LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Snail reprograms glucose metabolism by repressing PFKP allowing cancer cell survival under metabolic stress'.
Answer: Dynamic regulation of glucose flux between aerobic glycolysis and the pentose phosphate pathway (PPP) during epithelial-mesenchymal transition (EMT) is not well-understood. Here we show that Snail (SNAI1), a key transcriptional repressor of EMT, regulates glucose flux toward PPP, allowing cancer cell survival under metabolic stress. Mechanistically, Snail regulates glycolytic activity via repression of PFKP (phosphofructokinase, platelet), a major isoform of cancer-specific phosphofructokinase-1 (PFK-1), an enzyme involving the first rate-limiting step of glycolysis. The suppression of PFKP switches the glucose flux towards PPP, generating NADPH with increased metabolites of oxidative PPP. Functionally, dynamic regulation of PFKP significantly potentiates cancer cell survival under metabolic stress and increases metastatic capacities in vivo. Further, knockdown of PFKP rescues metabolic reprogramming and cell death induced by loss of Snail. Thus, the Snail-PFKP axis plays an important role in cancer cell survival via regulation of glucose flux between glycolysis and PPP.Dynamic regulation of glucose flux between aerobic glycolysis and the pentose phosphate pathway (PPP) during epithelial-mesenchymal transition (EMT) is not well-understood. Here we show that Snail (SNAI1), a key transcriptional repressor of EMT, regulates glucose flux toward PPP, allowing cancer cell survival under metabolic stress. Mechanistically, Snail regulates glycolytic activity via repression of PFKP (phosphofructokinase, platelet), a major isoform of cancer-specific phosphofructokinase-1 (PFK-1), an enzyme involving the first rate-limiting step of glycolysis. The suppression of PFKP switches the glucose flux towards PPP, generating NADPH with increased metabolites of oxidative PPP. Functionally, dynamic regulation of PFKP significantly potentiates cancer cell survival under metabolic stress and increases metastatic capacities in vivo. Further, knockdown of PFKP rescues metabolic reprogramming and cell death induced by loss of Snail. Thus, the Snail-PFKP axis plays an important role in cancer cell survival via regulation of glucose flux between glycolysis and PPP.
Question: Write a study description for the study titled 'Prediction of irritable bowel syndrome by integrating urine metabolites and gut microbiota'.
Answer: AbstractBackgroundIrritable bowel syndrome (IBS) is a functional gastrointestinal disorder characterized by recurrent abdominal pain and altered bowel habits. While gut microbiota alterations and metabolic disturbances have been implicated in IBS, their diagnostic utility remains unclear. This study aimed to evaluate the potential of integrating gut microbiota profiling and urinary metabolomics for improved IBS classification.MethodsFifty-four participants (27 healthy controls, 27 IBS patients) were recruited for gut microbiota and urinary metabolite analysis. Gut microbiota composition was assessed via 16S rRNA gene sequencing, and urinary metabolites were profiled using gas chromatography-mass spectrometry (GC-MS). Receiver operating characteristic (ROC) curve analysis was performed to assess the predictive accuracy of gut microbiota, urinary metabolites, and their combined model.ResultsLEfSe analysis identified that Bacteroides eggerthii and Desulfovibrio desulfuricans as enriched in IBS patients, whereas Hallella bergensis and Faecalitalea cylindroides were predominant in healthy individuals. Urinary metabolite analysis revealed significant structural variationsalterations in metabolite profiles, with IBS patients exhibiting elevated fructose levels and trends of increased serine, mannose, and galactose. ROC curve analysis demonstrated that urinary metabolomics outperformed gut microbiota profiling, while a combined approach integrating both datasets achieved the highest predictive accuracy.ConclusionThese findings highlight the predictive potential of integrating urinary metabolomics with gut microbiota profiling for IBS classification. The multi-marker approach demonstrated superior predictive accuracy, suggesting a promising non-invasive strategy for IBS classification and patient stratification.
Question: Write a study description for the study titled 'UHPLC-MS/MS-Based Identity Confirmation of Amino Acids Involved in Response to and Side Effects from Antiseizure Medications'.
Answer: Real-time breath analysis using secondary electrospray ionization coupled with high-resolution mass spectrometry is a fast and noninvasive method to access the metabolic state of a person. However, it lacks the ability to unequivocally assign mass spectral features to compounds due to the absence of chromatographic separation. This can be overcomed by using exhaled breath condensate and conventional liquid chromatography-mass spectrometry (LC-MS) systems. In this study, to the best of our knowledge, we confirm for the first time the presence of six amino acids (GABA, Oxo-Pro, Asp, Gln, Glu, and Tyr) previously reported to be involved in response to and side effects from antiseizure medications in exhaled breath condensate and by extension in exhaled human breath.
Question: Write a study description for the study titled 'Arginine-induced metabolomic perturbation in Streptococcus mutans'.
Answer: BACKGROUND: Streptococcus mutans is a major pathogen responsible for dental caries. Arginine is a promising potential caries preventive agent which can inhibit the growth of S. mutans. However, the mechanism whereby arginine inhibits S. mutans growth remains unclear.AIM: To assess the impact of arginine-induced metabolomic perturbations on S. mutans under biofilm conditions.METHODS: We identified 5,933 and 7,413 ions in positive (ESI+) and negative (ESI-) electrospray ion modes, respectively, with a total of 11.05% and 11.58% differential ions subsequently detected in two respective modes. Further analyses of these metabolites led to identification of 8 and 22 metabolic pathways that were affected by arginine treatment in ESI+ and ESI- modes.RESULTS: Once or twice daily treatments of S. mutans biofilms with arginine resulted in reductions in biofilm biomass. Significant reductions in EPS production were observed following twice daily arginine treatments. Identified metabolites that were significantly differentially abundant following arginine treatment were associated with glycolysis metabolism, amino sugar and nucleotide sugar metabolism, and peptidoglycan synthesis.CONCLUSIONS: Arginine can reduce S. mutans biofilm growth and acid production by inhibiting glycolysis, amino sugar and nucleotide sugar metabolism, and peptidoglycan synthesis.
Question: Write a study description for the study titled 'Serum lipidomics study looking for specific endometrial polyps biomarkers distinguishing from endometrial cancer or hyperplasia'.
Answer: Endometrial diseases are common gynecological diseases that disorder women of childbearing age and perimenopausal women, including endometrial polyps (EP), endometrial cancer (EC), and endometrial hyperplasia (EH). Clinically, biopsy or imaging methods are usually used to screen and diagnose endometrial diseases, but due to their invasiveness and heterogeneity, a noninvasive, convenient, objective and accurate biomarker is needed for the differential diagnosis of EP and EC or EH. In the present study, serum samples from 396 patients with endometrial disease and 225 healthy volunteers were analyzed by UPLC-Q-TOF/MS non-targeted lipidomics. A combination of multivariate (Orthogonal partial least-squares discriminant analysis) and univariate (Student t-test) analyses were used to identify and qualify 6, 8, and 7 potential biomarkers in serum from patients with EP, EC, and EH, respectively. With the aid of logistic regression algorithm and receiver operating characteristic (ROC) curve analysis, A biomarker panel including four specific EP biomarkers, 6-Keto-PGF1α, PA(37:4), LysoPC(20:1) and PS (36:0), had good classification and diagnostic ability in distinguishing EP from EC or EH. The biomarker panel can be used as a rapid diagnostic method to assist imaging examination to effectively differentially diagnose endometrial diseases, and provide a reference for clinicians in the identification and diagnosis of endometrial diseases.
Question: Write a study description for the study titled 'Human gut bacteria increase PFNA excretion in vivo'.
Answer: Per- and polyfluoroalkyl Substances (PFAS) – the so-called ‘forever chemicals’ – are a major cause of environmental and health concern due to their toxicity and long-term persistence. Yet, no efficient mechanisms for their removal have been identified. Here we report the potential of human gut bacteria to increase fecal PFNA excretion.
Question: Write a study description for the study titled 'Timing of unsaturated fat intake improves insulin sensitivity through gut microbiota-dependent regulation of bile acid metabolism: a randomized controlled trial'.
Answer: The timing of dietary fat intake influences metabolic health. However, the impact of the timing of unsaturated fat (USFA) intake on glycemic control has yet to be explored. This 12-week, double-blind, randomized, controlled, 2 x 2 factorial-designed feeding trial investigated the effects of timing (lunch or dinner) and types of dietary USFA (high monounsaturated fat or polyunsaturated fat diet) intake on glucose metabolism in seventy prediabetes participants (mean age, 57 years, fasting glucose (100-126 mg/dL) or postprandial glucose (140-199 mg/dL)). Sixty participants with completed fecal samples were included in the final analysis (n=15 for each group). Postprandial serum glucose (first primary outcome) and insulin (co-primary outcomes) levels from an oral glucose tolerance test were detected. Insulin sensitivity indices (co-primary outcomes) were calculated. Secondary outcomes were continuous glucose levels, serum fatty acid profile, gut microbiome (metagenomic sequencing) and fecal metabolites. Results showed no significant differences in postprandial glucose between groups. However, USFA intake at lunch (vs dinner) improved insulin sensitivity and reduced postprandial insulin and serum free saturated fatty acid (Ptiming < 0.05, Ptype > 0.05, Pinteraction > 0.05), which was associated with alterations in gut microbiome and bile acid metabolism, regardless of USFA type. Here we show, advancing timing of USFA intake improves insulin sensitivity through the gut microbiome and bile acid metabolism, while the type of USFA does not. A limitation is that sample size calculation and power were based on postprandial glucose changes, whereas other co-primary outcomes were not considered. However, the type I error was controlled (α/4) in their analysis. Trial registration: ChiCTR2100045645.
Question: Write a study description for the study titled 'The downside of metabolic diversity: Postingestive rearrangements by specialized insects'.
Answer: Deploying toxins in complex mixtures is thought to be advantageous and is observed during antagonistic interactions in nature. Toxin mixtures are widely utilized in medicine and pest control, as they are thought to slow the evolution of detoxification counterresponses in the targeted organisms. Here we show that caterpillars rearrange key constituents of two distinct plant defense pathways to postingestively disable the defensive properties of both pathways. Specifically, phenolic esters of quinic acid, chlorogenic acids (CAs), potent herbivore and ultraviolet (UV) defenses, are reesterified to decorate particular sugars of 17-hydroxygeranyllinalool diterpene glycosides (HGL-DTGs) and prevent their respective anti–herbivore defense functions. This was discovered through the employment of comparative metabolomics of the leaves of Nicotiana attenuata and the frass of this native tobacco’s specialist herbivore, Manduca sexta larvae. Feeding caterpillars on leaves of transgenic plants abrogated in each of the two pathways, separately and together, revealed that one of the fully characterized frass conjugates, caffeoylated HGL-DTG, originated from ingested CA and HGL-DTGs and that both had negative effects on the defensive function of the other compound class, as revealed by rates of larval mass gain. This negative defensive synergy was further explored in 183 N. attenuata natural accessions, which revealed a strong negative covariance between the two defense pathways. Further mapping analyses in a biparental recombinant inbred line (RIL) population imputed quantitative trait loci (QTLs) for the two pathways at distinct genomic locations. The postingestive repurposing of defense metabolism constituents reveals a downside of deploying toxins in mixtures, a downside which plants in nature have evolved to counter.
Question: Write a study description for the study titled 'Dual transcriptomic & metabolomic analysis of elicited flax sheds light on the kinetics of immune defense activation against the biotrophic pathogen Oidium lini.'.
Answer: Flax (Linum usitatissimum) grown under controlled conditions displayed genotype-dependent resistance to powdery mildew (Oidium lini) following COS-OGA (comprising chitosan- and pectin-derived oligomers) elicitor application. The present study reveals a two-step immune response in plants preventively challenged with the elicitor: an initial, rapid response characterized by the transcription of defense genes whose protein products act in contact with or within the cell wall, where biotrophic pathogens initially thrive, followed by a prolonged activation of cell wall peroxidases and accumulation of secondary metabolites. Thus, dozens of genes encoding membrane receptors, pathogenesis-related proteins, and wall peroxidases were initially overexpressed. Repeated COS-OGA treatments had a transient effect on the transcriptome response while cumulatively remodeling the metabolome over time, with a minimum of two applications required for maximal metabolomic shifts. Secondary metabolites, in particular terpenoids and phenylpropanoids, emerged as major components of this secondary defense response alongside pathogenesis-related proteins and wall peroxidases. The sustained accumulation of secondary metabolites, even after cessation of elicitation, contrasted with the short-lived transcriptomic response. Wall peroxidase enzyme activity also exhibited cumulative effects, increasing strongly for weeks after a third elicitor treatment. This underscores the plasticity of the plant immune response in the face of a potential infection, and the need for repeated preventive applications to achieve the full protective potential of the elicitor.
Question: Write a study description for the study titled 'The Leiden Longevity Study: Identification of biomarkers of the rate of ageing'.
Answer: The aim of the study is to identify genetic mechanisms of longevity and to characterize their interaction with the environment. Using the results the future health of people without familial longevity can be improved in old age. Long-lived siblings of European descent were recruited together with their offspring and the partners of the offspring. Families were recruited if at least two long-lived siblings were alive and fulfilled the age criterion of 89 years or older for males and 91 years or older for females, representing less than 0.5% of the Dutch population in 2001.
Question: Write a study description for the study titled 'Impact of collection conditions on the metabolite content of human urine samples as analyzed by liquid chromatography coupled to mass spectrometry and nuclear magnetic resonance spectroscopy (LC-MS assay)'.
Answer: There is a lack of comprehensive studies documenting the impact of sample collection conditions on metabolic composition of human urine. To address this issue, two experiments were performed at a three-month interval, in which midstream urine samples from healthy individuals were collected, pooled, divided into several aliquots and kept under specific conditions (room temperature, 4 °C, with or without preservative) up to 72 h before storage at -80 °C. Samples were analyzed by high-performance liquid chromatography coupled to high-resolution mass spectrometry and bacterial contamination was monitored by turbidimetry. Multivariate analyses showed that urinary metabolic fingerprints were affected by the presence of preservatives and also by storage at room temperature from 24 to 72 hours, whereas no change was observed for urine samples stored at 4 °C over a 72-hour period. Investigations were then focused on 280 metabolites previously identified in urine: 19 of them were impacted by the kind of sample collection protocol in both experiments, including 12 metabolites affected by bacterial contamination and 7 exhibiting poor chemical stability. Finally, our results emphasize that the use of preservative prevents bacterial overgrowth, but does not avoid metabolite instability in solution, whereas storage at 4 °C inhibits bacterial overgrowth at least over a 72-hour period and slows the chemical degradation process. Consequently, and for further LC/MS analyses, human urine samples should be maintained at 4 °C if their collection is performed over 24 hours.
Question: Write a study description for the study titled 'Gut-derived metabolites drive Th17 cell pathogenicity in multiple sclerosis'.
Answer: The gut-brain axis is an emerging factor in promoting multiple sclerosis (MS). However, the underlying mechanisms and strategies to target this axis are not established. Here, we investigated how the gut environment influences myelin-specific Th17 cell pathogenicity. We used the adoptive Th17 cell transfer experimental autoimmune encephalomyelitis (EAE) model and antibiotic treatment to disrupt the intestinal microbiome. We observed a reduced pathogenic Th17 cell signature in the colon of antibiotic-treated mice. Treatment with fecal filtrates enhanced myelin-specific Th17 cell encephalitogenic properties both in vitro and in vivo. Fecal metabolomic profiling identified altered tryptophan-derived metabolites, including indole-3-carboxylate (I3CA). Oral I3CA supplementation accelerated EAE development. I3CA concentration in blood samples from persons with MS (PwMS) was associated with increased disease severity mirrored by increased serum neurofilament light chain levels. Altogether, our study shows that microbiota-derived metabolites play a key role in the intestine during neuroinflammation, offering potential therapeutic insights for PwMS.
Question: Write a study description for the study titled 'Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach'.
Answer: The human gut microbiome establishes and matures during infancy, and dysregulation at this stage may lead to pathologies later in life. We conducted a multi-omics study comprising three generations of family members to investigate the early development of the gut microbiota. Fecal samples from 200 individuals, including infants (0-12 months old; 55% females, 45% males) and their respective mothers and grandmothers, were analyzed using two independent metabolomics platforms and metagenomics. For metabolomics, gas chromatography and capillary electrophoresis – using multisegment injection – coupled to mass spectrometry were applied. For metagenomics, both 16S rRNA gene and shotgun sequencing were performed. Here we show that infants greatly vary from their elders in fecal microbiota populations, function, and metabolome. Infants have a less diverse microbiota than adults and present differences in several metabolite classes, such as short- and branched-chain fatty acids, which are associated with shifts in bacterial populations. These findings provide innovative biochemical insights into the shaping of the gut microbiome within the same generational line that could be beneficial in improving childhood health outcomes.
Question: Write a study description for the study titled 'Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome'.
Answer: Although the gut microbiome plays important roles in host physiology, health and disease, we lack understanding of the complex interplay between host genetics and early life environment on the microbial and metabolic composition of the gut. We used the genetically diverse Collaborative Cross mouse system to discover that early life history impacts the microbiome composition, whereas dietary changes have only a moderate effect. By contrast, the gut metabolome was shaped mostly by diet, with specific non-dietary metabolites explained by microbial metabolism. Quantitative trait analysis identified mouse genetic trait loci (QTL) that impact the abundances of specific microbes. Human orthologues of genes in the mouse QTL are implicated in gastrointestinal cancer. Additionally, genes located in mouse QTL for Lactobacillales abundance are implicated in arthritis, rheumatic disease and diabetes. Furthermore, Lactobacillales abundance was predictive of higher host T-helper cell counts, suggesting an important link between Lactobacillales and host adaptive immunity. Correlations between specific operational taxonomic units (OTUs) and B-cell counts, body weight and neuromuscular function (rotarod performance) were also observed. This study is the first to determine and rank the complex contributions of built environment, host genetics and diet in shaping gut microbial and metabolite composition, host fitness and behavior.
Question: Write a study description for the study titled 'Metabolic responses induced by DNA damage and poly (ADP-ribose) polymerase (PARP) inhibition in MCF-7 cells'.
Answer: Genomic instability is one of the hallmarks of cancer. Several chemotherapeutic drugs and radiotherapy induce DNA damage to prevent cancer cell replication. Cells in turn activate different DNA damage response (DDR) pathways to either repair the damage or induce cell death. These DDR pathways also elicit metabolic alterations which can play a significant role in the proper functioning of the cells. The understanding of these metabolic effects resulting from different types of DNA damage and repair mechanisms is currently lacking. In this study, we used NMR metabolomics to identify metabolic pathways which are altered in response to different DNA damaging agents. By comparing the metabolic responses in MCF-7 cells, we identified the activation of poly (ADP-ribose) polymerase (PARP) in methyl methanesulfonate (MMS)-induced DNA damage. PARP activation led to a significant depletion of NAD+. PARP inhibition using veliparib (ABT-888) was able to successfully restore the NAD+ levels in MMS-treated cells. In addition, double strand break induction by MMS and veliparib exhibited similar metabolic responses as zeocin, suggesting an application of metabolomics to classify the types of DNA damage responses. This prediction was validated by studying the metabolic responses elicited by radiation. Our findings indicate that cancer cell metabolic responses depend on the type of DNA damage responses and can also be used to classify the type of DNA damage.