LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Plasma metabolomic profiling for hepatocellular carcinoma diagnosis and microvascular invasion prediction'.
Answer: Altered metabolites play a crucial role in the development and progression of hepatocellular carcinoma (HCC). In this study, an untargeted metabolomic analysis was conducted to identify novel biomarkers with high sensitivity and specificity for the early detection of HCC and to explore their functions. Plasma samples were collected from 138 HCC patients, 69 patients with benign hepatic lesions, and 35 healthy donors. These samples were divided into a discovery set of 171 and a validation set of 71, and analyzed using ultra high performance liquid chromatography mass spectrometry. Through paired t-tests and orthogonal partial least-squares discriminant analysis, nine metabolites with significant predictive value were selected out and incorporated into a model for HCC diagnosis. Area under curves for the discovery set, the validation set, and all samples were 0.97, 0.95, and 0.96 respectively. The satisfactory diagnostic performance was maintained regardless of the China liver cancer (CNLC) staging. Additionally, this model demonstrated better diagnostic performance than AFP when comparing HCC to controls in different CNLC stages. The metabolite pathway enrichment analysis showed that alterations in plasma bile acids were associated with cirrhosis. Univariate and multivariate analyses indicated that the ratio of L-Serine and Sarcosine was an independent predictor for MVI. An integrated analysis of metabolomic data with transcriptomic data from the Cancer Genome Atlas revealed that the low expression of AGXT and GATM was more likely related to MVI. To sum up, our research findings may offer valuable insights into HCC metabolic alterations and contribute to a better characterization of HCC.
Question: Write a study description for the study titled 'The microbiome is associated with obesity-related metabolome signature in the process of aging'.
Answer: The roles of specific microbial metabolites in aging remains understudied. Here we examine the microbiome’s contribution to the metabolic profile in aged mice. Fecal samples were collected from 8-week-old (young) and 18-month-old (aged) female Swiss-Webster mice raised conventionally (Conv) or germ free (GF). Bacterial DNA was sequenced and microbiome analysis predormed using QIIME2. Liquid chromatography mass spectrometry was used for untargeted metabolomics on Conv and GF samples.Significant differences were observed in bacterial composition and predicted functional pathways between young and aged mice. Age-related metabolome variance was greater in Conv than GF mice, highlighting microbial contribution. Moreover, microbiome-associated metabolites, predominantly lipids, were higher in aged mice, with linoleic acid metabolism enriched in this group. Our study underscores a microbiome-dependent component to age-related metabolic changes, particularly in lipid-associated pathways. These findings contribute to the growing body of literature linking gut microbiota with host metabolism in aging.
Question: Write a study description for the study titled 'Molecular characterization of firefly nuptial gifts: a multi-omics approach sheds light on postcopulatory sexual selection'.
Answer: Postcopulatory sexual selection is recognized as a key driver of reproductive trait evolution, including the machinery required to produce endogenous nuptial gifts. Despite the importance of such gifts, the molecular composition of the non-gametic components of male ejaculates and their interactions with female reproductive tracts remain poorly understood. During mating, male Photinus fireflies transfer to females a spermatophore gift manufactured by multiple reproductive glands. Here we combined transcriptomics of both male and female reproductive glands with proteomics and metabolomics to better understand the synthesis, composition and fate of the spermatophore in the common Eastern firefly, Photinus pyralis. Our transcriptome of male glands revealed up-regulation of proteases that may enhance male fertilization success and activate female immune response. Using bottom-up proteomics we identified 208 functionally annotated proteins that males transfer to the female in their spermatophore. Targeted metabolomic analysis also provided the first evidence that Photinus nuptial gifts contain lucibufagin, a firefly defensive toxin. The reproductive tracts of female fireflies showed increased gene expression for several proteases that may be involved in egg production. This study offers new insights into the molecular composition of male spermatophores, and extends our understanding of how nuptial gifts may mediate postcopulatory interactions between the sexes.
Question: Write a study description for the study titled 'Bioaccumulation of therapeutic drugs by human gut bacteria: cross-feeding metabolite analysis (FIA-MS) (E.rectale;S.salivarius assays)'.
Answer: Bacteria in the gut can modulate the availability and efficacy of therapeutic drugs. Interactions at this level have only recently started to being systematically mapped and the main underlying mechanism proposed is chemical transformation of drugs by microbes (biotransformation). Here, we investigated the depletion of 15 structurally diverse drugs by 25 representative gut bacterial strains. This revealed 70 bacteria-drug interactions, 29 of which had not been reported before.Over half of the new interactions can be ascribed to bioaccumulation, that is bacteria storing the drug without chemically modifying it, and in most cases without their growth being affected. As a case in point, we studied the molecular basis of bioaccumulation of the widely used antidepressant duloxetine by using click-chemistry, thermal proteome profiling and metabolomics. We find that duloxetine binds to several metabolic enzymes and changes metabolite secretion of the respective bacteria. When tested in a defined microbial community of accumulators and non-accumulators, duloxetine markedly altered the community composition through metabolic cross-feeding. We further validated our findings in an animal model, showing that bioaccumulating bacteria attenuate the behavioral response of Caenorhabditis elegans to duloxetine.Taken together, bioaccumulation by gut bacteria might be a common mechanism that alters drug availability and bacterial metabolism, with implications for microbiota composition, pharmacokinetics, side effects and drug responses, likely in an individual manner.Linked studies;UPLC-MS/MS assays of Bifidobacterium animalis subsp. lactis are reported in MTBLS1264.UPLC-MS/MS assay of Lacrimispora saccharolytica and Escherichia coli IAI1 is reported in MTBLS1319.UPLC-MS/MS assays of Escherichia coli ED1a, Clostridium saccharolyticum, Escherichia coli IAI1, Streptococcus salivarius, Eubacterium rectale, Lactobacillus plantarum WCFS1 and Lactococcus lactis subsp. lactis Il1403 are reported in MTBLS1627.UPLC-MS/MS assay of Bacteroides uniformis and Clostridium saccharolyticum is reported in MTBLS1757.UPLC-MS/MS assay of Clostridium saccharolyticum, Escherichia coli ED1a, Escherichia coli IAI1, Lactobacillus plantarum WCFS1, Lactococcus lactis subsp. lactis Il1403 and Streptococcus salivarius is reported in MTBLS1791.UPLC-MS/MS assay of Lacrimispora saccharolytica and standards is reported in MTBLS2885.
Question: Write a study description for the study titled 'Distinct metabolic responses of an ovarian cancer stem cell line'.
Answer: BackgroundCancer metabolism is emerging as an important focus area in cancer research. However, the in vitro cell culture conditions under which much cellular metabolism research is performed differ drastically from in vivo tumor conditions, which are characterized by variations in the levels of oxygen, nutrients like glucose, and other molecules like chemotherapeutics. Moreover, it is important to know how the diverse cell types in a tumor, including cancer stem cells that are believed to be a major cause of cancer recurrence, respond to these variations. Here, in vitro environmental perturbations designed to mimic different aspects of the in vivo environment were used to characterize how an ovarian cancer cell line and its derived, isogenic cancer stem cells metabolically respond to environmental cues.ResultsMass spectrometry was used to profile metabolite levels in response to in vitro environmental perturbations. Docetaxel, the chemotherapeutic used for this experiment, caused significant metabolic changes in amino acid and carbohydrate metabolism in ovarian cancer cells, but had virtually no metabolic effect on isogenic ovarian cancer stem cells. Glucose deprivation, hypoxia, and the combination thereof altered ovarian cancer cell and cancer stem cell metabolism to varying extents for the two cell types. Hypoxia had a much larger effect on ovarian cancer cell metabolism, while glucose deprivation had a greater effect on ovarian cancer stem cell metabolism. Core metabolites and pathways affected by these perturbations were identified, along with pathways that were unique to cell types or perturbations.ConclusionsThe metabolic responses of an ovarian cancer cell line and its derived isogenic cancer stem cells differ greatly under most conditions, suggesting that these two cell types may behave quite differently in an in vivo tumor microenvironment. While cancer metabolism and cancer stem cells are each promising potential therapeutic targets, such varied behaviors in vivo would need to be considered in the design and early testing of such treatments.
Question: Write a study description for the study titled 'Lipidomic analysis reveals altered lipid profiles of clinically healthy and periodontitis-affected gingival biopsies'.
Answer: AIM: The role of lipids in periodontitis has not been well studied. Thus, this study aimed to explore periodontitis-associated lipid profile changes and identify differentially expressed lipid metabolites in gingival tissues.MATERIALS AND METHODS: Gingival tissues from 38 patients with periodontitis (periodontitis group) and 38 periodontally healthy individuals (control group) were collected. A UHPLC-QTOF-MS-based non-targeted metabolomics platform was used to identify and compare the lipid profiles of the two groups. The distribution and expression of related proteins were subsequently analyzed via immunohistochemistry to further validate the identified lipids.RESULTS: Lipid profiles significantly differed between the two groups, and 20 differentially expressed lipid species were identified. Lysophosphatidylcholines (lysoPCs), diacylglycerols (DGs) and phosphatidylethanolamines (PEs) were significantly upregulated, while triacylglycerols (TGs) were downregulated in the periodontitis group. Moreover, the staining intensity of ABHD5/CGI-58, secretory phospholipase A2 (sPLA2), and sPLA2-IIA was significantly stronger in the gingival tissues of patients with periodontitis than in those of healthy controls.CONCLUSIONS: LysoPCs, DGs, and PEs were significantly upregulated, whereas TGs were downregulated in gingival tissues of patients with periodontitis. Correspondingly, the immunohistochemical staining of ABHD5/CGI-58, sPLA2 and sPLA2-IIA in gingival tissues was consistent with the downstream production of lipid classes (lysoPCs, TGs and DGs).
Question: Write a study description for the study titled 'Gluconeogenesis using glycerol as a substrate in bloodstream-form Trypanosoma brucei'.
Answer: Bloodstream form African trypanosomes are thought to rely exclusively upon glycolysis, using glucose as a substrate, for ATP production. Indeed, the pathway has long been considered a potential therapeutic target to tackle the devastating and neglected tropical diseases caused by these parasites. However, plasma membrane glucose and glycerol transporters are both expressed by trypanosomes and these parasites can infiltrate tissues that contain glycerol. Here, we show that bloodstream form trypanosomes can use glycerol for gluconeogenesis and for ATP production, particularly when deprived of glucose following hexose transporter depletion. We demonstrate that Trypanosoma brucei hexose transporters 1 and 2 (THT1 and THT2) are localized to the plasma membrane and that knockdown of THT1 expression leads to a growth defect that is more severe when THT2 is also knocked down. These data are consistent with THT1 and THT2 being the primary routes of glucose supply for the production of ATP by glycolysis. However, supplementation of the growth medium with glycerol substantially rescued the growth defect caused by THT1 and THT2 knockdown. Metabolomic analyses with heavy-isotope labelled glycerol demonstrated that trypanosomes take up glycerol and use it to synthesize intermediates of gluconeogenesis, including fructose 1,6-bisphosphate and hexose 6-phosphates, which feed the pentose phosphate pathway and variant surface glycoprotein biosynthesis. We used Cas9-mediated gene knockout to demonstrate a gluconeogenesis-specific, but fructose-1,6-bisphosphatase (Tb927.9.8720)-independent activity, converting fructose 1,6-bisphosphate into fructose 6-phosphate. In addition, we observed increased flux through the tricarboxylic acid cycle and the succinate shunt. Thus, contrary to prior thinking, gluconeogenesis can operate in bloodstream form T. brucei. This pathway, using glycerol as a physiological substrate, may be required in mammalian host tissues.
Question: Write a study description for the study titled 'Revealing the constituents of Egypt’s oldest beer using infrared and mass spectrometry'.
Answer: Previous studies have shown that the Ancient Egyptians used malted wheat and barley as the main ingredients in beer brewing, but the chemical determination of the exact recipe is still lacking. To investigate the constituents of ancient beer, we conducted a detailed IR and GC-MS based metabolite analyses targeting volatile and non-volatile metabolites on the residues recovered from the interior of vats in what is currently the world's oldest (c. 3600 BCE) installation for large-scale beer production located at the major pre-pharaonic political center at Hierakonpolis, Egypt. In addition to distinguishing the chemical signatures of various flavoring agents, such as dates, a significant result of our analysis is the finding, for the first time, of phosphoric acid in high level probably used as a preservative much like in modern beverages. This suggests that the early brewers had acquired the knowledge needed to efficiently produce and preserve large quantities of beer. This study provides the most detailed chemical profile of an ancient beer using modern spectrometric techniques and providing evidence for the likely starting materials used in beer brewing.
Question: Write a study description for the study titled 'Evaluation of ambient mass spectrometry tools for assessing inherent postharvest pepper quality'.
Answer: Horticulturists are interested in evaluating how cultivar, environment, or production system inputs can affect postharvest quality. Ambient mass spectrometry approaches enable analysis of minimally processed samples under ambient conditions and offer an attractive high-throughput alternative for assessing quality characteristics in plant products. Here, we evaluate direct analysis in real time (DART-MS) mass spectrometry and rapid evaporative ionization-mass spectrometry (REIMS) to assess quality characteristics in various pepper (Capsicum annuum L.) cultivars. DART-MS exhibited the ability to discriminate between pod colors and pungency based on chemical fingerprints, while REIMS could distinguish pepper market class (e.g., bell, lunchbox, and popper). Furthermore, DART-MS analysis resulted in the putative detection of important bioactive compounds in human diet such as vitamin C, p-coumaric acid, and capsaicin. The results of this study demonstrate the potential for these approaches as accessible and reliable tools for high throughput screening of pepper quality.
Question: Write a study description for the study titled 'Sex Differences in Colon Cancer Metabolism Reveal A Novel Subphenotype (UPLC-MS RP NEG assay)'.
Answer: Women have a lower incidence of colorectal cancer (CRC) than men, however, they have a higher incidence of right-sided colon cancer (RCC). This is of concern as patients with RCC have the poorest clinical outcomes among all CRC patients. Aberrant metabolism is a known hallmark and therapeutic target for cancer. We propose that metabolic subphenotypes exist between CRCs due to intertumoral molecular and genomic variation, and differences in environmental milieu of the colon which vary between the sexes. Metabolomics analysis of patient colon tumors (n = 197) and normal tissues (n = 39) revealed sex-specific metabolic subphenotypes dependent on anatomic location. Tumors from women with RCC were nutrient-deplete, showing enhanced energy production to fuel asparagine synthesis and amino acid uptake. The clinical importance of our findings were further investigated in an independent data set from The Cancer Genomic Atlas, and demonstrated that high asparagine synthetase (ASNS) expression correlated with poorer survival for women. This is the first study to show a unique, nutrient-deplete metabolic subphenotype in women with RCC, with implications for tumor progression and outcomes in CRC patients.UPLC-MS HILIC POS assay is reported in MTBLS1122.UPLC-MS HILIC NEG assay is reported in MTBLS1124.UPLC-MS RP POS assay is reported in MTBLS1129.UPLC-MS RP NEG assay is reported in MTBLS1130.
Question: Write a study description for the study titled 'Lipid Data Analyzer: Analysis of a complex biological system from murine liver samples (Murine liver lipidome experiment)'.
Answer: Lipid Data Analyzer (LDA; http://genome.tugraz.at/lda2) provides automated and reliable annotation of lipid species and their molecular structures in high-throughput data from chromatography-coupled tandem mass spectrometry using embedded rule sets. Using various low- and high-resolution mass spectrometry instruments with several collision energies, the method's platform independence is proved. The software's reliability, flexibility, and ability to identify novel lipid molecular species may now render current state-of-the-art lipid libraries obsolete.  The biological data was used to fine-tune the developed decision rule sets. In particular, the high numbers of isobaric species and structural isomers contained in these samples helped in the detection of decisive differences for many isobaric subclasses/adducts.  Control experiment 1 assays for this study can be found in the MetaboLights study MTBLS394. Control experiment 2 assays for this study can be found in the MetaboLights study MTBLS391. Control experiment 3 assays for this study can be found in the MetaboLights study MTBLS398. LipidBlast benchmarking assays for this study can be found in the MetaboLights study MTBLS397. HCD characterization and regioisomer detection assays for this study can be found in the MetaboLights study MTBLS462. Linked Studies: MTBLS391 MTBLS394 MTBLS397 MTBLS398 MTBLS462
Question: Write a study description for the study titled 'Integrated Proteomics and Metabolomics Analysis Reveals Differential Lipid Metabolism in HUVEC under high and low shear stress'.
Answer: OBJECTIVE: Atherosclerotic plaque development is closely associated with the hemodynamic forces applied to endothelial cells (EC). Among these, shear stress (SS) plays a key role in disease development since changes in flow intensity and direction could stimulate an atheroprone or atheroprotective phenotype. EC under low or oscillatory SS (LSS) shows upregulation of inflammatory, adhesion and cellular permeability molecules. On the contrary, cells under high or laminar SS (HSS) increase their expression of protective and anti-inflammatory factors. The mechanism behind SS regulation of an atheroprotective phenotype is not completely elucidated.APPROACH and RESULTS: Here we used proteomics and metabolomics to better understand the changes in endothelial cells (HUVECs) under in vitro LSS and HSS that promote an atheroprone or atheroprotective profile and how these modifications can be connected to atherosclerosis development. Our data showed that lipid metabolism, in special cholesterol metabolism, was downregulated in cells under LSS. The LDLR showed significant alterations both at the quantitative expression level, as well as regarding post-translational modifications. Under LSS, LDLR was seen at lower concentrations and with a different glycosylation profile. Finally, modulating LDLR with atorvastatin led to the recapitulation of a HSS metabolic phenotype in EC under LSS.CONCLUSIONS: Altogether, our data suggest that there is significant modulation of lipid metabolism in endothelial cells under different SS intensities and that this could contribute to the atheroprone phenotype of LSS. Statin treatment was able to partially recover the protective profile of these cells.
Question: Write a study description for the study titled 'Integrated multi-omics analysis of liver metabolic dysregulation in ACE2 knockout mice'.
Answer: This study systematically investigated the impact of ACE2 knockout (ACE2KO) on hepatic metabolic homeostasis and its molecular mechanisms, using integrated transcriptomic, proteomic, and metabolomic profiling. ACE2 deficiency exacerbates hepatic lipid accumulation, as evidenced by elevated total cholesterol and triglyceride levels, while disrupting the renin-angiotensin system equilibrium via increased angiotensin II (Ang II) and reduced Ang-(1-7). Histopathological analysis revealed hepatocyte edema, vacuolar degeneration, and inflammatory infiltration in the ACE2KO mice. Multi-omics integration uncovered systemic metabolic dysregulation: transcriptomics identified 1,004 differentially expressed genes (DEGs), including lipid metabolism regulators (Scd1, Fabp1) and circadian rhythm modulators (Arntl, Cry1), 191 differentially expressed proteins (DEPs) associated with interferon signaling activation (Oas1a, Rsad2) and lipid synthesis suppression (Scd1, Fasn), and metabolomics highlighted 193 differential metabolites (DEMs) indicative of bile acid dysregulation, glutathione redox imbalance, and amino acid metabolism anomalies. Cross-omics analysis indicated that the PPAR signaling pathway is a central regulatory hub driving lipid metabolic reprogramming and oxidative stress amplification. Furthermore, ACE2 deletion disrupted cytochrome P450-mediated detoxification and glutathione metabolism, thereby establishing a self-reinforcing oxidative injury cycle. These findings comprehensively delineate ACE2’s multifaceted role in hepatic metabolic homeostasis and provide mechanistic insights into and therapeutic targets for ACE2-associated liver diseases.