, NEDSST}, Slc2a1 (solute carrier family 2 (facilitated glucose transporter), member 1) [NCBI Gene 20525] {aka GT1, Glut-1, Glut1, M100200, Rgsc200}, Runx2 (runt related transcription factor 2) [NCBI Gene 12393] {aka AML3, CBF-alpha-1, Cbf, Cbfa-1, Cbfa1, LS3}, Zeb2 (zinc finger E-box binding homeobox 2) [NCBI Gene 24136] {aka 9130203F04Rik, D130016B08Rik, SIP1, Zfhx1b, Zfx1b, Zfxh1b}, Kdm6b (KDM1 lysine (K)-specific demethylase 6B) [NCBI Gene 216850] {aka 1700064E03Rik, Jmjd3}, Ctsb (cathepsin B) [NCBI Gene 13030] {aka APPM, CB}
- **Diseases:** X-linked hypophosphatemia (MESH:D053098), tooth loss (MESH:D016388), OIM (MESH:D012516), PDLSC (MESH:D010518), inflammatory (MESH:D007249), tumor (MESH:D009369), diabetes (MESH:D003920), metastasis (MESH:D009362), rheumatoid arthritis (MESH:D001172), toxicity (MESH:D064420), cardiovascular disease (MESH:D002318), glomerular disease (MESH:D007674), infectious disease (MESH:D003141), ectopic (MESH:C566852)
- **Chemicals:** oxygen (MESH:D010100), TCA (MESH:D014233), 2-DG (MESH:D003847), nitrogen (MESH:D009584), alizarin complexone (MESH:C070804), FITC (MESH:D016650), L-Lactate (MESH:D019344), Lactate sodium (MESH:D019354), TRIzol (MESH:C411644), lactoyl-CoA (MESH:C047009), FCCP (MESH:D002259), ethanol (MESH:D000431), ascorbic acid (MESH:D001205), SDS (MESH:D012967), Hematoxylin (MESH:D006416), puromycin (MESH:D011691), sodium (MESH:D012964), alpha-Ketoglutarate (MESH:D007656), phenol red (MESH:D010637), H&amp;E (MESH:D006371), methyl methacrylate (MESH:D020366), AA (-), Alizarin Red (MESH:C010078), GSK-J4 (MESH:C000593030), Lipofectamine 2000 (MESH:C086724), paraformaldehyde (MESH:C003043), Polybrene (MESH:D006583), Antimycin A (MESH:D000968), Rotenone (MESH:D012402), CO2 (MESH:D002245), ATP (MESH:D000255), calcium (MESH:D002118), alizarin red S (MESH:C004468), oligomycin (MESH:D009840), DAPI (MESH:C007293), Glucose (MESH:D005947), PVDF (MESH:C024865), PBS (MESH:D007854), eosin (MESH:D004801)
- **Species:** Mus musculus (house mouse, species) [taxon 10090], Homo sapiens (human, species) [taxon 9606]
- **Mutations:** S07921060E, lysine (K) to arginine (R), S07923050C
- **Cell lines:** C57BL/6 — Mus musculus (Mouse), Transformed cell line (CVCL_C0MU), OCCM-30 — Mus musculus (Mouse), Hybridoma (CVCL_J925)

## Full text

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## Figures

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## References

7 references — full list in the complete paper: https://tomesphere.com/paper/PMC12953700/full.md

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Source: https://tomesphere.com/paper/PMC12953700