Pyridoxine-dependent epilepsy, or PDE, is caused by loss-of-function mutations in a gene called ALDH7A1. People with the disorder experience severe seizures that, remarkably, can be ameliorated by high doses of pyridoxine, better known as vitamin B6. That response has been the cornerstone of treatment for decades. Yet the vitamin does not solve everything. Psychiatric and cognitive symptoms can persist even after the seizures are controlled, leaving patients and families grappling with problems that the standard therapy does not touch. That clinical observation raised a fundamental question for the Johns Hopkins team: do those lingering symptoms arise through the same mechanism as the seizures, or through something else entirely?

To find out, the researchers engineered mice in which ALDH7A1 could be selectively removed from either the liver or from astrocytes, the star-shaped brain cells that help maintain the chemical environment surrounding neurons. This precision approach allowed the team to disentangle contributions from different organ systems in a way that a conventional whole-body knockout could not. The results were unambiguous. Mice lacking ALDH7A1 in their liver cells became more susceptible to seizures but did not develop the changes in mood and behavior seen in mice lacking the gene throughout the body. Conversely, mice lacking the gene specifically in astrocytes developed behavioral deficits without becoming any more prone to seizures.

The behavioral changes observed in the astrocyte-specific mice were detailed and telling. The animals showed depressive-like behavior, reduced motivation, passive coping and decreased self-care — a constellation of deficits that mirrors the psychiatric burden reported by people with PDE whose seizures are well managed. The researchers traced these changes to a disruption of the normal antioxidant defenses that help cells manage reactive molecules and maintain normal function. In the astrocytes lacking ALDH7A1, that protective machinery faltered, and the disruption was associated with reduced activity among neurons in the prelimbic cortex, a brain region known to be involved in regulating emotional behavior.

That mechanistic chain — gene loss in astrocytes, weakened antioxidant defenses, disturbed redox balance, altered neuronal activity in an emotion-regulating circuit — gave the team a concrete therapeutic target. Because antioxidant defenses can help maintain the balance of reactive molecules in cells, the researchers turned to sulforaphane, an antioxidant compound found in broccoli sprouts that is known to activate NRF2, a cellular pathway that helps protect cells from oxidative stress. When the researchers incorporated sulforaphane into the mice’s diet, it increased NRF2 levels in the ALDH7A1-deficient astrocytes, suggesting increased antioxidant protection and an improved redox balance within the affected brain cells.

Crucially, the compound’s effects were selective. Sulforaphane did not correct the increased seizure susceptibility associated with loss of ALDH7A1 throughout the body. That distinction, the researchers say, provided additional evidence that the psychiatric and seizure symptoms are driven by separate mechanisms, with the psychiatric changes linked to astrocytes in the brain and seizure susceptibility linked to dysfunction involving the liver. For a field that has often treated a genetic mutation as a single point of failure, the finding is a powerful demonstration that one gene can produce distinct disease processes in different tissues.

“An important implication of this work is that the symptoms we see in a rare neurological disorder do not necessarily have to come from the same place or through the same mechanism,” says Akira Sawa, M.D., director of the Johns Hopkins Schizophrenia Center and professor of psychiatry and behavioral sciences at Johns Hopkins Medicine. “In this case, we found that the liver and brain each make distinct contributions to the disease, which gives us a much clearer picture of how these symptoms arise.”

The separation of mechanisms also reframes how the psychiatric burden of PDE might be treated. Vitamin B6 remains the standard for controlling seizures, but sulforaphane could potentially be added to treatment to address the psychiatric symptoms associated with the disorder. “The fact that sulforaphane could improve the psychiatric phenotype while not preventing seizures was especially informative,” says Sawa. “It suggests that targeting the biology of the brain directly may be able to address psychiatric symptoms that persist even when the seizures themselves are controlled.”

The study adds to a growing body of evidence that neurological and psychiatric symptoms arising from the same genetic mutation can stem from distinct biological and metabolic processes. That principle may extend well beyond PDE. If a single inherited mutation can produce seizures through liver-centered metabolic dysfunction and mood and motivational deficits through astrocyte redox imbalance in the brain, then other neurodevelopmental and neuropsychiatric conditions may similarly harbor organ-specific mechanisms that have been blurred together under a single diagnosis. Dissecting those mechanisms, as this study did with tissue-selective genetic engineering, could open the door to therapies aimed at each pathway individually rather than at the gene in the abstract.

The researchers caution that much work remains before sulforaphane reaches the clinic. The findings provide a foundation for further study of the compound as a potential supplemental treatment for psychiatric symptoms associated with pyridoxine-dependent epilepsy, but future research will be needed to determine whether targeting astrocyte redox imbalance can improve these symptoms in people with the disorder. Mechanism-driven clinical trials of sulforaphane represent a potential next step, and any such trials would need to establish whether the NRF2 activation seen in mice translates safely and effectively to human patients. The federally funded study was supported by the National Institute of Mental Health and the National Institute on Drug Abuse. Researchers from the Johns Hopkins University School of Medicine departments of neuroscience, psychiatry and behavioral sciences, physiology, pharmacology and therapeutics, biomedical engineering and genetic medicine led the work, with collaborators from the National Institute on Drug Abuse Intramural Research Program, Heidelberg University and the University of Maine. For now, the study stands as a vivid example of how a humble broccoli-sprout compound, guided by rigorous mechanistic science, can illuminate the hidden architecture of a rare disease — and perhaps point the way toward treating the symptoms that medicine has long left behind.

Subject of Research: Distinct liver and brain mechanisms underlying seizures and psychiatric symptoms in pyridoxine-dependent epilepsy

Article Title: Study reveals both liver and brain pathways in differing symptoms of inherited metabolic disorder

Article References: Study reveals both liver and brain pathways in differing symptoms of inherited metabolic disorder. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: pyridoxine-dependent epilepsy, ALDH7A1, astrocytes, liver, sulforaphane, NRF2, oxidative stress, vitamin B6, seizures, psychiatric symptoms, Johns Hopkins, Science Advances

Reactive oxygen species, or ROS, include free radicals such as superoxide and hydroxyl radicals as well as non-radical species like hydrogen peroxide and singlet oxygen. They arise from endogenous sources, chiefly mitochondrial metabolism, and from exogenous exposures including ultraviolet radiation, pollutants and drugs. In healthy cells, ROS act as essential signaling molecules, but when their production outpaces the cell’s antioxidant defenses, oxidative stress ensues. The review emphasizes that this imbalance is a hallmark of cancer cells, which typically generate more localized ROS than their normal counterparts due to elevated metabolic activity, mitochondrial dysfunction, oncogene activation and increased activity of oxidases, cyclooxygenases and lipoxygenases.

The consequences of excess ROS reach far beyond simple DNA breakage. Hydroxyl radicals can attack purines and pyrimidines, producing base modifications such as 8-oxo-7,8-dihydroguanine, one of the most reliable biomarkers of oxidative DNA damage. In normal human cells, 8-oxoGua adducts form at a rate of roughly one per 100,000 guanine residues, but in smokers this rate rises by more than 30 percent, and patients with lung, breast or prostate cancer show levels approximately 50 percent higher than healthy individuals. When repair mechanisms such as 8-oxoguanine glycosylase fail under persistent oxidative stress, mutations accumulate in critical genes including the RAS oncogene and the TP53 tumor suppressor, fueling genomic instability and malignant transformation.

Perhaps the most compelling section of the review concerns the epigenetic consequences of oxidative stress. ROS can drive both global DNA hypomethylation and site-specific hypermethylation of tumor suppressor gene promoters, a pattern reversal that is characteristic of cancer cells. The mechanistic links are intricate: oxidative stress alters the activity of DNA methyltransferases and histone modifiers, while depletion of glutathione reduces levels of S-adenosylmethionine, the universal methyl group donor required by DNA methyltransferases and histone methyltransferases. The oxidized base lesion 8-hydroxydeoxyguanosine interferes with methyltransferase binding to nearby cytosines, and hydroxylation of 5-methylcytosine to 5-hydroxymethylcytosine can reduce cytosine methylation by as much as 90 percent, according to work by Valinluck and Sowers cited in the review.

The authors also describe how hydrogen peroxide exposure recruits DNMT1 to damaged chromatin, where it joins complexes containing DNMT3B, sirtuins and members of the polycomb repressive complex 4, leading to silencing marks such as H3K27me3 and loss of active marks like H3K4me3 and H4K16ac. In kidney epithelial cells, chronic oxidative stress converted normal cells into cancerous ones, altering the expression of DNMT1, DNMT3a, MBD4, HDAC1, HMT1 and HAT1, and this malignant phenotype was partially reversed by treatment with the demethylating agent 5-aza-2′-deoxycytidine, underscoring the reversibility of the epigenetic machinery. Similar ROS-driven methylation changes have been documented for tumor suppressor genes such as RUNX3 in colorectal cancer and p16 in the progression from Barrett’s esophagus to esophageal adenocarcinoma.

ROS also orchestrate inflammation and immune evasion, two processes intimately entwined with epigenetics. Elevated ROS activates signaling cascades including NF-kB, MAPK, STAT3 and PI3K/AKT, promoting uncontrolled proliferation, angiogenesis and epithelial-mesenchymal transition, the program by which cancer cells acquire migratory and invasive properties. At the same time, ROS suppresses T cells and natural killer cells and skews macrophages toward an M2 phenotype that supports tumor vascularization. The Nrf2-KEAP1 pathway emerges as a double-edged sword: in normal cells, Nrf2 activation induces phase II detoxification and antioxidant enzymes, but in established cancers, sustained Nrf2 activation confers drug resistance and cellular immortality.

This duality is precisely where polyphenols display their therapeutic versatility. Compounds such as sulforaphane from cruciferous vegetables, curcumin from turmeric, epigallocatechin-3-gallate from green tea, genistein from soy, quercetin from onions and apples, and resveratrol from grapes and berries can each act as either antioxidant or pro-oxidant depending on context and concentration. As antioxidants, they activate Nrf2, promote its nuclear localization and stimulate the synthesis of glutathione S-transferase, heme oxygenase 1, NADPH quinone oxidoreductase, catalase and superoxide dismutase, thereby neutralizing ROS before they can damage the epigenome. As pro-oxidants, they raise ROS levels in drug-resistant cancer cells, inhibit Nrf2 and trigger apoptosis, sensitizing tumors to chemotherapy.

The epigenetic footprints of individual polyphenols are strikingly specific. Sulforaphane inhibited DNMT1 and DNMT3a in breast cancer cells, downregulated the telomerase reverse transcriptase hTERT, and remodeled chromatin at the hTERT promoter with increased H3K9 acetylation and decreased H3K9 and H3K27 trimethylation. Curcumin reversed hypermethylation of the glutathione S-transferase pi 1 promoter in MCF-7 breast cancer cells, re-expressed the hypermethylated BRCA1 gene through TET1-mediated demethylation, upregulated miR-15a and miR-16 to suppress the anti-apoptotic protein Bcl-2, and even reversed multidrug resistance in colorectal cancer cells by increasing ROS and diminishing Nrf2 expression. Genistein demethylated and reactivated p16INK4a and BTG3, while EGCG reactivated the silenced tumor suppressors p16INK4a, p21CIP/WAF1 and Wnt inhibitory factor 1 through promoter demethylation and histone acetylation changes.

The review is candid about the obstacles standing between laboratory promise and clinical practice. Most of the evidence comes from in vitro models, and animal studies must precede any prescription in clinical settings. Polyphenols suffer from poor water solubility and low oral bioavailability, although bio-based nanocarriers, including polymeric nanoparticles, nanocrystals, cyclodextrins, nano-caseins and electrospun nanofibers, are being developed to overcome these limitations. Dosing also demands caution: low concentrations of quercetin reduced ROS and antagonized the pro-oxidant mechanism of cisplatin in ovarian cancer cells, potentially undermining treatment, while high doses of green tea catechins have been associated with hepatotoxicity and worsened colon carcinogenesis in experimental animals. A study by Salvador and colleagues further showed that ROS-generating therapeutic agents can be more toxic to normal cells than to p53-negative tumors, highlighting the need to select agents and doses that spare healthy tissue.

Even with these caveats, the synthesis offered by Raina and colleagues is a compelling case that the epigenetic damage wrought by oxidative stress is not a one-way street. Because epigenetic modifications are inherently reversible, and because polyphenols can simultaneously scavenge ROS, modulate Nrf2, dampen NF-kB-driven inflammation and recalibrate DNA methyltransferases, histone acetyltransferases and histone deacetylases, these dietary compounds occupy a uniquely favorable position in the search for chemopreventive and chemosensitizing agents. The authors call for further research into the biological processes underlying ROS-induced epigenetic alterations, the interaction between polyphenols and the gut microbiome, and the precise concentrations required for anti-cancer effects. If those questions can be answered, the humble molecules found in broccoli, turmeric, green tea and grapes may yet earn a place alongside conventional therapies in the oncologist’s arsenal.

Subject of Research: ROS-induced epigenetic alterations in carcinogenesis and their reversal by dietary polyphenols

Article Title: Polyphenols reverse ROS induced epigenetic alterations in the process of carcinogenesis

Article References: Raina, R., Bhatt, R., Hussain, A., Afroze, N., & Hussain, A. (2025). Polyphenols reverse ROS induced epigenetic alterations in the process of carcinogenesis. Epigenetics Communications, 5(1), Article 5. https://doi.org/10.1186/s43682-025-00034-2

Image Credits: AI Generated

DOI: 10.1186/s43682-025-00034-2

Keywords: reactive oxygen species, polyphenols, epigenetics, carcinogenesis, Nrf2 pathway, DNA methylation, histone modification, sulforaphane, curcumin, EGCG, chemoprevention, oxidative stress