Project description:Tuberculosis (TB) remains a major public health problem and we lack a comprehensive understanding of how Mycobacterium tuberculosis (M. tb) infection impacts host immune responses. We compared, at two timepoints, the induced immune response to TB antigen, BCG and IL-1β stimulation between latently M. tb infected individuals (LTBI) and active TB patients. The immune response was assessed using the TruCulture system with a Null stimulation. samples were tested by Ultrahigh Performance Liquid Chromatography-Tandem Mass Spectroscopy (UPLC MS/MS) for a total of 696 metabolites.
Project description:Esophageal squamous cell carcinoma (ESCC) is characterized as a metabolic disorder characterized by lipid metabolic reprogramming. To investigate the regional characteristics of ESCC patients in Xinjiang Province, China, and lipid metabolism, in this study, we described the characteristics of the serum lipid composition in Kazakh ESCC patients by performing an integrated analysis of the transcriptome and lipidomic data. Serum samples from 30 Kazakh ESCC patients and 30 healthy individuals were subjected to targeted lipid metabolomics analysis via UPLC‒MS/MS, while 3 tumor samples and matched adjacent normal tissues from 30 ESCC patients were subjected to transcriptome analysis. Compared with those in the healthy group, we observed obvious changes in the serum lipid subclass content, chain length and unsaturation in the ESCC patients. Integrated lipidomic and transcriptomic analyses revealed that unsaturated fatty acid biosynthesis, fatty acid metabolism, lipid degradation, cholesterol metabolism and the AMPK signaling pathway were enriched in tumor tissues. In addition, RT–qPCR results demonstrated that genes closely related to these pathways were differentially expressed between the ESCC group and the healthy control group. Considering the key role of AMPK in lipid metabolism, we conducted a targeted lipid metabolomics analysis on AMPK-knockdown esophageal cancer cells by UPLC‒MS/MS. These findings suggested that AMPK might be correlated with lipid metabolism in Kazakh ESCC patients, identifying potential therapeutic targets of AMPK and other lipid metabolism-related markers against the progression of ESCC.
Project description:Purpose: The goal of this study is to integrate NGS-derived parotid salivary gland transcriptome profiling (RNA-seq) to metabolomics (UPLC-MS/MS) methods and identify mechanisms driving radiation-induced xerostomia, with potential clinical application to head and neck cancer patients. Methods: Parotid salvary gland mRNA profiles of 28-day-old wild-type (WT) and 5 Gy radiation treated mice were generated by deep sequencing, in triplicate, using Illumina TruSeq. The sequenced reads that passed quality filters were trimmed with Trimmomatic, mapped to mm10 genome with HISAT2, and summarized at the gene level with HTSeq-count and analyzed with DESeq2. Results: Using an optimized data analysis workflow, we mapped sequenced reads per sample to the mouse genome (build mm10) and identified 25422 genes with at least 1 read in the parotid glands of WT and radiation treated mice with HISTA2 workflow. RNA-seq data QA/QC by Principal Component Analysis showed a clear separation between conditions. 155 genes showed significant differential expression between the WT and radiation treated salivary gland, with an adjsuted p-value < 0.05. Pre ranked Gene Set Enrichment Analysis against the CPDB database led to 859 altered pathways with a p-value < 0.05. Integrative analysis pointed to 103 RNA-Seq/Metabolite joint enriched pathways with a p-value < 0.05.
Project description:The experiment is part of a study using systems biology approach to analyze muscle gene expression and UPLC-MS based plasma lipidomics profiling data to illuminate relevant biological pathways and to find potential biomarker candidates related to statin-induced changes in muscle metabolism.
2007-03-01 | E-TABM-116 | biostudies-arrayexpress
Project description:UPLC-QE-Orbitrap-MS-Based Metabolomics and Gut Microbiome Analysis to Reveal Codonopsis pilosula (Franch.) Nannf. Extract Improves Cyclophosphamide-Induced Immunosuppression in Mice
Project description:Intrauterine growth restriction (IUGR) is one of the most common adverse pregnancy outcomes with high risk of perinatal morbidity and mortality, and affects up to 7% of pregnancies. Here, seven pairs of placentas were employed for whole genomic promoter DNA methylation profiling and some of the candidate differentially methylated promoters were further validated in additional twelve pairs of samples. Consistent with previous report, our results further indicated that IUGR associated placentas harbored a distinct promoter DNA hypomethylation pattern and the result was further confirmed byultra-performance liquid chromatography/tandem mass spectrometry (UPLC-MS/MS)
Project description:Eriocitrin, found in lemon fruit, has shown a wide range of biological properties. Herein, to evaluate the intestinal metabolic profile of eriocitrin in colon, the flavonoids in mice colon contents were identified by ultra performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS), and a total of 136 flavonoids were found, including eriocitrin and its six metabolites (eriodictyol, homoeriodictyol, hesperetin, eriodictyol-3'-O-glucoside, hesperetin-7-O-glucoside and eriodictyol-7-O-(6''-O-galloyl) glucoside). Mice colon contents were used for 16S rDNA gene sequencing and gas chromatography-mass (GC-MS). Resultu showed that eriocitrin significantly alters the beta diversity of the gut microbiota, the probiotics such as Lachnospiraceae_UCG_006 were significantly enriched, and the production of butyrate, valerate and hexanoate in the colon pool of short-chain fatty acids (SCFAs) were significant increased. The spearman's association analysis performed some intestinal bacteria may be involved in the metabolism of eriocitrin. Collectively, our results preliminarily suggesting the metabolism of eriocitrin in the gut, demonstrate alterations of eriocitrin on gut microbiota, which warrants further investigation to determine its potential use in food and biomedical applications.