Our previous studies demonstrated that the fat mass and obesity-associated protein (FTO) is upregulated in colorectal cancer (CRC). It demethylates G6PD/PARP1 and SLC7A11/GPX4 mRNAs, thereby protecting CRC from DNA damage and ferroptotic cell death. However, the mechanisms underlying FTO upregulation in CRC remain unclear. Unexpectedly, we show Ubiquitin-specific peptidase 30 (USP30) binds serine/glycine and senses their levels to protect FTO from proteosome degradation. Stabilized FTO demethylates 3-phosphoglycerate dehydrogenase (PHGDH) and phosphoserine aminotransferase 1 (PSAT1) mRNAs and inhibits their degradation in an m6A-YTHDF2-dependent manner, thereby promoting serine synthesis and CRC tumor growth. Furthermore, we identify sodium 2, 2-dichloroacetate (DCA) as a novel inhibitor of USP30, and DCA inhibits CRC serine synthesis and tumor growth. Clinically, USP30, FTO, PHGDH, and PSAT1 levels are highly correlated in CRC tissues. This study provides mechanistic insights into how USP30 senses serine/glycine levels to regulate serine synthesis via the FTO-PHGDH/PSAT1 axis, offering a potential therapeutic strategy for targeting serine/glycine metabolism in cancer.

The role of glutamine/Nrf2-enhanced PHGDH in Cadmium-induced lactate utilization.

Transfecting neurons remains technically challenging due to their sensitivity. Conventional methods, such as Lipofectamine 2000 or Lipofectamine RNAiMAX, often result in significant cytotoxicity, which limits their utility. Although lentiviral transfection offers high efficiency, it is hindered by high costs and complex procedures. This experiment employs a small interfering RNA (siRNA)-specific transfection reagent from the Kermey company. This reagent is a novel nanoparticle-based lipid material designed for the efficient delivery of oligonucleotides, including siRNA, into a wide range of cell types. Its efficacy in achieving high transfection efficiency in neurons, however, has not yet been established. After several days of in vitro neuronal culture, researchers can perform a simple transfection procedure using this reagent to achieve robust transfection efficiency. Notably, the protocol does not require medium replacement 6-8 h post-transfection, streamlining the workflow and minimizing cellular stress. Key features • Based on Kermey's siRNA-specific transfection reagent, we present a method for efficient in vitro transfection of siRNA into primary cultured mouse cortical neurons. • No observable adverse effects are detected in the transfected neurons during the entire experiment. • This method enables consistent and efficient knockdown of the target protein. • Phosphoglycerate dehydrogenase (PHGDH) siRNA and siNC (negative control) siRNA can be transfected into neuronal cells after 72 h of in vitro culture.

Phosphoglycerate dehydrogenase deficiency is a rare neurometabolic disorder with clinical features of congenital microcephaly, psychomotor retardation, intractable seizures, and spasticity. We report a 2.5-year-old boy presenting with speech delay, seizures, microcephaly, and hyperactive behavior. Genetic testing detected a likely pathogenic homozygous variant c.1129G>A in the PHGDH gene. Parents were carrier for the detected variant. Biochemical analysis showed low serine and treatment with oral serine and glycine resulted in seizure control, followed by catchup of developmental milestones. This case illustrates the need for evaluating underlying neurometabolic causes, particularly treatable entities, in clinical presentations similar to cerebral palsy.

Enhancing cardiac serine biosynthesis mitigates the progression of dilated cardiomyopathy in mice.

ABSTRACT Plant development is a complex process governed by genetic regulatory networks in which metabolites play essential roles by modulating gene expression and cellular processes. While the functional importance of metabolites in plant development is increasingly recognized, their precise spatial and temporal accumulation patterns, which are closely tied to their mechanistic roles, remain poorly understood. This study highlights the need for high-resolution analyses finely tuned to specific developmental processes within the framework of plant developmental metabolomics. Using a Marchantia polymorpha mutant lacking 3-phosphoglycerate dehydrogenase (PGDH), an essential enzyme in serine biosynthesis and sperm formation, we demonstrated the importance of spatiotemporal metabolomics analysis. Conventional whole-organ metabolomics analysis failed to capture the difference between wild-type and mutant plants. Despite its limited resolution, however, spatial metabolomics analysis detected local metabolic changes caused by the mutation. Our results highlight the necessity of focusing on local metabolic alterations to better understand the influence of metabolism on plant development. This study illustrated how high-resolution spatial metabolomics analysis can provide new insights into the metabolic processes underlying plant development. Our findings highlight the need to refine metabolomics tools to better capture the spatial and temporal dynamics of metabolism during plant development, with broad implications for plant biology.

BackgroundUlcerative colitis (UC) is a chronic inflammatory bowel disorder with increasing incidence globally. However, the understanding of UC pathogenesis remains limited.MethodsDSS-induced UC mouse model and lipopolysaccharide (LPS)-treated colonic epithelial cell (CEC) model were established. The pathological changes in colons were evaluated by hematoxylin and eosin. Colon injury was graded by pathological scoring, evaluation of colon length and disease activity index. qRT-PCR, Western blot, immunofluorescent staining, and ELISA assay were used to detect the expression and secretion of key molecules. CCK-8 was employed to monitor cell viability. The m6A modification of phosphoglycerate dehydrogenase (PHGDH) was assessed by MeRIP assay, and the SUMOylation of PHGDH, as well as the association between PHGDH and ubiquitin conjugating enzyme 9 (UBC9), were detected by co-immunoprecipitation.ResultsPHGDH knockdown alleviated DSS-induced colitis in mice. Inhibiting PHGDH promoted autophagy and inhibited inflammation in DSS-induced colitis and LPS-treated CECs. Methyltransferase-like 3 (METTL3) mediated m6A modification of PHGDH in LPS-treated CECs. PHGDH overexpression reversed METTL3 knockdown-facilitated autophagy in the in vitro UC model. Additionally, UBC9-mediated SUMOylation regulated PHGDH protein stability in vitro. Enhanced SUMOylation of PHGDH rescued LPS-impaired cell viability via promoting autophagy. METTL3 inhibited autophagy in LPS-treated CECs by regulating UBC9/PHGDH axis. METTL3 knockdown and UBC9 overexpression synergistically alleviated DSS-induced colon injury. Furthermore, curcumin promoted autophagy via modulating METTL3/UBC9/PHGDH axis, thereby alleviating colonic damage in ulcerative colitis.Conclusionm6A modification and SUMOylation of PHGDH regulated UC through Beclin-1-dependent autophagy.Supplementary informationThe online version contains supplementary material available at 10.1007/s00018-025-05970-9.

Dietary sulfur amino acid restriction (SAAR) improves whole-body glucose homeostasis, elevates liver insulin action, and lowers liver triglycerides. These adaptations are associated with an increased expression of hepatic de novo serine synthesis enzymes, phosphoglycerate dehydrogenase (PHGDH) and phosphoserine aminotransferase 1 (PSAT1). This study tested the hypothesis that enhanced hepatic serine synthesis is necessary for glucose and lipid adaptations to SAAR. Hepatocyte-specific PSAT1 knockout (KO) mice and wild type (WT) littermates were fed a high-fat control or SAAR diet. In WT mice, SAAR increased liver PSAT1 protein (~70-fold), serine concentration (~2-fold), and 13C-serine (~20-fold) following an intravenous infusion of [U-13C]glucose. The elevated liver serine and partitioning of circulating glucose to liver serine by SAAR were attenuated in KO mice. This was accompanied by a blunted improvement in glucose tolerance in KO mice fed a SAAR diet. Interestingly, SAAR decreased liver lysine lactoylation, a SAA-supported post-translational modification known to inhibit PHGDH enzymatic activity. This suggests dietary SAAR may increase serine synthesis, in part, by lowering lysine lactoylation. Beyond glucose metabolism, dietary SAAR reduced body weight, adiposity, and liver triglycerides similarly in WT and KO mice. Collectively, these results demonstrate that hepatic PSAT1 is necessary for glucose, but not lipid, adaptations to SAAR.

Energy generation from oil, gas, or coal fired power plants results in significant CO2 emissions which are only expected to increase in the future. For such static point sources, monoethanolamine (MEA) represents an effective solvent for post combustion CO2 capture via gas scrubbing. Meanwhile, MEA finds additional industrial uses, including in detergents, emulsifiers, polishes, pharmaceuticals, and cosmetics. Since current methods for MEA production are energy intensive and unsustainable, this study investigated the systematic engineering of Escherichia coli for direct MEA biosynthesis from glucose. First, endogenous production of precursor serine was enhanced by i) deregulating feedback inhibition at phosphoglycerate dehydrogenase, ii) deleting multiple native serine deaminases and ethanolamine-ammonia lyase to prevent degradation, and iii) optimizing the carbon/nitrogen ratio in the culture medium. Two plant-derived serine decarboxylases (from Spinacia oleracea and Arabidopsis thaliana) were then evaluated with respect to their relative heterologous activity, of which the latter displayed the greatest activity in E. coli resting cells. The final engineered strain ultimately produced up to 515 mg/L MEA in shake flasks, and up to ~2.4 g/L MEA in a benchtop fed batch bioreactor. The collective data suggest that future improvements in MEA production should be possible via continued strain engineering to enhance the supply of precursor serine.

With the improvement of living standards, people's awareness of health care is becoming stronger and stronger. Rabbit meat is a very high-quality and healthy meat, but its consumption is low due to its poor flavor. To explore the regulatory mechanism of nutrition on the meat quality of rabbits, twenty-four rabbits were fed a control diet or a high-fat (5 percent lard) diet over 15 days. The contents and tissues of the jejunum were subjected to 16S sequencing and mRNA transcriptome sequencing, respectively. The results indicated that there were significant differences in species diversity through beta diversity analysis (p < 0.05). The diversity of alpha in the experimental group was also significantly reduced (p < 0.05). Based on gene function annotation, 8 bacteria at the phylum level and 11 bacteria at the genus level that are related to the metabolism of adipose tissue showed significant differences between the two groups (p < 0.05). The transcriptome results of the jejunum showed significant differences in 135 genes between the experimental group and control group (p < 0.05). Gene annotation revealed 10 differentially expressed genes related to fat metabolism, which regulate 36 signaling pathways. We speculated that Alloprevotella may influence drip loss and cooked meat rate by changing the expression of PHGDH through correlation analysis. In addition, Coprococcus may influence IMF by changing the expression of NEDD4, ANGPTL3, and CYP8B1. These results indicated that a high-fat diet changed the species and composition of bacteria in the rabbit jejunum. Alloprevotella and Coprococcus may influence rabbit meat quality and flavor by changing PHGDH, NEDD4, ANGPTL3, and CYP8B1 gene expression in the host. This study laid a molecular foundation for the improvement of rabbit meat quality through nutritional diets.

DNA-encoded libraries (DELs) have emerged as an effective and efficient selection strategy for lead compound discovery in academia and industry over the past few decades. Despite recent advancements in this field, DEL remains limited by sensitive DNA-based constructs, particularly with low selection success rates resulting from the random selection of targets. Here, we describe a chemoenzymatic on-DNA reaction for DEL syntheses and develop a chemoproteomic-guided DEL selection platform. This platform, termed FF tags-biocatDEL, integrates DEL technology, chemoenzymatic synthesis, and fully functionalized (FF) chemical tags to match DELs with selection targets, even with limited information about ligandable hotspots. Using two diazirine-based FF indole probes, we comprehensively surveyed binding partners in cells and identified phosphoglycerate dehydrogenase (PHGDH) as a potential target for DEL selection. DEL01 and DEL02 were designed, synthesized, and selected against PHGDH, leading to the identification of a novel enzyme-active compound with an IC50 value of 2.5 μM. Our strategy, utilizing FF tags-biocatDEL, establishes a generalizable workflow for rapid target hunting and ligand discovery. It provides an effective method for precisely matching DELs with potential targets, demonstrating its significant potential as a complementary approach to drug discovery based on DELs.

PHGDH as a therapeutic node: Natural modulators from TCM, degradation pathways, and emerging TPD strategies.

PHGDH-dependent serine metabolism in astrocytes: A key regulator of oxidative stress and pyroptosis in cerebral ischemia-reperfusion injury

In previous studies, we first reported that insulin resistancetogether with 3-phosphoglycerate dehydrogenase (PHGDH) overexpression, a key enzyme involved in de novo synthesis of endogenous serine (Ser), was observed in mice with a high selenium (Se) diet. This study aimed to investigate the effect of exogenous Ser on high-Se induced insulin resistance (IR) in mice. Thirty mice were randomized into three groups fed: (1) 0.1 mg/kg Se (non-IR control group), (2) 0.8 mg/kg Se (IR control group); and (3) 0.8 mg/kg Se with Ser supplement (IR Ser-intervention group). After IR was confirmed in mice both in two groups fed with a high-Se diet for 4months, mice in the intervention group were administered with Ser (215mg/kg body weight daily) whilst mice in the other two groups with saline by gavage for another month. Then, body weight, fasting blood glucose, plasma constituents (insulin, Se, Ser, homocysteine (HCY)), plasma lipid profiles (high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), total cholesterol (TCHO), triglycerides (TG)), tissue Se levels, glucose tolerance test (GTT) and insulin tolerance test (ITT) were measured in all mice before and after Ser intervention. Furthermore, the expression profiles of key enzymes participating in Ser synthesis and metabolism in the liver, skeletal muscle, and pancreas were also analyzed. Ser supplementation significantly improved insulin sensitivity in IR mice, evidenced by a 19.34% reduction in ITT area under the curve (AUC) compared to IR controls (P < 0.05). Compared to the IR control group, lower liver, skeletal muscle, and pancreas PHGDH expression as well as lower skeletal muscle glutathione peroxidase 1 (GPX1) expression were found in mice from the IR Ser-intervention group (P < 0.01). Plasma Ser levels increased by 13.91% (P < 0.05), while plasma HCY levels decreased by 18.4% (P < 0.001) after Ser intervention. Plasma lipid profiles improved significantly with reductions of 15.35% in HDL-C, 25.64% in LDL-C, 16.08% in TCHO, and 25.64% in TG versus IR controls (P < 0.05). Oral supplementation with Ser effectively alleviates insulin resistance and lipid metabolic disturbances in mice fed a high-Se diet via feedback inhibition of PHGDH enzyme gene overexpression. These findings highlight the potential translational value of Ser as a dietary intervention to mitigate metabolic dysfunction associated with high Se conditions.

Clioquinol as a New Therapy in Epilepsy: From Preclinical Evidence to a Proof-of-Concept Clinical Study Thevissen K, Ny A, Copmans D, Tits J, Kamata K, Gielis E, Longin K, Sourbron J, Thergarajan P, Tan TH, Ali I, Jones NC, O’Brien TJ, Monif M, Semple BD, Germeys C, Frizzi B, Minniti V, Perrone S, Linster CL, Elia I, Van Den Bosch L, Cammue BPA, Voet A, Lagae L, de Witte P. Epilepsia . 2025. doi:10.1111/epi.18536. Online ahead of print Objective: Drug-resistant epilepsy (DRE) affects &gt;25 million people worldwide and is often associated with neuroinflammation. Increasing evidence links deficiency or malfunctioning of the enzyme phosphoglycerate dehydrogenase (PHGDH), which converts 3-phosphoglycerate to generate serine and the neurotransmitter glycine, with (drug-resistant) epilepsy. Moreover, PHGDH, which is primarily expressed in astrocytes within the brain, has been identified as a critical enzyme in driving macrophage polarization toward an anti-inflammatory state. Hence, PHGDH activators may be beneficial for treating DRE by exhibiting both antiseizure and anti-inflammatory activity. The objective of this study was to identify such PHGDH activators. Methods: We screened a drug repurposing library for PHGDH activators and assessed their antiseizure and anti-inflammatory properties using various zebrafish and mouse epilepsy models and explored the mechanistic consequences of activating PHGDH in a cell line, in astrocytes, and in zebrafish heads. Finally, we assessed the efficacy of clioquinol as add-on treatment in three severe DRE patients in a clinical open pilot proof-of-concept study. Results: We identified haloquinolines from a drug repurposing library as potent activators of PHGDH. The most promising haloquinoline clioquinol can increase the catalytic activity of PHGDH up to 2.5-fold, thereby increasing de novo glycine biosynthesis and resulting in reduced glutamate levels. Moreover, we show that clioquinol has PHGDH-dependent antiseizure activity as well as anti-inflammatory properties in vivo using various zebrafish and mouse epilepsy models. Finally, we demonstrate the efficacy of clioquinol as add-on treatment in severe DRE patients; two patients showed a 37%-47% reduction in seizure frequency, and all three patients noted a positive impact on quality of life and seizure severity.

Abstract Diffuse midline gliomas (DMGs) are lethal pediatric brain tumors that are driven by a K27M mutation in histone H3 (H3K27M). We do not understand how the H3K27M mutation rewires DMG metabolism to facilitate growth within the metabolic constraints imposed by the brain. For instance, the brain is deficient in the amino acid serine, which is essential for the biosynthesis of molecules critical to proliferation (nucleotides, proteins, sphingolipids, phospholipids), redox balance (glutathione), and epigenetic reprogramming (S-adenosylmethionine). Here, we demonstrate the therapeutic potential of targeting serine biosynthesis in DMGs in vivo. Specifically, using murine and patient-derived cells and patient biopsies that differed only in H3K27M status, we demonstrated that H3K27M upregulated the expression of phosphoglycerate dehydrogenase (PHGDH), the rate-limiting enzyme in serine synthesis from glucose. Next, we examined the therapeutic potential of targeting PHGDH in DMGs. Silencing PHGDH expression using ASOs or pharmacological degradation of PHGDH using a novel molecular glue (PHGDH-deg) abrogated serine synthesis from [U-13C]-glucose in patient-derived DMG cells. The resulting depletion of nucleotides, sphingolipids, phospholipids, glutathione, and S-adenosylmethionine inhibited proliferation and induced oxidative stress, leading to lipid peroxidation and cell death by ferroptosis. Notably, in vivo stable isotope tracing confirmed that PHGDH-deg penetrated the blood-brain barrier and inhibited [U-13C]-glucose metabolism to serine in mice bearing intracranial DMG xenografts. Importantly, PHGDH-deg induced tumor regression and significantly extended the survival of mice bearing intracranial DMG xenografts (BT245, 24-B7, 24-C2, QCTB-R059). Furthermore, deuterium metabolic imaging of glucose metabolism provided an early readout of response to PHGDH-deg that preceded MRI-detectable volumetric alterations and predicted extended survival in vivo. Since PHGDH-deg is brain penetrant and deuterium metabolic imaging is clinically applicable, our studies have the potential for clinical translation. In essence, we have mechanistically validated serine biosynthesis as a metabolic vulnerability and developed an integrated metabolic therapy and imaging strategy for DMGs.

Dietary serine restriction increases venetoclax efficacy in Acute Myeloid Leukemia

Targeting serine metabolism vulnerability in omipalisib-resistant acute myeloid leukemia with phosphoglycerate dehydrogenase inhibitors.

As a critical component of amino acid metabolic reprogramming, serine metabolism has been demonstrated to be enhanced in a variety of cancer types, thereby supporting tumor progression. This enhancement is primarily driven by increased expression levels and augmented enzymatic activity of serine metabolic enzymes (phosphoglycerate dehydrogenase, phosphoserine aminotransferase 1, phosphoserine phosphatase and serine hydroxymethyltransferase). However, there is still lack of comprehensive summary on the regulation of serine metabolism in cancer. In this review, we provide a systematic overview of the currently discovered and proven regulatory mechanisms of serine metabolic enzymes in cancer, focusing on three levels: transcriptional, post-transcriptional, and post-translational regulation. Specifically, transcriptional regulation encompasses three major mechanisms: (1) transcription factor-mediated gene expression control, (2) histone modifications, and (3) DNA methylation. At the post-transcriptional level, regulation is primarily achieved through (1) non-coding RNAs, (2) RNA-binding proteins, and (3) RNA modifications. Post-translational regulation is predominantly mediated through diverse protein post-translational modifications. The transcriptional and post-transcriptional mechanisms primarily modulate the expression levels of serine metabolic enzymes, while post-translational modifications exert more diverse effects by altering the activity, protein stability or cellular localization of these enzymes. These regulations collectively modulate serine metabolism to influence tumor progression, offering promising targets for tumor-specific therapeutic interventions.

Twenty-three 4-anilinoquinazoline derivatives were successfully synthesized, including six new compounds (8, 9, 12, 17, 19, 20) and seventeen known compounds. Seventeen derivatives (10-26) were evaluated for cytotoxic activity against three cancer cell lines (A549, HepG2, and SH-SY5Y) using the MTT assay. The results showed that compound 13 exhibited high selectivity toward the SH-SY5Y cell line with an IC50 value of 13.1µM, while compound 26 displayed good inhibition against A549 and SH-SY5Y with IC50 values of 24.1 and 14.8µM, respectively. The ADME analysis further indicated that compounds 13 and 26 possess favorable drug-like and pharmacokinetic properties, supporting their potential suitability for further investigation. Furthermore, molecular docking and molecular dynamics simulations were performed on these two compounds (13 and 26) targeting phosphoglycerate dehydrogenase (PHGDH). The docking results revealed that the fluorine atom exhibited halogen interactions with Tyr173, and the -NH group formed hydrogen bonds with Asp174. Additional hydrogen bond interactions were observed for the nitro group of compound 13 with Gly156 and for the amine group of compound 26 with Leu152. Other interactions were dominated by van der Waals, π-π, π-sigma, alkyl, and π-alkyl contacts with the aromatic N-anilinoquinazoline scaffold. The molecular dynamics simulation demonstrated consistent RMSD, Rg, RMSF, hydrogen bond, and binding energy profiles, confirming the stability and reliability of the PHGDH-ligand complexes in aqueous solution. Notably, compound 13 maintained more persistent hydrogen bonding interactions and induced localized flexibility around the active site compared to compound 26.