LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Untargeted metabolomics profiling reveals exercise intensity-dependent alterations in Thoroughbred racehorses’ plasma after routine conditioning sessions'.
Answer: Thoroughbred (TB) racehorses are subjected to rigorous conditioning programs involving exercise sessions of various types, distances and intensities. These programs aim to optimize both their physical and mental capabilities, which are essential to achieve maximal performance. Conventional investigations of exercise-induced metabolic responses typically focus on a limited set of targeted hematological and biochemical parameters. This field study was conducted to comprehensively assess the metabolic responses triggered by exercise sessions routinely used in TB conditioning. To accomplish this, we employed an untargeted metabolomics approach. Blood samples were collected from 10 racehorses at rest and after completing a routine exercise session. The population was subsequently divided into two groups based on the intensity of the exercise performed: a high-intensity group (n = 6, gallop at ± 13.38 m/s, 1400 m) and a moderate-intensity group (n = 4, soft canter at ± 7.63 m/s, 2500 m). The exercise intensity was evaluated through monitoring of speed, heart rate, and targeted hematological and biochemical parameters (e.g., lactatemia, hematocrit, etc). Resting and 30 min post-exercise plasma samples were analyzed using an untargeted metabolomics approach based on ultra-performance liquid chromatography coupled with high-resolution mass spectrometry. Unsupervised principal component analysis revealed changes in the metabolome from pre- to post-exercise samples with greater alterations following high-intensity exercise. 54 metabolites, mainly related to amino acid, fatty acid, nucleic acid and vitamin metabolism, were altered following high-intensity exercise versus 23 metabolites, mainly related to fatty acid and amino acid metabolism, following moderate-intensity exercise. Untargeted metabolomics complemented the routine biochemical analyses, allowing a more comprehensive exploration of the exercise-induced response to exercises used in routine conditioning. As previously reported by traditional biochemistry, exercise-induced changes in energy metabolism in TB racehorses have been confirmed. Through metabolomics, the involvement of lipid and amino acid metabolism during routine exercise and recovery has been highlighted, aspects that had previously been largely overlooked in Thoroughbred racehorses.
Question: Write a study description for the study titled 'Characterization of the Human Exposome by a Comprehensive and Quantitative Large-Scale Multianalyte Metabolomics Platform'.
Answer: The exposome, defined as the cumulative measure of external exposures and associated biological responses throughout the lifespan, has emerged in recent years as a cornerstone in biomedical sciences. Metabolomics stands out here as one of the most powerful tools for investigating the interplay between the genetic background, exogenous, and endogenous factors within human health. However, to address the complexity of the exposome, novel methods are needed to characterize the human metabolome. In this work, we have optimized and validated a multianalyte metabolomics platform for large-scale quantitative exposome research in plasma and urine samples, based on the use of simple extraction methods and high-throughput metabolomic fingerprinting. The methodology enables, for the first time, the simultaneous characterization of the endogenous metabolome, food-related metabolites, pharmaceuticals, household chemicals, environmental pollutants, and microbiota derivatives, comprising more than 1000 metabolites in total. This comprehensive and quantitative investigation of the exposome is achieved in short run times, through simple extraction methods requiring small-sample volumes, and using integrated quality control procedures for ensuring data quality. This metabolomics approach was satisfactorily validated in terms of linearity, recovery, matrix effects, specificity, limits of quantification, intraday and interday precision, and carryover. Furthermore, the clinical potential of the methodology was demonstrated in a dietary intervention trial as a case study. In summary, this study describes the optimization, validation, and application of a multimetabolite platform for comprehensive and quantitative metabolomics-based exposome research with great utility in large-scale epidemiological studies.
Question: Write a study description for the study titled 'Androgens drive SLC1A5-dependent metabolic reprogramming in polycystic ovary syndrome-GC-MS analysis of KGN cells'.
Answer: Polycystic ovary syndrome (PCOS) is the primary cause of female infertility. Growing evidence suggests that dysregulation of amino acid metabolism plays a significant role in the onset and progression of PCOS. However, the underlying mechanism remains unclear. In this study, we conducted targeted metabolite profiling of human follicular fluid (FF) and granulosa cells (GCs). A significant increase in glutamine (Gln) uptake was observed in patients with hyperandrogenic-PCOS (HA-PCOS), mediated by the upregulation of SLC1A5, a specific Gln transporter. We subsequently confirmed that androgen excess primarily activates SLC1A5 expression. Furthermore, Slc1a5 overexpression in female mice induced PCOS-like phenotypes, including hyperandrogenism and abnormal follicle development. Additionally, the pharmacological blockade of SLC1A5 provided reproductive benefits to mice exhibiting PCOS-like symptoms. Mechanistically, we found that elevated flux of Gln-derived α-ketoglutarate (α-KG) enhanced HDAC5 expression and suppressed acetylation on histone 3 lysine residue 14 and lysine residue 56. The reduction in acetylation level correlated with the downregulation of several genes related to folliculogenesis, including CYP19A1, thereby exacerbating androgenic homeostasis imbalance. These findings indicate that androgen-induced aberrant Gln uptake via SLC1A5 is crucial for the development and progression of PCOS, suggesting pharmacological blockade of SLC1A5 as a potential therapeutic strategy for PCOS patients.
Question: Write a study description for the study titled 'Anti-anemia drug FG4592 retards the AKI to CKD transition by improving vascular regeneration and anti-oxidative capability (day 21)'.
Answer: Acute kidney injury (AKI) is a known risk factor for the development of chronic kidney disease (CKD), with no satisfactory strategy to prevent the progression of AKI to CKD. Damage to the renal vascular system and subsequent hypoxia are common contributors to both AKI and CKD. Hypoxia inducible factor (HIF) is reported to protect the kidney from acute ischemic damage and a novel HIF stabilizer, FG4592 (Roxadustat), has become available in the clinic as an anti-anemia drug. However, the role of FG4592 in the AKI-to-CKD transition remains elusive. In the present study, we investigated the role of FG4592 in the AKI-to-CKD transition induced by unilateral kidney ischemia-reperfusion (UIR). The results showed that FG4592, given to mice 3 days after UIR, markedly alleviated kidney fibrosis and enhanced renal vascular regeneration, possibly via activating the HIF-1α/vascular endothelial growth factor A (VEGFA)/VEGF receptor 1 (VEGFR1) signaling pathway and driving the expression of the endogenous antioxidant superoxide dismutase 2 (SOD2). In accordance with the improved renal vascular regeneration and redox balance, the metabolic disorders of the UIR mice kidneys were also attenuated by treatment with FG4592. However, the inflammatory response in the UIR kidneys was not affected significantly by FG-4592. Importantly, in the kidneys of CKD patients, we also observed enhanced HIF-1α expression which was positively correlated with the renal levels of VEGFA and SOD2. Together, these findings demonstrated the therapeutic effect of the anti-anemia drug FG-4592 in preventing the AKI-to-CKD transition related to ischemia and the redox imbalance.Linked study:UPLC-MS assay of mice kidney tissue sacrificed at day 10 after UIR is reported in MTBLS3056
Question: Write a study description for the study titled 'Integrated omics analysis of pathogenic host responses during pandemic H1N1 influenza virus infection: the crucial role of lipid metabolism'.
Answer: Pandemic influenza viruses modulate pro-inflammatory responses that can lead to immunopathogenesis. We present an extensive and systematic profiling of lipids, metabolites and proteins in respiratory compartments of ferrets infected with either 1918 or 2009 human pandemic H1N1 influenza viruses. Integrative analysis of high-throughput omics data with virologic and histopathologic data uncovered relationships between host responses and phenotypic outcomes of viral infection. Pro-inflammatory lipid precursors in the trachea following 1918 infection correlated with severe tracheal lesions. Using an algorithm to infer cell quantities changes from gene expression data, we found enrichment of distinct T cell subpopulations in the trachea. There was also a predicted increase in inflammatory monocytes in the lung of 1918 virus-infected animals that was sustained throughout infection. This study presents a unique resource to the influenza research community and demonstrates the utility of an integrative systems approach for characterization of lipid metabolism alterations underlying respiratory responses to viruses.
Question: Write a study description for the study titled 'An Integrated Biochemical, Proteomics, and Metabolomics Approach for Supporting Medicinal Value of Panax ginseng Fruits (GC-MS assay)'.
Answer: Panax ginseng roots are well known for their medicinal properties and have been used in Korean and Chinese traditional medicines for 1000s of years. However, the medicinal value of P. ginseng fruits remain poorly characterized. Using gas chromatography-time of flight mass spectrometry (GC-TOF MS), 66 metabolites including amino acids, sugars, organic acids, phenolic acids, phytosterols, tocopherols, and policosanols were identified and quantified. Some of these are well known medicinal compounds and were not previously identified in ginseng. Interestingly, the concentration of almost all metabolites was higher in the Chunpoong and Gumpoong cultivars. Parallel comparison of the four cultivars also revealed higher amounts of the medicinal metabolites in Chunpoong and Gumpoong cultivars. Taken together, our results demonstrate that ginseng fruits are a rich source of medicinal compounds with potential beneficial health effects.
Question: Write a study description for the study titled 'Multiomic analysis revealed the potential role of rumen microbes in heat stress'.
Answer: Heat stress is an important issue in dairy cattle feeding management affecting summer health and economic efficiency. In recent years, global climate change has led to an increase in atmospheric CO2 content and average daily temperature, making heat stress a major challenge in dairy farming. This experiment combined 16S rDNA sequencing, metagenomic sequencing and metabolomic analysis. In this experiment, 10 cows each of growing heifers, heifers and lactating cows were selected for sample collection in April and August. Ruminal fluid was collected and filtered through gauze, which was immediately transferred to liquid nitrogen prior to macrogenomic, 16S rDNA sequencing and metabolomic analyses.
Question: Write a study description for the study titled 'Proteomic analysis validates previous findings on wounding-responsive plant hormone signaling and primary metabolism contributing to the biosynthesis of secondary metabolites based on metabolomic analysis in harvested broccoli (Brassica oleracea L. var. italica)'.
Answer: The plant wound-response is a complex process that generates physiological modiﬁcations for protecting the wounded tissue. In this study, tandem mass tag (TMT)-based quantitative proteomic analysis was performed to clarify the comprehensive molecular mechanism for the wound-response of broccoli subjected to two wounding intensities (0.04 and 1.85 m2 kg−1 for florets and shreds, respectively). Furthermore, integrated proteomic and metabolomic analysis was performed to reveal the interaction among the critical metabolic pathway responses to wounding. The results show that a total of 399 proteins and 266 proteins were identified as differentially expressed proteins (DEPs) in florets and shreds broccoli compared to control, respectively. Bioinformatic analysis indicated that the DEPs were mainly involved in metabolism, genetic information processing, cellular process, environmental information processing and organismal systems. Salicylic acid (SA) and ethylene (ET) biosynthesis were more susceptible to being induced by wounding with lower intensities, whereas, jasmonic acid (JA) biosynthesis was more susceptible to being activated by wounding with higher intensities. Some carbohydrate metabolic pathways and amino acid biosynthesis-related pathways such as phenylalanine, cysteine and methionine metabolic pathways were significantly up-regulated, which promotes the precursor levels for phenolic substances and glucosinolate synthesis. Biosynthesis of secondary metabolites was activated by wounding through regulation of critical proteins involved in the corresponding metabolic pathways.
Question: Write a study description for the study titled 'Mechanistic insights revealed by lipid profiling in monogenic insulin resistance syndromes (Human data)'.
Answer: Evidence from several recent metabolomic studies suggests that increased concentrations of triacylglycerols (TAGs) with shorter (14-16 carbon atoms), saturated fatty acids are associated with insulin resistance and the risk of type 2 diabetes. Although causality cannot be inferred from association studies, patients in whom the primary cause of insulin resistance can be genetically defined, offer unique opportunities to address this challenge. Therefore, we compared metabolite profiles in patients with congenital lipodystrophy or loss-of-function insulin resistance (INSR) mutations with healthy controls. The absence of significant differences in TAG species in the INSR group suggest that changes previously observed in epidemiological studies are not purely a consequence of insulin resistance. The presence of TAGs with lower carbon numbers and high saturation in patients with lipodystrophy suggests that these metabolite changes may be associated with primary adipose tissue dysfunction. The observed pattern of TAG species is indicative of increased de novo lipogenesis (DNL). To test this we investigated the distribution of these TAGs in lipoprotein fractions using size exclusion chromatography prior to mass spectrometry. This associated these TAGs with VLDL particles, and hence release of TAGs into the blood from the liver. To test further the hepatic origin of these TAGs we induced DNL in the mouse, comparing ob/ob and wild type mice on a chow or high fat diet, confirming that DNL induced an increase in relatively shorter, more saturated fatty acids. Overall, these studies highlight DNL in the pathogenesis of metabolic dyslipidaemia in states where energy intake exceeds the capacity of adipose tissue. The protocols and data for human samples are reported in the current study MTBLS162. The protocols and data for mice samples are reported in the study MTBSL327.
Question: Write a study description for the study titled 'Modification of erythrocyte membrane phospholipid composition in preterm newborns with retinopathy of prematurity: The omegaROP study'.
Answer: N-3 polyunsaturated fatty acids (PUFAs) may prevent retinal vascular abnormalities observed in oxygen-induced retinopathy, a model of retinopathy of prematurity (ROP). In the OmegaROP prospective cohort study, we showed that preterm infants who will develop ROP accumulate the n-6 PUFA arachidonic acid (ARA) at the expense of the n-3 PUFA docosahexaenoic acid (DHA) in erythrocytes with advancing gestational age (GA). As mice lacking plasmalogens ―that are specific phospholipids considered as reservoirs of n-6 and n-3 PUFAs― display a ROP-like phenotype, the aim of this study was to determine whether plasmalogens are responsible for the changes observed in subjects from the OmegaROP study. Accordingly, preterm infants aged less than 29 weeks GA were recruited at birth in the Neonatal Intensive Care Unit of University Hospital Dijon, France. Blood was sampled very early after birth to avoid any nutritional influence on its lipid composition. The lipid composition of erythrocytes and the structure of phospholipids including plasmalogens were determined by global lipidomics using liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS). LC-HRMS data confirmed our previous observations by showing a negative association between the erythrocyte content in phospholipid esterified to n-6 PUFAs and GA in infants without ROP (rho = -0.485, p = 0.013 and rho = -0.477, p = 0.015 for ethanolamine and choline total phospholipids, respectively). Phosphatidylcholine (PtdCho) and phosphatidylethanolamine (PtdEtn) species with ARA, namely PtdCho16:0/20:4 (rho = -0.511, p < 0.01) and PtdEtn18:1/20:4 (rho = -0.479, p = 0.015), were the major contributors to the relationship observed. On the contrary, preterm infants developing ROP displayed negative association between PtdEtn species with n-3 PUFAs and GA (rho = -0.380, p = 0.034). They were also characterized by a positive association between GA and the ratio of ethanolamine plasmalogens (PlsEtn) with n-6 PUFA to PlsEtn with n-3 PUFAs (rho = 0.420, p = 0.029), as well as the ratio of PlsEtn with ARA to PlsEtn with DHA (rho = 0.843, p = 0.011). Altogether, these data confirm the potential accumulation of n-6 PUFAs with advancing GA in erythrocytes of infants developing ROP. These changes may be partly due to plasmalogens.
Question: Write a study description for the study titled 'Metabolomics study of COVID-19 patients in four different clinical stages'.
Answer: SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is the coronavirus strain causing the respiratory pandemic COVID-19 (coronavirus disease 2019). To understand the pathobiology of SARS-CoV-2 in humans it is necessary to unravel the metabolic changes that are produced in the individuals once the infection has taken place. The goal of this work is to provide new information about the altered biomolecule profile and with that the altered biological pathways of patients in different clinical situations due to SARS-CoV-2 infection. This is done via metabolomics using HPLC-QTOF-MS analysis of plasma samples at COVID-diagnose from a total of 145 adult patients, divided into different clinical stages based on their subsequent clinical outcome (25 negative controls (non-COVID); 28 positive patients with asymptomatic disease not requiring hospitalization; 27 positive patients with mild disease defined by a total time in hospital lower than 10 days; 36 positive patients with severe disease defined by a total time in hospital over 20 days and/or admission at the ICU; and 29 positive patients with fatal outcome or deceased). Moreover, follow up samples between 2 and 3 months after hospital discharge were also obtained from the hospitalized patients with mild prognosis. The final goal of this work is to provide biomarkers that can help to better understand how the COVID-19 illness evolves and to predict how a patient could progress based on the metabolites profile of plasma obtained at an early stage of the infection. In the present work, several metabolites were found as potential biomarkers to distinguish between the end-stage and the early-stage (or non-COVID) disease groups. These metabolites are mainly involved in the metabolism of carnitines, ketone bodies, fatty acids, lysophosphatidylcholines/phosphatidylcholines, tryptophan, bile acids and purines, but also omeprazole. In addition, the levels of several of these metabolites decreased to “normal” values at hospital discharge, suggesting some of them as early prognosis biomarkers in COVID-19 at diagnose.
Question: Write a study description for the study titled 'Aspartate aminotransferase Rv3722c governs aspartate-dependent nitrogen metabolism in Mycobacterium tuberculosis'.
Answer: Gene rv3722c of Mycobacterium tuberculosis is essential for in vitro growth, and encodes a putative pyridoxal phosphate-binding protein of unknown function. Here we use metabolomic, genetic and structural approaches to show that Rv3722c is the primary aspartate aminotransferase of M. tuberculosis, and mediates an essential but underrecognized role in metabolism: nitrogen distribution. Rv3722c deficiency leads to virulence attenuation in macrophages and mice. Our results identify aspartate biosynthesis and nitrogen distribution as potential species-selective drug targets in M. tuberculosis.
Question: Write a study description for the study titled 'Liquid Chromatography-Mass Spectrometry Quantification of Phytochemicals in Withania somnifera Using Data-Dependent Acquisition, Multiple-Reaction-Monitoring, and Parallel-Reaction-Monitoring with an Inclusion List'.
Answer: Characterization of botanical extracts by mass spectrometry-based metabolomics analysis helps in determining the phytochemical composition that underlies their bioactivity and potential health benefits, while also supporting reproducibility of effects in clinical trials. The quantification of seven withanolides in Withania somnifera using three mass-spectrometry methods was evaluated using Deming regression. Two high-resolution time-of-flight mass spectrometry methods were used, one operating in data-dependent acquisition mode and the other in parallel-reaction-monitoring mode with an inclusion list. The two high-resolution time-of-flight mass spectrometry methods were compared to a multiple-reaction-monitoring method. We evaluated in-source fragmentation of steroidal glycosides and optimized the methods accordingly. A novel software approach to integrating parallel-reaction-monitoring data acquired with an inclusion list was developed. Combining and comparing quantitative results allowed for quantitative specificity, good precision, and adjustment of instrument source conditions for optimal quantification by multiple-reaction-monitoring mass spectrometry, an analytical method that is widely accessible in analytical and phytochemical laboratories.Linked R ScriptAn R script for PRM data analysis collected with an inclusion list is available in Github.
Question: Write a study description for the study titled 'Myocardial metabolic alterations in mice with diet-induced atherosclerosis: linking sulfur amino acid and lipid metabolism.'.
Answer: Atherosclerosis is a leading cause of cardiovascular disease (CVD), but the effect of diet on the atherosclerotic heart's metabolism is unclear. We used an integrated metabolomics and lipidomics approach to evaluate metabolic perturbations in heart and serum from mice fed an atherogenic diet (AD) for 8, 16, and 25 weeks. Nuclear magnetic resonance (NMR)-based metabolomics revealed significant changes in sulfur amino acid (SAA) and lipid metabolism in heart from AD mice compared with heart from normal diet mice. Higher SAA levels in AD mice were quantitatively verified using liquid chromatography-mass spectrometry (LC/MS). Lipidomic profiling revealed that fatty acid and triglyceride (TG) levels in the AD group were altered depending on the degree of unsaturation. Additionally, levels of SCD1, SREBP-1, and PPARγ were reduced in AD mice after 25 weeks, while levels of reactive oxygen species were elevated. The results suggest that a long-term AD leads to SAA metabolism dysregulation and increased oxidative stress in the heart, causing SCD1 activity suppression and accumulation of toxic TGs with a low degree of unsaturation. These findings demonstrate that the SAA metabolic pathway is a promising therapeutic target for CVD treatment and that metabolomics can be used to investigate the metabolic signature of atherosclerosis.