Serine Pathway Research Articles

Exertional Exhaustion (Post-Exertional Malaise, PEM) Evaluated by the Effects of Exercise on Cerebrospinal Fluid Metabolomics–Lipidomics and Serine Pathway in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome

Post-exertional malaise (PEM) is a defining condition of myalgic encephalomyelitis (ME/CFS). The concept requires that a provocation causes disabling limitation of cognitive and functional effort (“fatigue”) that does not respond to rest. Cerebrospinal fluid was examined as a proxy for brain metabolite and lipid flux and to provide objective evidence of pathophysiological dysfunction. Two cohorts of ME/CFS and sedentary control subjects had lumbar punctures at baseline (non-exercise) or after submaximal exercise (post-exercise). Cerebrospinal fluid metabolites and lipids were quantified by targeted Biocrates mass spectrometry methods. Significant differences between ME/CFS and control, non-exercise vs. post-exercise, and by gender were examined by multivariate general linear regression and Bayesian regression methods. Differences were found at baseline between ME/CFS and control groups indicating disease-related pathologies, and between non-exercise and post-exercise groups implicating PEM-related pathologies. A new, novel finding was elevated serine and its derivatives sarcosine and phospholipids with a decrease in 5-methyltetrahydrofolate (5MTHF), which suggests general dysfunction of folate and one-carbon metabolism in ME/CFS. Exercise led to consumption of lipids in ME/CFS and controls while metabolites were consumed in ME/CFS but generated in controls. In general, the frequentist and Bayesian analyses generated complementary but not identical sets of analytes that matched the metabolic modules and pathway analysis. Cerebrospinal fluid is unique because it samples the choroid plexus, brain interstitial fluid, and cells of the brain parenchyma. The quantitative outcomes were placed into the context of the cell danger response hypothesis to explain shifts in serine and phospholipid synthesis; folate and one-carbon metabolism that affect sarcosine, creatine, purines, and thymidylate; aromatic and anaplerotic amino acids; glucose, TCA cycle, trans-aconitate, and coenzyme A in energy metabolism; and vitamin activities that may be altered by exertion. The metabolic and phospholipid profiles suggest the additional hypothesis that white matter dysfunction may contribute to the cognitive dysfunction in ME/CFS.

P0146 Phosphoglycerate dehydrogenase plays a vital role in ER-stress-related intestinal inflammation

Abstract Background Inflammatory Bowel Disease (IBD) is characterized by chronic inflammation and metabolic dysregulation in the intestinal epithelium. Serine, a non-essential amino acid synthesized via the rate-limiting enzyme phosphoglycerate dehydrogenase (PHGDH) maintains cellular redox balance. Serine metabolism is upregulated in cancer and immune cells, supporting survival and growth. Our previous story shows ER stress-mediated rewiring of serine metabolism is a key molecular feature in IBD. However, the mechanism of how it influences ER stress in IBD remains unclear. Methods To explore the molecular regulation of de novo serine synthesis via PHGDH, we used murine intestinal epithelial cells (Mode-K cells) and murine intestinal organoids. WB and IHC were performed in vivo to analyze ER stress and PHGDH on DSS colitis model. Mode-K cells were subjected to serine starvation and co-treated with LPS. Proinflammatory cytokines (Cxcl1, Tnfα, Il6) were evaluated by qPCR and ELISA. Metabolic supplement formate and hypoxanthine were tested to mitigate hyperinflammation. Total starvation was assessed by using serine deprivation medium and PHGDH inhibitor BI-4916. Tunicamycin, NAC, Y27632, and rapamycin were used to study the biofunction under ER stress effect by using qPCR, WB, and IF. Cell viability was performed by CellTiter-Glo® 2.0 Cell Viability Assay. RNA sequencing and proteomic analyses were performed to investigate molecular mechanisms. Clinical analysis of PHGDH was assessed in two cross-sectional IBD cohorts correlating PHGDH expression with endoscopic or clinical disease activity. Results We show elevated ER stress and de novo serine synthesis in DSS colitis model. Using total starvation to completely block serine pathway, we observed increased ER stress which subsequently leads to dramatically enhanced inflammation signature under LPS treatment. ER stress induced by total starvation also leads to mitochondria dysfunction as assessed by Seahorse and JC-1 assay. By using cell viability assay and IF, we show ER stress induces AIF-mediated anoikis. Autophagy induced by ROS under ER stress conditions can protect cells from anoikis and inflammation. Combining RNAseq and proteomic analysis, we identified CEBPB as the critical regulator in mediating cellular anoikis and inflammation during ER stress which were further confirmed by IF and qPCR. Finally, we observed unregulated PHGDH in IBD patients showing a strong association between serine metabolism and IBD severity. Conclusion In this study, we demonstrate the critical roles of PHGDH and Serine metabolism in regulating cellular inflammatory responses under ER stress. Notably, we reveal a protective role of ROS in ER stress and inflammation, providing new insights into ER stress and IBD severity.

Differences in the composition of plasma metabolites and intestinal flora of piglets with different weaning weights revealed by untargeted metabolomics and 16S rRNA gene sequencing.

Piglets with different weaning body weights exhibit varying growth performance. This study explores the relationship between their plasma metabolites and gut microbiota to reveal differences in metabolic regulation and microbial composition. Plasma and colon content samples from piglets of different weaning weights were collected. Untargeted metabolomics, 16S rRNA gene sequencing, multivariate statistics, and bioinformatics were used to identify and compare metabolites. Six key findings emerged. First, 23 differential metabolites were found, with three upregulated in high-weight piglets and 20 downregulated in low-weight piglets. A total of 15 were lipids or lipid-like molecules. Second, metabolic pathway enrichment analysis indicated that the sphingolipid signaling pathway, HIF-1 signaling pathway, sphingolipid metabolism pathway, ascorbate and aldarate metabolism pathway, and glycine, serine, and threonine metabolism pathway were the most significantly affected pathways in the plasma of piglets with different weaning body weights. Third, alpha diversity was lower in low-weight weaned piglets. Fourth, Lactobacillus was 23.16% in high-weight piglets, higher than 19.62% in low-weight ones. Fifth, linear discriminant analysis effect size (LEfSe) analysis showed that Faecalibacterium is a biomarker for low-body-weight piglets and Oscillospira is a biomarker for high-body-weight piglets. Finally, Spearman correlation analysis indicated that Lactobacillus, Prevotella, Ruminococcus, and Oscillospira were negatively correlated with differential metabolites in plasma. The plasma metabolites and colon microbiota differed between piglets of different body weights. Lipid-related plasma metabolites contributed to weight variation, being lower in heavier piglets. The colonic microbiota, especially Oscillospira and Roseburia, exhibited strong correlations with these metabolites. © 2025 Society of Chemical Industry.

The Metabolome Characteristics of Aerobic Endurance Development in Adolescent Male Rowers Using Polarized and Threshold Model: An Original Research.

This study aimed to explore the molecular response mechanisms of differential blood metabolites before and after 8 weeks of threshold and polarized training models using metabolomics technology combined with changes in athletic performance. Twenty-four male rowers aged 14-16 were randomly divided into a THR group and a POL group (12 participants each). The THR group followed a threshold training model (72%, 24%, and 4% of training time in low-, moderate-, and high-intensity zones, respectively), while the POL group followed a polarized training model (78%, 8%, and 14% training-intensity distribution). Both groups underwent an 8-week training program. Aerobic endurance changes were assessed using a 2 km maximal rowing performance test, and untargeted metabolome analysis was conducted to examine blood metabolomic changes before and after the different training interventions. Aerobic endurance changes were assessed through a 2 km maximal rowing test. Non-targeted metabolomics analysis was employed to evaluate changes in blood metabolome profiles before and after the different training interventions. After 8 weeks of training, both the THR and POL groups exhibited significant improvements in 2 km maximal rowing performance (p < 0.05), with no significant differences between the groups. The THR and POL groups had 46 shared differential metabolites before and after the intervention, primarily enriched in sphingolipid metabolism, glutathione metabolism, and glycine, serine, and threonine metabolism pathways. Nine unique differential metabolites were identified in the THR group, mainly enriched in pyruvate metabolism, glycine, serine, and threonine metabolism, glutathione metabolism, and sphingolipid metabolism. A total of 14 unique differential metabolites were identified in the POL group, predominantly enriched in sphingolipid metabolism, glycine, serine, and threonine metabolism, aminoacyl-tRNA biosynthesis, and glutathione metabolism. The 8-week THR and POL training models demonstrated similar effects on enhancing aerobic performance in adolescent male rowers, indicating that both training modalities share similar blood metabolic mechanisms for improving aerobic endurance. Furthermore, both the THR group and the POL group exhibited numerous shared metabolites and some differential metabolites, suggesting that the two endurance training models share common pathways but also have distinct aspects in enhancing aerobic endurance.

Methyloraptor flagellatus gen. nov., sp. nov., novel Ancalomicrobiaceae-affiliated facultatively methylotrophic bacteria that feed on methanotrophs of the genus Methylococcus.

A morphologically conspicuous microbial association was detected in a bioreactor running in a continuous mode with methanotrophic bacteria of the genus Methylococcus and natural gas as a growth substrate. The association consisted of spherical Methylococcus cells colonized by elongated rods, which produced rosette-like aggregates and inhibited the cultivation process. An isolate of these bacteria, strain S20T, was obtained and identified as belonging to the alphaproteobacterial family Ancalomicrobiaceae but displaying only a distant relationship (93.9-95.1% 16S rRNA gene sequence similarity) to characterized members of this family. Strain S20T was represented by aerobic, motile, facultatively methylotrophic bacteria, which grew between 10 and 45°C (optimum 30-35°C) in a pH range of 4.5-8.5 (optimum pH6.0). These bacteria were capable of attaching to Methylococcus cells and breaking the integrity of methanotroph cell walls, presumably to feed on methanol. The same interaction was observed with Methylomonas species. The finished genome sequence of strain S20T consisted of a 5.0Mb chromosome and one plasmid, 0.26Mb in size; the DNA G+C content was 68.4%. The genome encoded 3 rRNA operons and∼4400 proteins including MxaFI- and XoxF-like methanol dehydrogenases, all enzymes of the serine pathway as well as a complete chemotaxis pathway, a unipolar polysaccharide adhesin, and a wide range of peptidases. The genome sequence displayed 67.20-69.56% average amino acid identity to those of earlier described Ancalomicrobiaceae species. We propose to classify these bacteria as representing a novel genus and species, Methyloraptor flagellatus gen. nov., sp. nov., with the type strain S20T (=KCTC 8649T=VKM B-3853T).

CNSC-68. SEX DIFFERENCES IN GLYCINE BIOSYNTHESIS DRIVE RESPONSES TO COMBINED NUTRIENT DEPRIVATION AND PHARMACOLOGICAL INHIBITION IN PEDIATRIC HGG

Abstract In children and adults, high-grade gliomas (HGGs) are the most common and deadly primary brain malignancies. Generally, male HGGs occur at higher incidence and demonstrate more rapid proliferation, resulting in shorter overall male survival. Obscurity of molecular mechanisms driving this phenomenon prevents implementation of clinically effective treatments. Recently, a positive correlation between HGG cellular proliferation and metabolic reprogramming toward glycine biosynthesis was identified. By analyzing pediatric and adult HGG patient data, we discovered significantly worse outcomes unique to pediatric males bearing upregulation of serine and glycine biosynthesis transcripts. Previously, we have identified differential flux of glucose into serine and glycine biosynthesis drives sex differences in lung cancer. Therefore, we sought to confirm and target this paradigm in our NF1-/- DNp53 model of HGG. By performing metabolic tracing with [13C]-labeled glucose in male and female cells, we identified higher enrichment of [13C]-labeled serine and glycine in male cells relative to female cells. Through Western blotting, we identify male-specific upregulation of serine and glycine biosynthetic pathway enzymes in transformed cells, supporting our labelling results. Next, we sought to determine if inhibition of de-novo serine and glycine biosynthesis was similarly sex-biased. Utilizing serine-and-glycine-deprived media conditions, we identified a male-biased decrease in proliferation following pharmacological inhibition of de-novo serine and glycine biosynthesis. More precisely, in the absence of exogenous glycine, we discovered that inhibition of de-novo synthesis of glycine from serine drove male-specific decreases in proliferation. Additionally, we identified that transformed female cell robustness against inhibition of glycine biosynthesis is driven by the uptake of exogenous nucleotide precursors. These data confirm that sex differences in de-novo glycine biosynthesis drive sex differences in HGG cellular proliferation. As well, our work suggests that dietary restriction of serine and glycine, in-combination with pharmacological inhibition of de-novo glycine biosynthesis, represents a novel treatment paradigm.

The ‘photosynthetic C1 pathway’ links carbon assimilation and growth in California poplar

Although primarily studied in relation to photorespiration, serine metabolism in chloroplasts may play a key role in plant CO2 fertilization responses by linking CO2 assimilation with growth. Here, we show that the phosphorylated serine pathway is part of a ‘photosynthetic C1 pathway’ and demonstrate its high activity in foliage of a C3 tree where it rapidly integrates photosynthesis and C1 metabolism contributing to new biomass via methyl transfer reactions, imparting a large natural 13C-depleted signature. Using 13CO2-labelling, we show that leaf serine, the S-methyl group of leaf methionine, pectin methyl esters, and the associated methanol released during cell wall expansion during growth, are directly produced from photosynthetically-linked C1 metabolism, within minutes of light exposure. We speculate that the photosynthetic C1 pathway is highly conserved across the photosynthetic tree of life, is responsible for synthesis of the greenhouse gas methane, and may have evolved with oxygenic photosynthesis by providing a mechanism of directly linking carbon and ammonia assimilation with growth. Although the rise in atmospheric CO2 inhibits major metabolic pathways like photorespiration, our results suggest that the photosynthetic C1 pathway may accelerate and represents a missing link between enhanced photosynthesis and plant growth rates during CO2 fertilization under a changing climate.

Interleukin 6 blockage alters the plasma metabolome in out-of-hospital cardiac arrest

BackgroundComatose patients resuscitated from out-of-hospital cardiac arrest (OHCA) exhibit a systemic inflammatory response, as indicated by elevated interleukin-6 (IL-6) levels, which is associated with increased mortality. Tocilizumab, an IL-6 receptor antagonist that reduced C-reactive protein response and markers of myocardial injury in a phase II OHCA trial. AimTo describe the early effects of tocilizumab on circulating levels of metabolites in comatose patients resuscitated from OHCA. MethodPatients from the phase-II double-blinded randomized trial (NCT: 03863015) were included in this substudy. A total of 85 comatose patients resuscitated from OHCA were randomized at the time of arrival to the hospital to either tocilizumab 8 mg/kg or placebo, of which 80 received the intervention and did not later withdraw from the study. Plasma samples before randomization and 48 h later were analyzed by a targeted metabolomics approach quantifying 60 circulating metabolites. ResultsOf 80 enrolled patients (median age 62 years (IQR: 54–72), men 66 (83 %)), 39 were randomized to tocilizumab group and 41 to placebo. Comorbidities and cardiac arrest characteristics were overall well-balanced. At hospital arrival, levels of metabolites from the tricarboxylic acid (TCA) cycle were associated with time to return of spontaneous circulation and independently with early levels of IL-6 (all p < 0.05). The early levels of medium-chain acylcarnitines were associated with age, NT-proBNP, estimated glomerular filtration rate, and marker of neurological injury (neurofilament light chain) (all p < 0.01). At 48 h, tocilizumab increased the levels of plasma amino acids, especially threonine, glycine, and serine, by more than a factor of 1.5 (p < 0.01). Two eicosanoids 15(S)-HETE and 12(S)-HETE were 1.9 times higher (p < 0.01). ConclusionBlocking the IL-6 receptor with tocilizumab early after OHCA impacts circulating metabolites, particularly those within the glycine, serine, and threonine pathways, highlighting the connection between acute systemic inflammation and metabolism. Further, early levels of TCA metabolites are independently associated with early inflammatory response and early medium-chain acylcarnitine with later markers of neurological injury.

Response mechanisms of submerged macrophytes and epiphytic biofilms to single and coexisting per-and poly-fluoroalkyl substances and antibiotics stress

Combined pollutants of per- and poly-fluoroalkyl substances (PFAS) and antibiotics are commonly found in aquatic environments. This study aimed to investigate the effects of PFAS (perfluorobutyric acid (PFBA) and perfluorooctanoic acid (PFOA)) and antibiotics (tetracycline (TC) and chloramphenicol (CAP)) on Vallisneria natans (V. natans) and their epiphytic biofilms. The changes in photosynthetic pigments and oxidative damage in V. natans were altered by these pollutants. For example, the total chlorophyll was increased from 4.64 to 8.10 mg/L due to the combined pollutant of PFOA and TC. When exposed to the combined pollutant of PFBA and TC, a concentration of malondialdehyde of 28.4 nmol/g was measured, which was significantly higher than that in the control group. For combined toxicity, the PFAS and antibiotics primarily exhibited antagonistic effects within V. natans. The glycine, serine, and threonine metabolism pathways were mainly affected by the combined stress of PFBA and TC. Single pollutants of TC and CAP were found to inhibit the uptake of nutrients by V. natans, while the coexisting antibiotics enhanced the inhibitory effects of PFBA and PFOA in combined pollutant treatments. The growth of microorganisms in the epiphytic biofilms was significantly promoted by PFBA and PFOA, whereas their growth was notably inhibited by CAP. The composition of biofilms could be altered by single and combined pollutants, with antibiotics being more likely than PFAS to change the microbial communities within the biofilms. When exposed to TC and CAP, the ACE indices decreased from 1171.5 to 466.4 and 703.8, respectively.

MYC-dependent upregulation of the de novo serine and glycine synthesis pathway is a targetable metabolic vulnerability in group 3 medulloblastoma.

Group 3 medulloblastoma (MBGRP3) represents around 25% of medulloblastomas and is strongly associated with c-MYC (MYC) amplification, which confers significantly worse patient survival. Although elevated MYC expression is a significant molecular feature in MBGRP3, direct targeting of MYC remains elusive, and alternative strategies are needed. The metabolic landscape of MYC-driven MBGRP3 is largely unexplored and may offer novel opportunities for therapies. To study MYC-induced metabolic alterations in MBGRP3, we depleted MYC in isogenic cell-based model systems, followed by 1H high-resolution magic-angle spectroscopy (HRMAS) and stable isotope-resolved metabolomics, to assess changes in intracellular metabolites and pathway dynamics. Steady-state metabolic profiling revealed consistent MYC-dependent alterations in metabolites involved in one-carbon metabolism such as glycine. 13C-glucose tracing further revealed a reduction in glucose-derived serine and glycine (de novo synthesis) following MYC knockdown, which coincided with lower expression and activity of phosphoglycerate dehydrogenase (PHGDH), the rate-limiting enzyme in this pathway. Furthermore, MYC-overexpressing MBGRP3 cells were more vulnerable to pharmacological inhibition of PHGDH compared to those with low expression. Using in vivo tumor-bearing genetically engineered and xenograft mouse models, pharmacological inhibition of PHGDH increased survival, implicating the de novo serine/glycine synthesis pathway as a pro-survival mechanism sustaining tumor progression. Critically, in primary human medulloblastomas, increased PHGDH expression correlated strongly with both MYC amplification and poorer clinical outcomes. Our findings support a MYC-induced dependency on the serine/glycine pathway in MBGRP3 that represents a novel therapeutic treatment strategy for this poor prognosis disease group.

Metabolomic profiles differentiate between porto-sinusoidal vascular disorder, cirrhosis, and healthy individuals

Background & AimsPorto-sinusoidal vascular disorder (PSVD) is a rare and diagnostically challenging vascular liver disease. This study aimed to identify distinct metabolomic signatures in patients with PSVD, cirrhosis, and healthy volunteers (HV) to facilitate non-invasive diagnosis and elucidate perturbed metabolic pathways. MethodsSerum samples from 20 HV and patients with histologically confirmed PSVD or cirrhosis were analyzed. Metabolites were measured using liquid chromatography-mass spectrometry (LC-MS). Differential abundance was evaluated with Limma’s moderated t-statistics. Artificial neural network (ANN) and support vector machine (SVM) models were developed to classify PSVD against cirrhosis or HV metabolomic profiles. An independent cohort was used for validation. ResultsA total of 283 metabolites were included for downstream analysis. Clustering effectively separated PSVD metabolomes from HV, although a subset of PSVD patients (n=5, 25%) overlapped with cirrhosis. Differential testing revealed significant PSVD-linked metabolic perturbations, including taurocholic and adipic acids, distinguishing PSVD from both HV and cirrhosis. Alterations in pyrimidine, glycine, serine, and threonine pathways were exclusively associated with PSVD. Machine learning models utilizing selected metabolic signatures reliably differentiated PSVD from HV or cirrhosis using only 4 to 6 metabolites. Validation in an independent cohort demonstrated the high discriminative ability of taurocholic acid (AUROC 0.899) for PSVD vs HV and the taurocholic acid/aspartic acid ratio (AUROC 0.720) for PSVD vs cirrhosis. ConclusionsHigh-throughput metabolomics enabled the identification of distinct metabolic profiles for differentiating PSVD, cirrhosis, and healthy individuals. Unique alterations in the glycine, serine, and threonine pathways suggest their potential involvement in PSVD pathogenesis. Impact And ImplicationsPorto-sinusoidal vascular disorder (PSVD) is a vascular liver disease that can lead to pre-sinusoidal portal hypertension in the absence of cirrhosis, with poorly understood pathophysiology and no established treatment. Our study demonstrates that analyzing the serum metabolome could reveal distinct metabolic signatures in PSVD patients, including alterations in the pyrimidine, glycine, serine and threonine pathways and potentially shedding light on the disease's underlying pathways. These findings hold potential for earlier and non-invasive diagnosis of PSVD, potentially reducing reliance on invasive procedures like liver biopsy and guiding diagnostic pathways.

242. BRD4 INHIBITION ENHANCES THE RADIOSENSITIVITY OF ESOPHAGEAL SQUAMOUS CELL CARCINOMA THROUGH REGULATING ATF3-MEDIATED SERINE AND NUCLEOTIDE SYNTHESIS

Abstract Background Radioresistance is a major culprit for radiotherapy failure in esophageal squamous cell carcinoma (ESCC). This study aimed to investigate the underlying mechanism of Brd4 in radiosensitivity of ESCC. Methods Brd2/3/4 proteins were assessed in radiosensitive and radioresistant ESCC tissues using IHC. A serial of functional experiments was performed to verify the significance of Brd4 in ESCC. RNA-seq and bioinformatics analyses were used to determine the potential downstream targets. The dual-luciferase reporter and ChIP assay were further examined the underlying regulatory mechanism among targets. Besides, we further verified the importance of ATF3-mediated serine and nucleotide metabolism in radiated ESCC cells. Results Brd4 is highly expressed in radio-resistant ESCC tissue. Knockdown of Brd4 led to increased DNA damage and cell apoptosis in irradiated ESCC cells. RNA-seq analyses exhibited that ATF3 was a potential downstream target of Brd4. The dual-luciferase reporter and ChIP assay demonstrated that Brd4 upregulated ATF3 expression via activation its promoter region. Besides, we found that ATF3 could facilitate the enzyme activities involved in serine and nucleotide biosynthesis pathway to promote radiation-induced DNA damage repair. Conclusion Brd4 facilitates ATF3 expression via binding to and activating ATF3 promoter region. Enhanced ATF3 further increases crucial enzymes activity in serine and nucleotide biosynthesis pathway to promote radiation-induced DNA damage repair. Targeting Brd4 is a promising treatment strategy to improve radiosensitivity in ESCC.

An Analysis of the Intestinal Microbiome Combined with Metabolomics to Explore the Mechanism of How Jasmine Tea Improves Depression in CUMS-Treated Rats.

Recently, research has confirmed that jasmine tea may help improve the depressive symptoms that are associated with psychiatric disorders. Our team previously found that jasmine tea improved the depressive-like behavior that is induced by chronic unpredictable mild stress (CUMS) in Sprague Dawley (SD) rats. We hypothesized that the metabolic disorder component of depression may be related to the gut microbiota, which may be reflected in the metabolome in plasma. The influence of jasmine tea on gut microbiota composition and the association with depressive-related indexes were explored. Furthermore, the metabolites in plasma that are related to the gut microbiota were identified. SD rats were treated with control or CUMS and administrated jasmine tea for 8 weeks. The 16S rRNA gene amplicon sequencing was used to analyze the gut microbiota in feces samples, and untargeted metabolomics was used to analyze the metabolites in plasma. The results found that jasmine tea significantly ameliorated the depressive behavior induced by CUMS, significantly improved the neurotransmitter concentration (BDNF and 5-HT), and decreased the pro-inflammation levels (TNF-α and NF-κB). The intervention of jasmine tea also alleviated the dysbiosis caused by CUMS; increased the relative abundance of Bacteroides, Blautia, Clostridium, and Lactobacillus; and decreased Ruminococcus and Butyrivibrio in the CUMS-treated rats. Furthermore, the serum metabolites of the CUMS-treated rats were reversed after the jasmine tea intervention, i.e., 22 were up-regulated and 18 were down-regulated, which may have a close relationship with glycerophospholipid metabolism pathways, glycine serine and threonine metabolism pathways, and nicotinate and nicotinamide metabolism pathways. Finally, there were 30 genera of gut microbiota related to the depressive-related indexes, and 30 metabolites in the plasma had a strong predictive ability for depressive behavior. Potentially, our research implies that the intervention of jasmine tea can ameliorate the depression induced by CUMS via controlling the gut flora and the host's metabolism, which is an innovative approach for the prevention and management of depression.

Epigenome-wide association study on the plasma metabolome suggests self-regulation of the glycine and serine pathway through DNA methylation

BackgroundThe plasma metabolome reflects the physiological state of various biological processes and can serve as a proxy for disease risk. Plasma metabolite variation, influenced by genetic and epigenetic mechanisms, can also affect the cellular microenvironment and blood cell epigenetics. The interplay between the plasma metabolome and the blood cell epigenome remains elusive. In this study, we performed an epigenome-wide association study (EWAS) of 1183 plasma metabolites in 693 participants from the LifeLines-DEEP cohort and investigated the causal relationships in DNA methylation–metabolite associations using bidirectional Mendelian randomization and mediation analysis.ResultsAfter rigorously adjusting for potential confounders, including genetics, we identified five robust associations between two plasma metabolites (l-serine and glycine) and three CpG sites located in two independent genomic regions (cg14476101 and cg16246545 in PHGDH and cg02711608 in SLC1A5) at a false discovery rate of less than 0.05. Further analysis revealed a complex bidirectional relationship between plasma glycine/serine levels and DNA methylation. Moreover, we observed a strong mediating role of DNA methylation in the effect of glycine/serine on the expression of their metabolism/transport genes, with the proportion of the mediated effect ranging from 11.8 to 54.3%. This result was also replicated in an independent population-based cohort, the Rotterdam Study. To validate our findings, we conducted in vitro cell studies which confirmed the mediating role of DNA methylation in the regulation of PHGDH gene expression.ConclusionsOur findings reveal a potential feedback mechanism in which glycine and serine regulate gene expression through DNA methylation.

Plantaginis Semen Ameliorates Hyperuricemia Induced by Potassium Oxonate.

Plantaginis semen is the dried ripe seed of Plantago asiatica L. or Plantago depressa Willd., which has a long history in alleviating hyperuricemia (HUA) and chronic kidney diseases. While the major chemical ingredients and mechanism remained to be illustrated. Therefore, this work aimed to elucidate the chemicals and working mechanisms of PS for HUA. UPLC-QE-Orbitrap-MS was applied to identify the main components of PS in vitro and in vivo. RNA sequencing (RNA-seq) was conducted to explore the gene expression profile, and the genes involved were further confirmed by real-time quantitative PCR (RT-qPCR). A total of 39 components were identified from PS, and 13 of them were detected in the rat serum after treating the rat with PS. The kidney tissue injury and serum uric acid (UA), xanthine oxidase (XOD), and cytokine levels were reversed by PS. Meanwhile, renal urate anion transporter 1 (Urat1) and glucose transporter 9 (Glut9) levels were reversed with PS treatment. RNA-seq analysis showed that the PPAR signaling pathway; glycine, serine, and threonine metabolism signaling pathway; and fatty acid metabolism signaling pathway were significantly modified by PS treatment. Further, the gene expression of Slc7a8, Pck1, Mgll, and Bhmt were significantly elevated, and Fkbp5 was downregulated, consistent with RNA-seq results. The PPAR signaling pathway involved Pparα, Pparγ, Lpl, Plin5, Atgl, and Hsl were elevated by PS treatment. URAT1 and PPARα proteins levels were confirmed by Western blotting. In conclusion, this study elucidates the chemical profile and working mechanisms of PS for prevention and therapy of HUA and provides a promising traditional Chinese medicine agency for HUA prophylaxis.

Unlocking the formate utilization of wild-type Yarrowia lipolytica through adaptive laboratory evolution.

Synthetic biology is contributing to the advancement of the global net-negative carbon economy, with emphasis on formate as a member of the one-carbon substrate garnering substantial attention. In this study, we employed base editing tools to facilitate adaptive evolution, achieving a formate tolerance of Yarrowia lipolytica to 1M within 2 months. This effort resulted in two mutant strains, designated as M25-70 and M25-14, both exhibiting significantly enhanced formate utilization capabilities. Transcriptomic analysis revealed the upregulation of nine endogenous genes encoding formate dehydrogenases when cultivated utilizing formate as the sole carbon source. Furthermore, we uncovered the pivotal role of the glyoxylate and threonine-based serine pathway in enhancing glycine supply to promote formate assimilation. The full potential of Y. lipolytica to tolerate and utilize formate establishing the foundation for pyruvate carboxylase-based carbon sequestration pathways. Importantly, this study highlights the existence of a natural formate metabolic pathway in Y. lipolytica.

USP9X-mediated REV1 deubiquitination promotes lung cancer radioresistance via the action of REV1 as a Rad18 molecular scaffold for cystathionine γ-lyase.

Radioresistance is a key clinical constraint on the efficacy of radiotherapy in lung cancer patients. REV1 DNA directed polymerase (REV1) plays an important role in repairing DNA damage and maintaining genomic stability. However, its role in the resistance to radiotherapy in lung cancer is not clear. This study aims to clarify the role of REV1 in lung cancer radioresistance, identify the intrinsic mechanisms involved, and provide a theoretical basis for the clinical translation of this new target for lung cancer treatment. The effect of targeting REV1 on the radiosensitivity was verified by in vivo and in vitro experiments. RNA sequencing (RNA-seq) combined with nontargeted metabolomics analysis was used to explore the downstream targets of REV1. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to quantify the content of specific amino acids. The coimmunoprecipitation (co-IP) and GST pull-down assays were used to validate the interaction between proteins. A ubiquitination library screening system was constructed to investigate the regulatory proteins upstream of REV1. Targeting REV1 could enhance the radiosensitivity in vivo, while this effect was not obvious in vitro. RNA sequencing combined with nontargeted metabolomics revealed that the difference result was related to metabolism, and that the expression of glycine, serine, and threonine (Gly/Ser/Thr) metabolism signaling pathways was downregulated following REV1 knockdown. LC-MS/MS demonstrated that REV1 knockdown results in reduced levels of these three amino acids and that cystathionine γ-lyase (CTH) was the key to its function. REV1 enhances the interaction of CTH with the E3 ubiquitin ligase Rad18 and promotes ubiquitination degradation of CTH by Rad18. Screening of the ubiquitination compound library revealed that the ubiquitin-specific peptidase 9 X-linked (USP9X) is the upstream regulatory protein of REV1 by the ubiquitin-proteasome system, which remodels the intracellular Gly/Ser/Thr metabolism. USP9X mediates the deubiquitination of REV1, and aberrantly expressed REV1 acts as a scaffolding protein to assist Rad18 in interacting with CTH, promoting the ubiquitination and degradation of CTH and inducing remodeling of the Gly/Ser/Thr metabolism, which leads to radioresistance. A novel inhibitor of REV1, JH-RE-06, was shown to enhance lung cancer cell radiosensitivity, with good prospects for clinical translation.

Multi-omics reveals the molecular mechanism of the combined toxic effects of PFOA and 4-HBP exposure in MCF-7 cells and the key player: mTORC1

With the discovery of evidence that many endocrine-disrupting chemicals (EDCs) in the environment influence human health, their toxic effects and mechanisms have become a hot topic of research. However, investigations into their endocrine-disrupting toxicity under combined binary exposure, especially the molecular mechanism of combined effects, have rarely been documented. In this study, two typical EDCs, perfluorooctanoic acid (PFOA) and 4-hydroxybenzophenone (4-HBP), were selected to examine their combined effects and molecular mechanism on MCF-7 cell proliferation at environmentally relevant exposure concentrations. We have successfully established a model to evaluate the binary combined toxic effects of endocrine disruptors, presenting combined effects in a simple and direct way. Results indicated that the combined effect changed from additive to synergistic from 1.25 × 10−8 M to 4 × 10−7 M. Metabolomics analyses suggested that exposure to PFOA and 4-HBP caused significant alterations in purine metabolism, arginine, and proline metabolism and had superimposed influences on metabolism. Enhanced combined effects were observed in glycine, serine, and threonine metabolic pathways compared to exposure to PFOS and 4-HBP alone. Additionally, the differentially expressed genes (DEGs) are primarily involved in Biological Processes, especially protein targeting the endoplasmic reticulum, and significantly impact the oxidative phosphorylation and thermogenesis-related KEGG pathway. By integrating metabolome and transcriptome analyses, PFOA and 4-HBP regulate purine metabolism, the TCA cycle, and endoplasmic reticulum protein synthesis in MCF-7 cells via mTORC1, which provides genetic material, protein, and energy for cell proliferation. Furthermore, molecular docking confirmed the ability of PFOA and 4-HBP to stably bind the estrogen receptor, indicating that they have different binding pockets. Collectively, these findings will offer new insights into understanding the mechanisms by which EDCs produce combined toxicity.

The gluconeogenesis enzyme PCK2 has a non-enzymatic role in proteostasis in endothelial cells

Endothelial cells (ECs) are highly glycolytic, but whether they generate glycolytic intermediates via gluconeogenesis (GNG) in glucose-deprived conditions remains unknown. Here, we report that glucose-deprived ECs upregulate the GNG enzyme PCK2 and rely on a PCK2-dependent truncated GNG, whereby lactate and glutamine are used for the synthesis of lower glycolytic intermediates that enter the serine and glycerophospholipid biosynthesis pathways, which can play key roles in redox homeostasis and phospholipid synthesis, respectively. Unexpectedly, however, even in normal glucose conditions, and independent of its enzymatic activity, PCK2 silencing perturbs proteostasis, beyond its traditional GNG role. Indeed, PCK2-silenced ECs have an impaired unfolded protein response, leading to accumulation of misfolded proteins, which due to defective proteasomes and impaired autophagy, results in the accumulation of protein aggregates in lysosomes and EC demise. Ultimately, loss of PCK2 in ECs impaired vessel sprouting. This study identifies a role for PCK2 in proteostasis beyond GNG.

Abstract PO5-08-06: Metabolic shift to serine pathway induced by lipids confers oncogenic properties in non-transformed breast cells

Abstract Introduction. Oncogenic factors that are local/in-breast are of great interest as they may be more specifically targetable for breast cancer prevention than systemic factors. We have identified a lipid metabolism gene signature that is enriched in breast tissue at risk for estrogen negative breast cancer (ER- BC). Utilizing the medium chain fatty acid Octanoic acid (OA) to probe lipid metabolism in non-transformed breast epithelial cells, we observed increased flux through several metabolic reactions and altered histone methylation with consequent changes in gene expression (e.g. neural genes). Neuronal signaling and regulatory circuits are observed in cancer cells of multiple origins, not just ones with ontological relationships to neurons. We hypothesize that the first and rate limiting step in the de novo serine pathway, which is catalyzed by Phosphoglycerate Dehydrogenase (PHGDH) is key to these observations. In the forward direction, PHGDH participates in the serine, one-carbon, glycine (SOG) and methionine pathways that produce the methyl donor S-adenosylmethionine (SAM) and in the reverse direction produces the oncometabolite 2-Hydroxyglycerate (2-HG). Methods. Non-transformed MCF-10A cells exposed to OA were utilized for U13C-glucose tracing. SAM and 2-HG concentrations following treatment with OA ± PHGDH inhibitor were measured by liquid chromatography. CUT&amp;RUN for H3K4me3 was performed and genes affected by OA (PMID: 28263391) were compared with OA-responsive peaks. Single cell RNA-sequencing was carried out using breast microstructures derived from reduction mammoplasty tissue exposed to vehicle or OA. Microstructures were dissociated into single cells and sequenced using the 10x Genomics platform. The digital expression matrix file containing UMIs were analyzed with Seurat. Alkaline comet assay was performed to detect DNA breaks. Results. U13C-glucose tracing in presence of OA revealed that one-carbon-THF was redirected to the methionine cycle increasing flux to methylation. Concentrations of SAM and 2-HG increased after 15- and 30-min OA exposure, respectively; PHGDH inhibitor blocked these increases. H3K4me3 CUT&amp;RUN revealed 661 differential peaks (FDR &amp;lt; 0.05) comparing OA to control. 73% of H3K4me3 OA-associated peaks were in regulatory regions of OA-induced genes (FDR &amp;lt; 0.01), these genes are involved in neural pathways, EMT and ER- BC. Motif analysis revealed an overrepresentation of binding sites for transcription factors ATF3/4 (p &amp;lt; 0.05), which are regulators of the serine pathway. Single cell RNA-sequencing revealed OA not only affected the distribution of cell subpopulations but also modulated the expression of many genes within each subcluster. The percentage of luminal progenitor subcluster 3 increased upon OA from less than 1% to about 13%. Within basal subcluster 3, OA drives the expression of ATF3, along with two of the enzymes in the de novo serine pathway: PHGDH and PSAT1. Alkaline comet assay showed DNA breaks in OA- and control 2-HG- treated cells. Conclusions. Metabolism of OA in preference to glucose and glutamine results in a metabolic shift toward the serine pathway increasing the production of SAM and 2-HG, with implications for oncogenesis: 1. SAM production results in epigenetic fostered plasticity leading to reprogramming/selecting cells that express genes consistent with a neural/neural crest-like state. These co-opted neuronal regulatory mechanisms can make critical contributions to the acquired functional capabilities that drive cancer development. 2. 2-HG exposure results in appearance of DNA breaks, which are likely consequent to the inhibition of the alpha-ketoglutarate-dependent dioxygenases KDM 4A/B by 2-HG. Their catalytic activity is required for homologous recombination repair; inhibition results in metabolic “BRCAness”. Citation Format: Mariana Bustamante Eduardo, Gannon Cottone, Shiyu Liu, Maria Paula Zappia, Elizaveta V. Benevolenskaya, Abul Bashar Mir Md. Khademul Islam, Maxim V. Frolov, Seema Khan, Susan Clare. Metabolic shift to serine pathway induced by lipids confers oncogenic properties in non-transformed breast cells [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-08-06.