LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'A lipidomic human population and translational feeding study of hepatic steatosis and de novo lipogenesis (Human plasma assay)'.
Answer: Background: Diet is a major contributor to metabolic disease risk, but there is controversy as to whether increased incidences of diseases such as non-alcoholic fatty liver disease arise from consumption of saturated fats or free sugars. Our aims were to investigate whether a sub-set of TAGs were associated with hepatic steatosis and whether they arise from de novo lipogenesis (DNL) from the consumption of carbohydrates.  Results: We conducted direct infusion mass spectrometry of lipids in plasma to study the association between specific triacylglycerols (TAGs) and hepatic steatosis assessed by ultrasound and fatty liver index in volunteers from the UK-based Fenland Study (n=1507), and evaluated clustering of TAGs in the National Survey of Health and Development UK cohort (n=1701). TAGs formed 3 clusters, with those TAGs containing saturated and monounsaturated fatty acids with 16-18 carbons being specifically associated with hepatic steatosis. These TAGs were associated with higher consumption of carbohydrate and saturated fat, hepatic steatosis, and variations in the gene for protein phosphatase 1, regulatory subunit 3b (PPP1R3B), which in part regulates glycogen synthesis. DNL was measured in hyperphagic ob/ob mice, mice on a Western diet (high in fat and free sugar) and in healthy humans using stable isotope techniques following high carbohydrate meals, demonstrating the rate of DNL correlates with increased synthesis of this cluster of TAGs. Furthermore, these TAGs were increased in plasma from patients with biopsy-confirmed steatosis.  Conclusion: A sub-set of TAGs are associated with hepatic steatosis, even when correcting for common confounding factors. We suggest that hepatic steatosis risk in Western populations is in part driven by increased DNL following carbohydrate rich meals.  The protocols and data of the murine study of de novo lipogenesis are included in the study MTBLS614.  Linked Studies: MTBLS614
Question: Write a study description for the study titled 'Serum metabolomic profiles identify ER-positive early breast cancer patients at increased risk of disease recurrence in a multicentre population'.
Answer: PURPOSE: Detecting signals of micrometastatic disease in early breast cancer (EBC) patients could improve risk stratification and allow better tailoring of adjuvant therapies. We have previously shown that postoperative serum metabolomic profiles are predictive of relapse in a single-centre cohort of ERnegative EBC patients. Here, we investigated this further using pre-operative serum samples from ER-positive, premenopausal women with EBC who were enrolled in an international phase III trial. METHODS: Proton nuclear magnetic resonance (NMR) spectroscopy of 590 EBC samples (319 with relapse or =6 years clinical follow up) and 109 metastatic breast cancer (MBC) samples was performed. A Random Forest (RF) classification model was built using a training set of 85 EBC and all MBC samples. The model was then applied to a test set of 234 EBC samples, and a risk of recurrence score was generated based on the likelihood of the sample being misclassified as metastatic. RESULTS: In the training set, the RF model separated EBC from MBC with discrimination accuracy of 84.9%. In the test set, the RF recurrence risk score correlated with relapse, with an area under the curve of 0.747 in receiver operator characteristics analysis. Accuracy was maximised at 71.3% (sensitivity 70.8%, specificity 71.4%). The model performed independently of age, tumor size, grade, HER2 status and nodal status, and also of AdjuvantOnline risk of relapse score.CONCLUSIONS: In a multicentre group of EBC patients, we developed a model based on preoperative serum metabolomic profiles that was prognostic for disease recurrence, independent of traditional clinicopathological risk factors.
Question: Write a study description for the study titled 'Metabolomics analysis was used to resolve metabolites affecting the protein oil content of soybean.'.
Answer: Soybean (Glycine max (L.)) originated in China more than 5000 years ago, and the country is currently the third largest producer of soybeans in the world (Hymowitz et al., 2015). Based on a wild soybean Chromosome Segment Substitution Line (CSSL) population were constructed by crossing with the cultivar Suinong14 and ZYD00006 (the donor parent, a wild soybean variety) (Xin et al. 2016). A high-oil, low-protein (LPHO) and a high-protein, low-oil (HPLO) lines were screened out. In this study, a global interstitial microorganisms map were constructed, including Rhizosphere microorganisms, Phyllosphere microorganisms, Stem-interstitial microorganisms and interstitial microorganisms at the seeds developmental stage of early maturity stage (EM), mid-seed maturity stage (MM), late maturing stage (LM) and dry seed stage (DS). Whether the interstitial microorganisms may affect the growth of soybeans and the protein and oil content, as well as whether metabolites related to protein and oil content affect the surface and interior of soybeans in terms of beneficial microbial enrichment. To address these questions, we performed transcriptome sequencing, metabolomics, and microbial diversity analyses and examined significantly different microbial enrichment in LPHO/HPLO lines to screen out beneficial microbes associated with influencing soybean growth and affecting the protein and oil content. This finding will provide new ideas for further research on microorganisms affecting the protein and oil content of soybean seeds.
Question: Write a study description for the study titled 'Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community; Interaction between the kefir isolates Lactococcus lactis and Acetobacter (spent-medium assay, measured untargeted (FIA-qTOF) and targeted (HILIC, LC-MS)'.
Answer: Microbial communities often undergo intricate compositional changes yet also maintain stable coexistence of diverse species. The mechanisms underlying long-term coexistence remain unclear, as system-wide studies have been largely limited to engineered communities, ex situ adapted cultures, or synthetic assemblies. Here we show how kefir, a natural milk-fermenting community of prokaryotes and yeasts, realises stable coexistence through spatiotemporal orchestration of species and metabolite dynamics. During milk fermentation, kefir grains (a polysaccharide matrix synthesized by kefir microbes) grow in mass but remain unchanged in composition. In contrast, the milk is colonized in a sequential manner in which early members open metabolic niches for followers. Through metabolomics and large-scale mapping of inter-species interactions, we show how microbes poorly suited for milk survive in, and even dominate the community, through metabolic cooperation and uneven partitioning between grain and milk. Overall, our findings reveal how inter-species interactions partitioned in space and time lead to stable coexistence.Linked metabolomics studies:MTBLS1829 Kefir fermentation curve (FIA-MS)MTBLS1830 Interaction between the kefir isolates Lactococcus lactis and Acetobacter fabarum (GC-MS)Linked cross omic data:Genomes of isolated kefir species are available in the NCBI database under the accession: PRJNA375758 (bioproject ID: 375758).Metatranscriptomic sequencing reads can be accessed from ENA under the project id PRJEB37001.Genome-scale metabolic models for kefir bacteria can be found at github.com/cdanielmachado/kefir_models.
Question: Write a study description for the study titled 'Flow cytometry has a significant impact on the cellular metabolome (General LC-MS assay)'.
Answer: The characterization of specialized cell subpopulations in a heterogeneous tissue is essential for understanding organ function in health and disease. A popular method of cell isolation is fluorescence-activated cell sorting (FACS) based on probes that bind surface or intracellular markers. In this study, we analyse the impact of FACS on the cell metabolome of mouse peritoneal macrophages. Compared with directly pelleted macrophages, FACS-treated cells had an altered content of metabolites related to the plasma membrane, activating a mechanosensory signalling cascade causing inflammation-like stress. The procedure also triggered alterations related to energy consumption and cell damage. The observed changes mostly derive from the physical impact on cells during their passage through the instrument. These findings provide evidence of FACS-induced biochemical changes, which should be taken into account in the design of robust metabolic assays of cells separated by flow cytometry.  The General LC-MS assay is reported in the current study MTBLS629.  The Lipidomic LC-MS assay is reported in MTBLS631.  The CE-MS assay is reported in MTBLS633.  The GC-MS assay is reported in MTBLS634.  Linked Studies: MTBLS631 MTBLS633 MTBLS634
Question: Write a study description for the study titled 'Comparing Campylobacter jejuni to three other enteric pathogens in OligoMM 12 mice reveals pathogen-specific host and microbiota responses'.
Answer: Campylobacter jejuni, non-typhoidal Salmonella spp., Listeria monocytogenes and enteropathogenic/enterohemorrhagic Escherichia coli (EPEC/EHEC) are leading causes of food-borne illness worldwide. Citrobacter rodentium has been used to model EPEC and EHEC infection in mice. The gut microbiome is well-known to affect gut colonization and host responses to many food-borne pathogens. Recent progress has established gnotobiotic mice as valuable models to study how microbiota affect the enteric infections by S. Typhimurium, C. rodentium and L. monocytogenes. However, for C. jejuni, we are still lacking a suitable gnotobiotic mouse model. Moreover, the limited comparability of data across laboratories is often negatively affected by variations between different research facilities or murine microbiotas. In this study, we applied the standardized gnotobiotic OligoMM12 microbiota mouse model and compared the infections in the same facility. We provide evidence of robust colonization and significant pathological changes in OligoMM12 mice following infection with these pathogens. Moreover, we offer insights into pathogen-specific host responses and metabolite signatures, highlighting the advantages of a standardized mouse model for direct comparisons of factors influencing the pathogenesis of major food-borne pathogens. Notably, we reveal for the first time that C. jejuni stably colonizes OligoMM12 mice, triggering inflammation. Additionally, our comparative approach successfully identifies pathogen-specific responses, including the detection of genes uniquely associated with C. jejuni infection in humans. These findings underscore the potential of the OligoMM12 model as a versatile tool for advancing our understanding of food-borne pathogen interactions.
Question: Write a study description for the study titled 'Identification of AK4 and RHOC as novel oncogenes addicted by adult T-cell leukemia'.
Answer: Adult T-cell leukemia (ATL) is a highly aggressive T-cell malignancy characterized by human T-cell leukemia virus type 1 (HTLV-1) infection. ATL has a very poor prognosis and lacks satisfactory treatments; therefore, it is critical to identify novel targets in ATL cells in order to develop effective targeted therapeutics. Here we report the identification of two novel oncogenes, AK4 and RHOC, as target genes of miR-455-3p, a tumor suppressive microRNA in ATL patients. Importantly, AK4 and RHOC are highly expressed in ATL and exhibit oncogenic potentials in vitro and in vivo. Interestingly, transcriptome and metabolome analyses reveal a functional overlap of AK4 and RHOC, including activating oncogenic pathways such as Myc targets and deregulating lipid metabolism such as enhancing the production of sphingomyelin, a tumor-promoting lipid. In particular, compared to other types of T-cell malignancy such as T-ALL and CTCL, ATL is sensitive to sphingomyelin inhibition and AK4 or RHOC depletion. Altogether, we report a distinct dependency of ATL on newly characterized oncogenes AK4 and RHOC and an oncometabolite sphingomyelin, which together represent novel targetable vulnerabilities of ATL that could be exploited for developing effective therapeutics.
Question: Write a study description for the study titled 'Marine metabolomics: measurement of metabolites in seawater by gas chromatography mass spectrometry (Cell culture sampling)'.
Answer: "One of the major bottlenecks in describing marine ecosystems is characterizing the metabolome of seawater, as salt prevents metabolite analysis. We present SeaMet, a method that can detect hundreds of metabolites in less than one ml of seawater and quantifies them down to nano-molar levels using gas chromatography-mass spectrometry. Our method provides a major advance in marine metabolomics by enabling the unbiased analysis of primary metabolites across saltwater habitats. Cell culture sampling is reported in the current study.Method development is reported in MTBLS826The effect of salt and water on metabolite detection is reported in MTBLS839Environmental sampling is reported in MTBLS844Method quantification is reported in MTBLS848Solid phase extraction is reported in MTBLS849"
Question: Write a study description for the study titled 'Multiomics implicate gut microbiota in altered lipid and energy metabolism in Parkinson’s disease'.
Answer: We aimed to investigate the link between serum metabolites, gut bacterial community composition, and clinical variables in Parkinson’s disease (PD) and healthy control subjects (HC). A total of 124 subjects were part of the study (63 PD patients and 61 HC subjects). 139 metabolite features were found to be predictive between the PD and Control groups. No associations were found between metabolite features and within-PD clinical variables. The results suggest alterations in serum metabolite profiles in PD, and the results of correlation analysis between metabolite features and microbiota suggest that several bacterial taxa are associated with altered lipid and energy metabolism in PD.
Question: Write a study description for the study titled 'CD36 palmitoylation regulates the lipid metabolic homeostasis'.
Answer: Alterations in myocardial energy substrate metabolism following myocardial infarction (MI) results in structural and functional abnormalities of the heart. The fatty acid translocase CD36 (CD36), acrucial membrane protein, plays a pivotal role in regulating fatty acid (FA) uptake and lipid homeostasis. Here, we employed a comprehensive multi-omics analysis using a mouse MI model, integrating molecular biology, histological, transcriptomic and proteomic analyses. Our findings unveiled dysregulation in lipid metabolism, mitochondrial oxidative phosphorylation and related genes.
Question: Write a study description for the study titled 'Botanical collections as an opportunity to explore nature through the time: An untargeted metabolomic study in historical and modern Nicotiana leaves'.
Answer: The living and dried specimens in botanical collections play an important role in society for scientific and recreational purposes, offering the opportunity to obtain both macroscopic and molecular information for individual plants, ecosystems, and environmental studies. Untargeted metabolomics is an analytical approach that permits the simultaneous study of multiple small molecules present in an organism, which allows us to statistically compare different conditions of interest. Metabolomic approaches have been used on living specimens in botanical collections, but, until now, not on historical dried material. Using the Nicotiana genus herbaceous plant (tobacco) as a case study, we propose an untargeted metabolomic study to evaluate the potential of dried historical specimens as a source of metabolomic information on the past. The metabolomic profile from polar and less-polar/apolar aqueous extracts of four modern handmade tobacco cigars (split into wrapper, binder, and filler leaves), and a set of eight late-19th to early-20th century tobacco specimens (seven tobacco leaves and one snuff powder) from the collection of the Royal Botanical Gardens at Kew (London, UK) were analysed by liquid chromatography coupled to high resolution mass spectrometry. Results showed a wide range of polar and less-polar/apolar molecules which are preserved in dried botanical material, providing information optimal for metabolomic studies. The metabolomic profiles of historical dried samples were distinct enough to classify as Nicotiana tabacum or Nicotiana rustica, and showed differences based on geographic provenance or product transformation/processing. Statistical models based on the molecular data from the historical material permitted us to validate the labelling of the historical collection, which identified one possible mislabelled specimen and offered some clues as to the species of one unknown Nicotiana sample. Finally, metabolomic differences in profiles between Nicotiana tabacum and modern cigars showed that both share a large proportion of their metabolomic profile, where molecular differences could be possibly associated with both location of growth and anthropogenic transformation suffered by the plant in the last two centuries. This study demonstrates that dry botanical collections are a feasible source of information, and, if applied to a large set of individuals, conclusions may be drawn about the possible evolution and anthropogenic modification over time in plant material. The results are significant for disciplines interested in the history of plants, such as botany, history and archaeology.
Question: Write a study description for the study titled 'Dynamics of Plasma Lipidome in Progression to Islet Autoimmunity and Type 1 Diabetes: Type 1 Diabetes Prediction and Prevention Study (DIPP)'.
Answer: Type 1 diabetes (T1D) is one of the most prevalent autoimmune diseases among children in Western countries. Earlier metabolomics studies suggest that T1D is preceded by dysregulation of lipid metabolism. Here we used a lipidomics approach to analyze molecular lipids in a prospective series of 428 plasma samples from 40 children who progressed to T1D (PT1D), 40 children who developed at least a single islet autoantibody but did not progress to T1D during the follow-up (P1Ab) and 40 matched controls (CTR). Sphingomyelins were found to be persistently downregulated in PT1D when compared to the P1Ab and CTR groups. Triacylglycerols and phosphatidylcholines were mainly downregulated in PT1D as compared to P1Ab at the age of 3 months. Our study suggests that children who progressed to islet autoimmunity or overt T1D are characterized by distinct lipidomic signatures, which may be helpful in the identification of at-risk children before the initiation of autoimmunity.
Question: Write a study description for the study titled 'Clostridium butyricum-induced ω-3 fatty acid 18-HEPE elicits anti-influenza virus pneumonia effects through interferon-λ upregulation'.
Answer: The precise mechanism by which butyrate-producing bacteria in the gut contribute to resistance to respiratory viral infections remains to be elucidated. Here, we describe a gut-lung axis mechanism and report that orally administered Clostridium butyricum (CB) enhances influenza virus infection resistance through upregulation of interferon (IFN)-λ in lung epithelial cells. Gut microbiome-induced ω-3 fatty acid 18-hydroxy eicosapentaenoic acid (18-HEPE) promotes IFN-λ production through the G protein-coupled receptor (GPR)120 and IFN regulatory factor (IRF)-1/-7 activations. CB promotes 18-HEPE production in the gut and enhances ω-3 fatty acid sensitivity in the lungs by promoting GPR120 expression. This study finds a gut-lung axis mechanism and provides insights into the treatments and prophylaxis for viral respiratory infections.
Question: Write a study description for the study titled 'Integrative of Single-Cell RNA Sequencing and Metabolomics Decipher the Imbalanced Lipid-Metabolism in Maladaptive Immune Responses during Sepsis'.
Answer: To identify differentially expressed lipid metabolism-related genes (DE-LMRGs) responsible for immune dysfunction in sepsis. Machine learning algorithms were applied for screening hubgenes related to lipid metabolism. CIBERSORT and Single-sample GSEA were employed for assessing the immune cell infiltration of hubgenes. Next, the immune function of these hubgenes at the single cell level were validated by comparing multiregional immune landscapes between septic patients (SP) and healthy control (HC). Then, support vector machine - recursive feature elimination (SVM-RFE) algorithm was conducted to explore significantly altered metabolites critical to hubgenes using non-targeted liquid chromatography–high resolution mass spectrometry metabolomics from SP and HC. Furthermore, the role of most significant hubgene was verified in sepsis rats and LPS-induced cardiomyoctes, respectively. A total of 508 DE-LMRGs were identified between SP and HC and 5 hubgenes relevant to lipid metabolism-MAPK14, EPHX2, BMX, FCER1A and PAFAH2- were screened via multiple machine learning algorithms. Then, the correlation between hub genes and immune-cell infiltrations was analyzed and suggested an immunosuppressive microenvironment in sepsis. The role of hubgenes in immune cells was further confirmed by single-cell RNA landscape. Moreover, significantly altered metabolites were mainly enriched in lipid metabolism-related signaling pathways and was associated with MAPK14. Finally, inhibiting MAPK14 could decrease the levels of inflammatory cytokines, and improve the survival and myocardial injury of sepsis. This study indicates that these lipid-metabolic hubgenes may has great potential in prognosis prediction and precise treatment of sepsis.
Question: Write a study description for the study titled 'Adipocyte-specific Zeb1 confers breast cancer progression by triggering the tumor-associated adipose microenvironment remodeling_Medium and long chain fatty acids'.
Answer: Upon penetrating the basement membrane, breast cancer cells directly interact with their surrounding adipose tissue, which forms a unique tumor-associated adipose microenvironment (TAME). However, the underlying mechanism involved in the regulation of lipid metabolic remodeling in the TAME remains elusive. Herein, we identified a Zeb1-orchestrated bidirectional communication between breast cancer cells and their adjacent cancer-associated adipocytes (CAAs). At the molecular level, breast cancer cells, through the secretion of adrenomedullin (AM), induce downregulation of Zeb1 expression to activate the Atgl/Hsl/Scd-depedent lipolysis in CAAs, which subsequently results in the release of palmitoleic acid (POA) into the TAME. In turn, accumulated POA triggers the malignant growth and metastasis of breast cancer cells and their production of AM via an ARA-PDG2-mediated membrane phospholipid replacement mechanism. Importantly, disruption of Zeb1-dependent lipolytic activity and/or membrane phospholipid remodeling within the TAME, severely diminishes the aggressiveness of breast cancer in vitro and in vivo.