Frataxin Gene Emerges as Biomarker and Protective Switch in Glaucoma

Glaucoma steals sight silently. More than 11 million people worldwide live with the disease, and primary open-angle glaucoma (POAG) accounts for nearly 70 percent of all cases. Once retinal ganglion cells die and the optic nerve degenerates, the lost vision never returns. Current therapy focuses on lowering intraocular pressure with drops or surgery, yet even successfully controlled pressure does not always halt the relentless apoptosis of the neurons that carry visual signals to the brain. That therapeutic gap has pushed researchers to hunt for the molecular drivers of the disease, and a new study published in the Journal of Molecular Medicine points to an unexpected pair of players: the mitochondrial protein frataxin, known as FXN, and the master genome organizer CTCF.

The research team, led by Ziyao Liu of the Second Affiliated Hospital of Xi’an Jiaotong University, began with a simple premise. Oxidative stress, the imbalance that lets reactive oxygen species overwhelm cellular antioxidant defenses, is a well-established contributor to optic nerve degeneration. But which of the hundreds of oxidation-related genes actually matter in POAG? To find out, the investigators assembled a comprehensive set of 885 oxidative stress-related genes from the GeneCards and MSigDB databases, then mined five public transcriptomic datasets from the Gene Expression Omnibus, using optic nerve head astrocyte samples from the GSE9963 cohort as their discovery set.

The screening pipeline was deliberately redundant. Weighted gene co-expression network analysis grouped genes into modules correlated with disease status, while two independent machine learning algorithms, LASSO regression and support vector machine recursive feature elimination, each flagged candidate genes under ten-fold cross-validation. When the three approaches were intersected, only two genes survived: FXN and CYP1B1. Of these, FXN proved the sharper diagnostic blade. Receiver operating characteristic analysis in the discovery cohort yielded an area under the curve of 0.945 for FXN, far exceeding CYP1B1’s 0.700, and the result held up across four independent validation datasets with AUC values ranging from 0.708 to 0.946.

A diagnostic meta-analysis pooling the five datasets strengthened the case further. Elevated FXN expression was significantly associated with POAG status, with an overall odds ratio of 6.35. Notably, FXN levels tracked with disease sample type but not with race, gender, or age, suggesting the signal reflects disease biology rather than demographic confounders. Bioinformatic characterization placed the protein in the cytosol and mitochondria, consistent with its known role in mitochondrial iron transport and respiration, and the team retrieved its three-dimensional structure from the AlphaFold database to support future drug design efforts.

The immune dimension added another layer of intrigue. CIBERSORT deconvolution showed that POAG samples with high FXN expression differed in estimated immune cell abundance, with M1 and M2 macrophage subtypes significantly reduced in the discovery cohort. Single-sample gene set enrichment analysis linked high FXN expression to signatures including antigen-presenting cell function, chemokine receptor interaction, and inflammation promotion, although these immune associations were less consistent across the validation cohorts. Metabolic profiling told a clearer story: gene set enrichment analysis repeatedly tied high FXN expression to glycolysis and pyruvate metabolism gene sets, hinting that FXN may participate in the metabolic reprogramming that accompanies glaucomatous degeneration.

Bioinformatics alone, however, could not establish causation. The team turned to an in vitro model in which retinal ganglion cell-derived R28 cells are injured by a 12-hour exposure to 200 micromolar hydrogen peroxide, a widely used simulation of oxidative stress injury in glaucoma research. Interestingly, while FXN was upregulated in patient tissue samples, hydrogen peroxide sharply decreased FXN expression in the cultured cells. That inverse response suggested a defensive role: the stressed cells were losing a protective factor. The researchers tested this by manipulating FXN with overexpression vectors and short hairpin RNAs, verifying the changes by quantitative PCR and western blot.

The functional assays were strikingly consistent. CCK8 and EdU assays showed that hydrogen peroxide suppressed cell survival, that FXN overexpression blunted this loss of viability, and that FXN knockdown made it worse. Flow cytometry using the BODIPY-C11 probe revealed that FXN overexpression significantly reduced the reactive oxygen species surge induced by peroxide treatment, while silencing FXN accelerated ROS accumulation. Annexin V staining and TUNEL assays confirmed the anti-apoptotic effect, with FXN overexpression defending cells against both early and late apoptosis. Western blots added a mechanistic clue: FXN overexpression increased levels of the antioxidant proteins NRF2, HO-1, and SOD1, while knockdown decreased them, indicating that frataxin bolsters the cell’s endogenous antioxidant defenses.

The deeper question was who controls FXN in the first place. Mining the hTFtarget and GeneCards databases produced four candidate transcription factors: MAX, YY1, RAD21, and CTCF. Cross-referencing public knockdown data from the KnockTF database and expression correlations in the discovery dataset narrowed the field, and PCR experiments in R28 cells delivered the verdict: only silencing CTCF downregulated FXN. CTCF, a zinc-finger protein famous for organizing chromatin into loops and insulating genes from inappropriate regulatory influences, emerged as the upstream switch. Chromatin immunoprecipitation sealed the argument, showing that CTCF antibody pulled down the FXN promoter sequence spanning bases 1797 to 1815 upstream of the transcription start site, one of four predicted binding sites.

The rescue experiments tied the axis together. CTCF expression itself dropped in the hydrogen peroxide model, mirroring FXN. Overexpressing CTCF preserved cell viability, reduced ROS accumulation, and curbed apoptosis just as FXN overexpression did, but when the researchers simultaneously knocked down FXN, much of that protection evaporated. In other words, CTCF shields retinal ganglion cells largely by switching on frataxin. Because CTCF is a global regulator, the team also intersected their 125 oxidative stress-related differentially expressed genes with predicted CTCF targets and found 79 overlaps, suggesting the CTCF-FXN axis may sit within a broader oxidative stress transcriptional network in POAG.

The authors are candid about the limitations. There is no animal model yet, the acute hydrogen peroxide model cannot fully reproduce the chronic oxidative environment of human glaucoma, and the regulatory mechanism still needs confirmation through promoter mutation assays and in vivo work. The immune findings require experimental validation, and whether FXN directly modulates mitochondrial ROS production remains open. Even so, the study delivers something glaucoma research has lacked: a biomarker with validated diagnostic performance across multiple cohorts, a plausible mechanistic story connecting oxidative stress, mitochondrial biology, and chromatin regulation, and a therapeutic hypothesis that could be tested. If frataxin’s protective power holds up in living retinae, the CTCF-FXN axis may become more than a molecular curiosity. It could become a target, and for a disease that currently can only be slowed, that would be a genuinely new frontier.

Subject of Research: The role of the CTCF-FXN regulatory axis in oxidative stress, diagnosis, and progression of primary open-angle glaucoma

Article Title: CTCF-FXN regulatory axis plays critical roles in clinical assessments and disease progression of primary open-angle glaucoma

Article References: Cai, D., Yu, Y., Ma, J., Li, T., & Liu, Z. (2026). CTCF-FXN regulatory axis plays critical roles in clinical assessments and disease progression of primary open-angle glaucoma. Journal of Molecular Medicine, 104(1), Article 114. https://doi.org/10.1007/s00109-026-02717-2

Image Credits: AI Generated

DOI: 10.1007/s00109-026-02717-2

Keywords: primary open-angle glaucoma, FXN, frataxin, CTCF, oxidative stress, retinal ganglion cells, reactive oxygen species, biomarker, transcriptional regulation, machine learning, mitochondria, neurodegeneration