LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Epithelial-Cell-Derived Phospholipase A2 Group 1B Is an Endogenous Anthelmintic'.
Answer: Immunity to intestinal helminth infections has been well studied, but the mechanism of helminth killing prior to expulsion remains unclear. Here we identify epithelial-cell-derived phospholipase A2 group 1B (PLA2g1B) as a host-derived endogenous anthelmintic. PLA2g1B is elevated in resistant mice and is responsible for killing tissue-embedded larvae. Despite comparable activities of other essential type-2-dependent immune mechanisms, Pla2g1b-/- mice failed to expel the intestinal helminths Heligmosomoides polygyrus or Nippostrongylus brasiliensis. Expression of Pla2g1b by epithelial cells was dependent upon intestinal microbiota, adaptive immunity, and common-gamma chain-dependent signaling. Notably, Pla2g1b was downregulated in susceptible mice and inhibited by IL-4R-signaling in vitro, uncoupling parasite killing from expulsion mechanisms. Resistance was restored in Pla2g1b-/- mice by treating infective H. polygyrus L3 larvae with PLA2g1B, which reduced larval phospholipid abundance. These findings uncover epithelial-cell-derived Pla2g1b as an essential mediator of helminth killing, highlighting a previously overlooked mechanism of anti-helminth immunity.
Question: Write a study description for the study titled 'Fecal microbiota transplantation plus anti-PD-1 immunotherapy in advanced melanoma: a phase I trial'.
Answer: Fecal microbiota transplantation (FMT) represents a potential strategy to overcome resistance to immune checkpoint inhibitors in patients with refractory melanoma; however, the role of FMT in first-line treatment settings has not been evaluated. We conducted a multicenter phase I trial combining healthy donor FMT with the PD-1 inhibitors nivolumab or pembrolizumab in 20 previously untreated patients with advanced melanoma. The primary end point was safety. No grade 3 adverse events were reported from FMT alone. Five patients (25%) experienced grade 3 immune-related adverse events from combination therapy. Key secondary end points were objective response rate, changes in gut microbiome composition and systemic immune and metabolomics analyses. The objective response rate was 65% (13 of 20), including four (20%) complete responses. Longitudinal microbiome profiling revealed that all patients engrafted strains from their respective donors; however, the acquired similarity between donor and patient microbiomes only increased over time in responders. Responders experienced an enrichment of immunogenic and a loss of deleterious bacteria following FMT. Avatar mouse models confirmed the role of healthy donor feces in increasing anti-PD-1 efficacy. Our results show that FMT from healthy donors is safe in the first-line setting and warrants further investigation in combination with immune checkpoint inhibitors. ClinicalTrials.gov identifier NCT03772899 .
Question: Write a study description for the study titled 'A multi-omic profiles of fruits regarding the maturation of Olive (Olea europaea L.) (Tyrosol only UPLC-MS assay)'.
Answer: Olive (Olea europaea) has a long history of medicinal and nutritional values own to it rich in polyphenol and fatty acids (FAs) in fruits. In order to better understand the biosynthesis important of these metabolites, we generated comprehensive Iso-Seq full-length and illumina RNA-seq transcriptome, and targeted metabolomics dataset of different olive fruits maturity. The targeted metabolomics by using both GC/MS and LC/MS were totally quantified 35 FAs and 13 polyphenols. Iso-Seq library was constructed and sequenced by PacBio Sequel System, and a total of 5,891,652 (10.55 G) with an average length of 1,791 subreads were obtained. 492,350 circular consensus sequences (CCSs) were formed after merging and error correction through subread comparison. Of the 492,350 CCSs, 399,263 were found to be full-length non chimera (FLNC) reads, and 187,517 consensus reads were finally obtained by using clustering algorithm of Iterative clustering for error (IEC). These multiomics data provide a foundation to elucidate the mechanisms regulating biosynthesis of polyphenol and FAs during the maturation of olive fruits.Tyrosol only UPLC-MS protocols and data associated to this study are reported in the current study MTBLS1127.Polyphenols UPLC-MS protocols and data associated to this study are reported in MTBLS814.GC-MS protocols and data associated to this study are reported in MTBLS855.
Question: Write a study description for the study titled 'Prediction, detection, and validation of isotope peaks in mass spectrometry data (Supplemental data for manuscript)'.
Answer: Mass spectrometry is a key analytical platform for metabolomics. The precise quantification and identification of small molecules is a prerequisite for elucidating the metabolism and the detection, validation, and evaluation of isotope clusters in LC-MS data is important for this task. Here, we present an approach for the improved detection of isotope clusters using chemical prior knowledge and the validation of detected isotope clusters depending on the substance mass using database statistics. We find remarkable improvements regarding the number of detected isotope clusters and are able to predict the correct molecular formula in the top three ranks in 92% of the cases. We make our methodology freely available as part of the Bioconductor packages xcms and CAMERA.
Question: Write a study description for the study titled 'Alterations in gut microbiota composition, plasma lipids, and brain activity, suggest inter-connected pathways influencing malnutrition-associated cognitive and neurodevelopmental changes.'.
Answer: Malnutrition affects over 30 million children annually and has profound immediate and enduring repercussions, with nearly half of child deaths under five linked to malnutrition. Survivors face lasting consequences, including impaired neurocognitive development, leading to cognitive and behavioural deficits, impacting academic performance and socioeconomic outcomes. Despite extensive literature on malnutrition’s associations with infections, metabolism, microbiome and genomics, knowledge gaps persist around how these changes are mechanistically connected. The objective of this study was to identify gut microbiome mediated associations between Moderate Acute Malnutrition (MAM) and cognitive development. Despite limitations, this study provides evidence supporting the hypothesis that inter-connected pathways between the gut microbiome, microbial metabolism mediate plasma lipids, brain activity and cognitive functions. Causality between gut microbiome, plasma metabolite changes and MAM phenotype remains unclear, necessitating further research. However, these findings offer insights to optimize interventions for MAM-associated neurodevelopmental changes.
Question: Write a study description for the study titled 'α-ketoglutarate maintains AMPK translation for energy sensing in human cancer cells_targeted metabolites'.
Answer: The energy sensor AMPK promotes tumor cell survival under stress, but how to prevent AMPK activation to blunt tumor progression remains unclear. Here we show that the metabolite α-ketoglutarate (α-KG) controls AMPK translation through a TET-YBX1 axis, which can be exploited to sensitize human cancer cells to energy stress. α-KG-deficient cells fail to activate AMPK under glucose starvation, which elicits cytosolic NADPH depletion and cell death . Mechanistically, α-KG insufficiency inhibits TET-dependent transcription of YBX1, an RNA-binding protein required for human-specific AMPK translation. Similarly, α-KG competitors including succinate and itaconate inhibit the YBX1-AMPK axis and sensitize cancer cells to glucose starvation. Finally, co-targeting oncogenic YBX1 and GLUT1 creates a synthetic lethality and therapeutically blunts tumor growth in vivo. Together, our findings link α-KG to energy sensing through AMPK translation, and propose that targeting α-KG-YBX1-dependent AMPK translation can sensitize human cancer cells to energy stress for treatment.
Question: Write a study description for the study titled 'Molecular Basis Underlying Common Cutworm Resistance of the Primitive Soybean Landrace Peking'.
Answer: The common cutworm (CCW; Spodoptera litura) is one of the major insect pests of soybean in Asia and Oceania. Although quantitative trail loci related to CCW resistance have been introduced into leading soybean cultivars, these do not exhibit sufficient resistance against CCW. Thus, understanding the genetic and metabolic resistance mechanisms of CCW as well as integrating other new resistance genes are required. In this study, we focused on a primitive soybean landrace, Peking, which has retained resistances to various pests. We found a resistance to CCW in Peking by the detached-leaf feeding assay, and subsequently determined the genetic and metabolic basis of the resistance mechanism using chromosome segment substitution lines (CSSLs) of Peking. Several characteristic metabolites for Peking were identified by the metabolomic approach using liquid chromatography/mass spectrometry combined with a principle component analysis. The structure of seven metabolites were determined by nuclear magnetic resonance (NMR) analysis. The genomic segments of Peking on chromosome 06 (Chr06) and Chr20 had a clear association with these metabolites. Moreover, a line possessing a Peking genomic segment on Chr20 inhibited growth of the CCW. The genetic factors and the metabolites on Chr20 in Peking will be useful for understanding mechanisms underlying CCW resistance and breeding resistant soybean cultivars.
Question: Write a study description for the study titled 'Metabolome and exposome profiling of the biospecimens from COVID-19 patients in India (Nasopharyngeal swab assay)'.
Answer: INTRODUCTION: COVID-19 has become a global impediment by bringing everything to a halt starting from January 2020. India underwent the lockdown starting from 22nd March 2020 with the sudden spike in the number of COVID-19 patients in major cities and states. This study focused on how metabolites play a crucial role in SARSCoV-2 prognosis.MATERIALS AND METHODS: Metabolome profiling of 106 plasma samples and 24 swab samples from symptomatic patients in the Indian population of the Mumbai region was done. COVID-19 positive samples were further segregated under the non-severe COVID-19 and severe COVID-19 patient cohort for both plasma and swab.RESULTS: After analyzing the raw files, total 7,949 and 12,871 metabolites in plasma and swab were found. 11 and 35 significantly altered metabolites were found in COVID-19 positive compared to COVID-19 negative plasma and swab samples, respectively. Also, 9 and 23 significantly altered metabolites were found in severe COVID-19 positive to non-severe COVID-19 positive plasma and swab samples, respectively. The majorly affected pathways in COVID-19 patients were found to be the amino acid metabolism pathway, sphingosine metabolism pathway, and bile salt metabolism pathway.CONCLUSION: This study facilitates identification of potential metabolite-based biomarker candidates for rapid diagnosis and prognosis for clinical applications.Nasopharyngeal swab assay is reported in the current study MTBLS2349.Blood plasma assay is reported in MTBLS2291.
Question: Write a study description for the study titled 'Integration of magnetic resonance imaging and protein and metabolite CSF measurements to enable early diagnosis of secondary progressive multiple sclerosis'.
Answer: Molecular networks in neurological diseases are complex. Despite this fact, contemporary biomarkers are in most cases interpreted in isolation, leading to a significant loss of information and power. We present an analytical approach to scrutinize and combine information from biomarkers originating from multiple sources with the aim of discovering a condensed set of biomarkers that in combination could distinguish the progressive degenerative phenotype of multiple sclerosis (SPMS) from the relapsing-remitting phenotype (RRMS).METHODS: Clinical and magnetic resonance imaging (MRI) data were integrated with data from protein and metabolite measurements of cerebrospinal fluid, and a method was developed to sift through all the variables to establish a small set of highly informative measurements. This prospective study included 16 SPMS patients, 30 RRMS patients and 10 controls. Protein concentrations were quantitated with multiplexed fluorescent bead-based immunoassays and ELISA. The metabolome was recorded using liquid chromatography-mass spectrometry. Clinical follow-up data of the SPMS patients were used to assess disease progression and development of disability.RESULTS: Eleven variables were in combination able to distinguish SPMS from RRMS patients with high confidence superior to any single measurement. The identified variables consisted of three MRI variables: the size of the spinal cord and the third ventricle and the total number of T1 hypointense lesions; six proteins: galectin-9, monocyte chemoattractant protein-1 (MCP-1), transforming growth factor alpha (TGF-α), tumor necrosis factor alpha (TNF-α), soluble CD40L (sCD40L) and platelet-derived growth factor AA (PDGF-AA); and two metabolites: 20β-dihydrocortisol (20β-DHF) and indolepyruvate.The proteins myelin basic protein (MBP) and macrophage-derived chemokine (MDC), as well as the metabolites 20β-DHF and 5,6-dihydroxyprostaglandin F1a (5,6-DH-PGF1), were identified as potential biomarkers of disability progression.CONCLUSION: Our study demonstrates, in a limited but well-defined and data-rich cohort, the importance and value of combining multiple biomarkers to aid diagnostics and track disease progression.Cohort 2 assays are reported in the current study MTBLS558.Cohort 1 assays are reported in MTBLS1464.
Question: Write a study description for the study titled 'The microbiome interacts with the circadian clock and dietary composition to regulate metabolite cycling in the gut'.
Answer: Gut microbiomes play a key role in the maintenance of host metabolic homeostasis and health. An important aspect of metabolism is its circadian regulation, but how the microbiome regulates metabolite cycling under different conditions, including variations in dietary composition, remains undefined. In this study, we utilized high temporal resolution metabolite profiling of the Drosophila gut to investigate the role of the microbiome in metabolite cycling. We find that, in contrast to its effect on transcript cycling, the microbiome increases metabolite cycling in the gut. In the absence of a circadian clock, the microbiome has minimal effect on the number of metabolites cycling, but profoundly affects phase, suggesting that the clock stabilizes circadian phase in the face of microbial changes. Interestingly, the impact of the microbiome is also reduced in a timed feeding paradigm, and vice versa, suggesting that timed feeding and the microbiome have similar circadian effects. Finally, the microbiome increases metabolite cycling but does not alter phase in flies fed high protein diets, but suppresses metabolite cycling and changes cycling phase in flies fed high sugar diets. Enrichment analysis of cycling metabolites found that amino acid metabolism is particularly sensitive to changes in the microbiome, the circadian clock and timed feeding. Collectively, our observations highlight a key role of the microbiome in producing robust metabolite cycling, in conjunction with the circadian clock and dietary composition.
Question: Write a study description for the study titled 'Metabolic memory underlying minimal residual disease in breast cancer'.
Answer: Tumor relapse from treatment-resistant cells (minimal residual disease, MRD) underlies most breast cancer related deaths. Yet, the molecular characteristics defining their malignancy have largely remained elusive. Here we integrated multi-omics data from a tractable organoid system with a metabolic modelling approach to uncover the metabolic and regulatory idiosyncrasies of the MRD. We find that the resistant cells, despite their non-proliferative phenotype and the absence of oncogenic signaling, feature increased glycolysis and activity of certain urea cycle enzymes reminiscent of the tumor. This metabolic distinctiveness was also evident in a mouse model and in transcriptomic data from patients following neo-adjuvant therapy. We further identified a marked similarity in DNA methylation profiles between tumor and residual cells. Taken together, our data reveal a metabolic and epigenetic memory of the treatment-resistant cells. We further demonstrate that the memorized elevated glycolysis in MRD is crucial for their survival and can be targeted using a small molecule inhibitor without impacting normal cells. The metabolic aberrances of MRD thus offer new therapeutic opportunities for post-treatment care to prevent breast tumor recurrence.
Question: Write a study description for the study titled 'The diversity of quinoa morphological traits and seed metabolic composition'.
Answer: Quinoa (Chenopodium quinoa Willd.) is an herbaceous annual crop of the amaranth family (Amaranthaceae). It is increasingly cultivated for its nutritious grains, which are rich in protein and essential amino acids, lipids, and minerals. Quinoa exhibits a high tolerance towards various abiotic stresses including drought and salinity, which supports its agricultural cultivation under climate change conditions. The use of quinoa grains is compromised by anti-nutritional saponins, a terpenoid class of secondary metabolites deposited in the seed coat; their removal before consumption requires extensive washing, an economically and environmentally unfavorable process; or their accumulation can be reduced through breeding. In this study, we analyzed the seed metabolomes, including amino acids, fatty acids, and saponins, from 471 quinoa cultivars, including two related species, by liquid chromatography - mass spectrometry. Additionally, we determined a large number of agronomic traits including biomass, flowering time, and seed yield. The results revealed considerable diversity between genotypes and provide a knowledge base for future breeding or genome editing of quinoa.
Question: Write a study description for the study titled 'Reactive Oxygen Species Deficiency Due to Ncf1-Mutation Leads to Development of Adenocarcinoma and Metabolomic and Lipidomic Remodeling in a New Mouse Model of Dextran Sulfate Sodium-Induced Colitis'.
Answer: Inflammatory bowel disease is characterized by chronic relapsing idiopathic inflammation of the gastrointestinal tract and persistent inflammation. Studies focusing on the immune-regulatory function of reactive oxygen species (ROS) are still largely missing. In this study, we analyzed an ROS-deficient mouse model leading to colon adenocarcinoma. Colitis was induced with dextran sulfate sodium (DSS) supplied via the drinking water in wild-type (WT) and Ncf1-mutant (Ncf1) B10.Q mice using two different protocols, one mimicking recovery after acute colitis and another simulating chronic colitis. Disease progression was monitored by evaluation of clinical parameters, histopathological analysis, and the blood serum metabolome using 1H nuclear magnetic resonance spectroscopy. At each experimental time point, colons and spleens from some mice were removed for histopathological analysis and internal clinical parameters. Clinical scores for weight variation, stool consistency, colorectal bleeding, colon length, and spleen weight were significantly worse for Ncf1 than for WT mice. Ncf1 mice with only a 7-day exposure to DSS followed by a 14-day resting period developed colonic distal high-grade dysplasia in contrast to the low-grade dysplasia found in the colon of WT mice. After a 21-day resting period, there was still β-catenin-rich inflammatory infiltration in the Ncf1 mice together with high-grade dysplasia and invasive well-differentiated adenocarcinoma, while in the WT mice, high-grade dysplasia was prominent without malignant invasion and only low inflammation. Although exposure to DSS generated less severe histopathological changes in the WT group, the blood serum metabolome revealed an increased fatty acid content with moderate-to-strong correlations to inflammation score, weight variation, colon length, and spleen weight. Ncf1 mice also displayed a similar pattern but with lower coefficients and showed consistently lower glucose and/or higher lactate levels which correlated with inflammation score, weight variation, and spleen weight. In our novel, DSS-induced colitis animal model, the lack of an oxidative burst ROS was sufficient to develop adenocarcinoma, and display altered blood plasma metabolic and lipid profiles. Thus, oxidative burst seems to be necessary to prevent evolution toward cancer and may confer a protective role in a ROS-mediated self-control mechanism.
Question: Write a study description for the study titled 'The prognostic value of hydroxybutyrate dehydrogenase in diffuse large B-cell lymphoma'.
Answer: In our investigation, we examined biochemical parameters and identified hydroxybutyrate dehydrogenase (HBDH) as a significant predictor for diffuse large B-cell lymphoma (DLBCL) patients. A group of 100 patients was used to explore potential biomarkers related to progression-free survival (PFS). Subsequently, an independent cohort of 404 patients from a separate hospital was recruited to validate our findings. Our results revealed a strong association between elevated HBDH levels and poor PFS. Furthermore, while overexpression of LDHB, but not LDHA, was notably linked to poorer outcomes, HBDH expression emerged as a more robust predictor of clinical prognosis compared to LDH expression. Our investigations, which included metabolic and genetic pathway enrichment analyses, indicated that patients exhibiting heightened HBDH expression were characterized by distinct pathways related to energy metabolism and lymphoma progression. In conclusion, elevated HBDH levels were correlated with adverse survival and might serve as an independent parameter for evaluating patient outcomes.
Question: Write a study description for the study titled 'Intracellular and extracellular metabolites from three strains of Prochlorococcus'.
Answer: Prochlorococcus is an abundant, cosmopolitan, marine cyanobacterium with ecotypes that vary temporally and spatially across oligotrophic regions of the global ocean. This group of organisms can serve as a model system to understand the accumulation of organic compounds synthesized by primary producers in marine ecosystems. We applied targeted metabolomics to three axenic cultures of strains that span the Prochlorococcus phylogeny: a high-light adapted HLII-clade strain, a low-light adapted LLI-clade strain, and a low-light adapted LLIV-clade strain. Intracellular metabolites were extracted from cells captured in exponential growth and extracellular metabolites were adsorbed, from the same samples, to solid-phase extraction resin. Both pools were quantified using a triple quadrupole mass spectrometer. The resulting data reveal intraspecific differences in metabolites that provide clues about the selective pressures shaping the meta-metabolism of the Prochlorococcus collective, and its interactions with the surrounding microbes that depend on them.