# Aberrant maintenance of developmental transcription factor PAX6 promotes neuronal cell death via JNK3 signaling

**Authors:** Ji-Young Kim, Mi-Jin An, Jinho Kim, Chul-Hong Kim, Yuna Park, Geun-Seup Shin, Hyun-Min Lee, Ah-Ra Jo, Mi Jin Kim, Yujeong Hwangbo, Tae Kyung Hong, Jee Taek Kim, Uimook Choi, Jung-Woong Kim

PMC · DOI: 10.1038/s41419-026-08417-6 · Cell Death & Disease · 2026-01-29

## TL;DR

The study shows how the developmental protein PAX6, when abnormally active, contributes to nerve cell death in the retina through a stress-related signaling pathway.

## Contribution

The study reveals a novel transcriptional mechanism where PAX6, under JNK3 signaling, promotes neuronal apoptosis in mature retinal neurons.

## Key findings

- PAX6 is phosphorylated by JNK3 during excitotoxic stress, enhancing its chromatin binding.
- PAX6 and JNK3 form a complex that activates pro-apoptotic genes like Bax and Gadd45a.
- Knockdown of PAX6 or JNK3 reduces excitotoxic retinal ganglion cell death in vivo.

## Abstract

Retinal ganglion cell (RGC) degeneration is a hallmark of glaucoma and other optic neuropathies, yet the transcriptional mechanisms that drive stress-induced neuronal apoptosis remain incompletely understood. Here, we identify the developmental transcription factor PAX6 as an aberrantly sustained and stress-responsive regulator in mature retinal neurons. Upon NMDA-induced excitotoxic stress, PAX6 is phosphorylated by the neuronal stress kinase JNK3, without changes in total expression levels. In vitro kinase assays confirm direct phosphorylation of PAX6 by JNK3, while genetic ablation of JNK3 abolishes PAX6 activation. This phosphorylation enhances PAX6 chromatin binding and enables its co-recruitment with JNK3 to promoters of pro-apoptotic genes, including Bax and Gadd45a. Genome-wide ChIP-seq and transcriptomic analyses reveal that PAX6 and JNK3 form a transcriptional complex that drives apoptotic gene expression. In vivo, AAV-shRNA-mediated knockdown of either PAX6 or JNK3 significantly attenuates excitotoxic RGC death. These findings define a previously unrecognized transcriptional mechanism by which JNK3-mediated phosphorylation of persistently expressed PAX6 converts a developmental factor into a driver of neuronal apoptosis. More broadly, this study highlights how the dysregulation of developmental transcriptional programs in postmitotic neurons can contribute to neurodegeneration, offering new mechanistic insights into stress-induced neuronal loss in chronic neurodegenerative diseases.

## Linked entities

- **Genes:** PAX6 (paired box 6) [NCBI Gene 5080], MAPK10 (mitogen-activated protein kinase 10) [NCBI Gene 5602], BAX (BCL2 associated X, apoptosis regulator) [NCBI Gene 581], GADD45A (growth arrest and DNA damage inducible alpha) [NCBI Gene 1647]
- **Diseases:** glaucoma (MONDO:0005041)

## Full-text entities

- **Genes:** Mapk9 (mitogen-activated protein kinase 9) [NCBI Gene 26420] {aka JNK2, Prkm9, p54aSAPK}, Mapk8 (mitogen-activated protein kinase 8) [NCBI Gene 26419] {aka JNK, JNK1, Prkm8, SAPK1}, Trp53-ps (transformation related protein 53, pseudogene) [NCBI Gene 22060], Kat2a (K(lysine) acetyltransferase 2A) [NCBI Gene 14534] {aka 1110051E14Rik, Gcn5, Gcn5l2, mmGCN5}, Pou4f1 (POU domain, class 4, transcription factor 1) [NCBI Gene 18996] {aka Brn-3, Brn-3.0, Brn3, Brn3.0, Brn3a, E130119J07Rik}, Gadd45a (growth arrest and DNA-damage-inducible 45 alpha) [NCBI Gene 13197] {aka Ddit1, GADD45}, Mapk10 (mitogen-activated protein kinase 10) [NCBI Gene 26414] {aka C230008H04Rik, JNK3, JNK3B1, JNK3B2, SAPK(beta), Serk2}, CYCS (cytochrome c, somatic) [NCBI Gene 54205] {aka CYC, HCS, THC4}, PAX6 (paired box 6) [NCBI Gene 5080] {aka AN, AN1, AN2, ASGD5, D11S812E, FVH1}, BAX (BCL2 associated X, apoptosis regulator) [NCBI Gene 581] {aka BCL2L4}, MAPK8 (mitogen-activated protein kinase 8) [NCBI Gene 5599] {aka JNK, JNK-46, JNK1, JNK1A2, JNK21B1/2, PRKM8}, Map2k1 (mitogen-activated protein kinase kinase 1) [NCBI Gene 26395] {aka MAPKK1, MEKK1, Mek1, Prkmk1}, Jun (Jun proto-oncogene, AP-1 transcription factor subunit) [NCBI Gene 16476] {aka AP-1, Junc, c-jun}, Calb1 (calbindin 1) [NCBI Gene 12307] {aka Brain-2, CB, Calb, Calb-1}, Hipk2 (homeodomain interacting protein kinase 2) [NCBI Gene 15258] {aka 1110014O20Rik, B230339E18Rik, Stank}, 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}, GADD45A (growth arrest and DNA damage inducible alpha) [NCBI Gene 1647] {aka DDIT1, GADD45}, Chat (choline O-acetyltransferase) [NCBI Gene 12647] {aka B230380D24Rik, CHOACTase}, Mapk14 (mitogen-activated protein kinase 14) [NCBI Gene 26416] {aka CSBP2, Crk1, Csbp1, Mxi2, PRKM14, PRKM15}, Nrl (neural retina leucine zipper gene) [NCBI Gene 18185] {aka D14H14S46E}, MAPK10 (mitogen-activated protein kinase 10) [NCBI Gene 5602] {aka JNK3, JNK3A, PRKM10, SAPK1b, p493F12, p54bSAPK}, Rps6ka1 (ribosomal protein S6 kinase A1) [NCBI Gene 20111] {aka Mapkapk-1a, Rsk, Rsk-1, Rsk1, S6K-alpha-1, p90-Rsk1}, Bax (BCL2-associated X protein) [NCBI Gene 12028], Map2k6 (mitogen-activated protein kinase kinase 6) [NCBI Gene 26399] {aka MAPKK 6, MAPKK6, MEK6, MKK6, Prkmk6, SAPKK3}, Dnase1 (deoxyribonuclease I) [NCBI Gene 13419] {aka DNaseI, Dnl1}, BCL2L1 (BCL2 like 1) [NCBI Gene 598] {aka BCL-XL/S, BCL2L, BCLX, Bcl-X, PPP1R52}, Mapk1 (mitogen-activated protein kinase 1) [NCBI Gene 26413] {aka 9030612K14Rik, ERK, Erk2, MAPK2, PRKM2, Prkm1}, Pax6 (paired box 6) [NCBI Gene 18508] {aka 1500038E17Rik, AEY11, Dey, Gsfaey11, Pax-6, Sey}
- **Diseases:** neuronal apoptosis (MESH:D065703), optic neuropathies (MESH:D009901), inflammation (MESH:D007249), retinal neurodegeneration (MESH:D012164), blindness (MESH:D001766), RGC (MESH:D012173), excitotoxic injury (MESH:D014947), Glaucoma (MESH:D005901), hypoxia (MESH:D000860), calcium (MESH:D002128), excitotoxic damage (MESH:D020263), microphthalmia (MESH:D008850), congenital eye diseases (MESH:D015785), axonal injury (MESH:D001480), aniridia (MESH:D015783), excitotoxic neuronal injury (MESH:D009410), glaucomatous neurodegeneration (MESH:D019636), RGC degeneration (MESH:D012162), functional deterioration of the visual field (MESH:D014786), mitochondrial dysfunction (MESH:D028361)
- **Chemicals:** GC (MESH:C057580), water (MESH:D014867), NaCl (MESH:D012965), SP600125 (MESH:C432165), HEPES (MESH:D006531), DTT (MESH:D004229), brimonidine (MESH:D000068438), Hematoxylin (MESH:D006416), PBS (MESH:D007854), ATP (MESH:D000255), H&amp;E (MESH:D006371), sucrose (MESH:D013395), Thr (MESH:D013912), eosin (MESH:D004801), Ser (MESH:D012694), oligo dT (MESH:C027903), ethanol (MESH:D000431), EDTA (MESH:D004492), NaHCO3 (MESH:D017693), Tween-20 (MESH:D011136), beta-glycerophosphate (MESH:C031463), Triton X-100 (MESH:D017830), IGEPAL CA-630 (MESH:C010615), paraformaldehyde (MESH:C003043), glycine (MESH:D005998), BrdU (MESH:D001973), sodium citrate (MESH:D000077559), MgC12 (-), OCT (MESH:C051883), LiCl (MESH:D018021), agarose (MESH:D012685), deoxycholate (MESH:D003840), luminol (MESH:D008165), 4',6-diamidino-2-phenylindole (MESH:C007293), DEPC (MESH:D004047), SDS (MESH:D012967), IPTG (MESH:D007544), glutamate (MESH:D018698), TRIzol (MESH:C411644), calcium (MESH:D002118), NMDA (MESH:D016202), glutathione (MESH:D005978), lipid (MESH:D008055)
- **Species:** Homo sapiens (human, species) [taxon 9606], Escherichia coli BL21(DE3) (strain) [taxon 469008], Mus musculus (house mouse, species) [taxon 10090]
- **Cell lines:** /2 — Homo sapiens (Human), Colon carcinoma, Cancer cell line (CVCL_A628)

## Full text

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## Figures

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## References

3 references — full list in the complete paper: https://tomesphere.com/paper/PMC12876059/full.md

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Source: https://tomesphere.com/paper/PMC12876059