The team zeroed in on nucleus pulposus cells, the specialized cells that populate the gel-like core of each disc and are responsible for producing and maintaining its extracellular matrix. This matrix, rich in collagen II and aggrecan, gives the disc its remarkable ability to absorb compressive loads. When these cells die or stop producing healthy matrix components, the disc dehydrates, loses height, and can no longer cushion the spine effectively. Understanding what drives nucleus pulposus cells into decline is therefore a central question in disc biology, and mitochondria have emerged as key players. These organelles supply the energy the cells need to build and repair their matrix, and when mitochondria malfunction, the cells quickly deteriorate.

Cells protect themselves from damaged mitochondria through a process called mitophagy, a selective form of autophagy in which defective mitochondria are tagged and delivered to lysosomes for destruction and recycling. The best-characterized mitophagy pathway depends on two proteins, PINK1 and Parkin. When a mitochondrion loses its membrane potential, PINK1 accumulates on its outer surface and recruits Parkin, which ubiquitinates outer membrane proteins, marking the organelle for engulfment by autophagosomes marked with the lipidated form of LC3, known as LC3II. The cargo receptor p62, encoded by the SQSTM1 gene, helps bridge the tagged mitochondria to the autophagic machinery. When this system works, cellular ATP production stays healthy and damaged mitochondria do not accumulate. When it fails, dysfunctional mitochondria linger, generate reactive oxygen species, and can trigger apoptosis.

The new study examined Chromobox protein homolog 3, or CBX3, a component of heterochromatin protein 1 complexes that is better known for its roles in packaging DNA and regulating gene expression during development and in cancers. Using an in vitro model of disc degeneration in which nucleus pulposus cells are stimulated with the inflammatory cytokine interleukin-1 beta, the researchers found that CBX3 levels rose sharply in the stressed cells. This observation suggested that CBX3 might not be a passive bystander in the degenerating disc but an active participant in the damage response.

To test that idea, the team used molecular tools to reduce CBX3 expression in the interleukin-1 beta-treated cells and then measured a battery of outcomes. Knocking down CBX3 significantly reduced apoptosis, as assessed by flow cytometry, and improved cell viability as measured with the CCK-8 assay. Just as importantly, the composition of the extracellular matrix shifted in a favorable direction: levels of matrix metalloproteinase 3, an enzyme that chews up matrix components, fell, while the signature disc matrix proteins collagen II and aggrecan rebounded. In other words, removing CBX3 made the stressed disc cells behave more like healthy ones, both in terms of survival and in terms of the structural proteins they produced.

The mechanism behind this rescue turned out to run directly through mitophagy. When CBX3 was depleted, the researchers documented a restoration of PINK1 and Parkin levels, an increased ratio of LC3II to LC3I, and a drop in the p62 protein, all hallmarks of enhanced autophagic flux. Immunofluorescence imaging showed greater colocalization between mitochondria, labeled with MitoTracker Red, and LC3-positive autophagosomes, indicating that more mitochondria were being actively engulfed for degradation. Consistent with improved mitochondrial quality, cellular ATP content rose in the CBX3-depleted cells. The causal chain was confirmed in the opposite direction: when the researchers applied Mdivi-1, a chemical inhibitor of mitophagy, the protective effects of CBX3 knockdown were reversed, and the cells once again showed signs of apoptosis and matrix degradation. This pharmacological experiment demonstrated that functional mitophagy was not merely correlated with the rescue but was required for it.

Having established that CBX3 suppresses mitophagy, the team then asked how a chromatin protein could influence a cytoplasmic quality-control pathway. The answer lay in sestrin 2, or SESN2, a stress-inducible protein that has previously been shown in other contexts to support PINK1-Parkin-mediated mitophagy and to balance mitochondrial turnover against apoptosis. Using chromatin immunoprecipitation, peptide pull-down assays, and luciferase reporter assays, the researchers showed that CBX3 binds to the SESN2 promoter and transcriptionally represses it in a manner dependent on H3K9me3, the trimethylation of histone 3 at lysine 9. This histone mark is a classic signature of compact, transcriptionally silent heterochromatin, and CBX3’s chromodomain is known to recognize and bind it. By depositing or stabilizing this repressive mark at the SESN2 locus, CBX3 effectively locks the door on a gene that the stressed disc cells desperately need.

The final piece of evidence came from an epistasis experiment. When the researchers silenced SESN2 in cells in which CBX3 had already been knocked down, the benefits of CBX3 depletion disappeared. Apoptosis returned, matrix degradation resumed, and the mitophagy markers fell back toward their stressed baseline. This result places SESN2 squarely downstream of CBX3 in the pathway: CBX3 acts as a brake on SESN2 transcription, and loss of SESN2 in turn weakens PINK1-Parkin mitophagy, leaving mitochondria damaged, ATP production compromised, and the cell vulnerable to programmed death. The full pathway, from a histone mark to a mitochondrial recycling system to the structural integrity of the spinal disc, is now mapped in a single coherent chain.

The implications of this work extend beyond basic cell biology. Intervertebral disc degeneration affects a large fraction of the adult population and currently has few treatment options short of surgery for advanced cases. If the CBX3-SESN2-mitophagy axis operates similarly in disc tissue in vivo, it offers two attractive intervention points. Small molecules or gene-based approaches could aim to relieve CBX3-mediated repression of SESN2, or they could directly boost mitophagy in nucleus pulposus cells, an approach already being explored with compounds such as taurine and daphnetin in related studies. The finding also connects disc degeneration to a broader family of diseases in which CBX3 and the H3K9me3 machinery have been implicated, including kidney ischemia-reperfusion injury and several cancers, suggesting that epigenetic control of mitochondrial quality control may be a recurring theme in chronic degenerative conditions.

Important caveats remain. The study was conducted entirely in vitro, using interleukin-1 beta stimulation as a stand-in for the inflammatory environment of a degenerating disc, and the authors note that all data are contained within the published article. Whether CBX3 is upregulated in human disc tissue during natural degeneration, whether the same H3K9me3-dependent repression of SESN2 occurs in living discs under mechanical load, and whether restoring SESN2 expression can halt or reverse degeneration in animal models are questions that will require further work. Still, by tracing a line from a specific histone modification through a stress-response gene to the mitochondrial housekeeping that keeps disc cells alive, the study provides a mechanistically precise target for a condition that has long lacked one. For the millions of people whose discs are slowly failing, that precision may eventually translate into therapies that address the degeneration itself rather than merely its painful symptoms.

Subject of Research: Epigenetic regulation of mitophagy in intervertebral disc degeneration

Article Title: CBX3 aggravates nucleus pulposus cell apoptosis and extracellular matrix degradation in vitro via repressing SESN2-mediated mitophagy in an H3K9me3-dependent manner

Article References: Liu, X., Lei, J., Luo, P., Du, Y., Zhou, H., & Hu, P. (2026). CBX3 aggravates nucleus pulposus cell apoptosis and extracellular matrix degradation in vitro via repressing SESN2-mediated mitophagy in an H3K9me3-dependent manner. Molecular Biology Reports, 53(1), Article 1611. https://doi.org/10.1007/s11033-026-12744-4

Image Credits: AI Generated

DOI: 10.1007/s11033-026-12744-4

Keywords: intervertebral disc degeneration, CBX3, SESN2, mitophagy, PINK1, Parkin, H3K9me3, nucleus pulposus cells, apoptosis, extracellular matrix, epigenetics, back pain