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Genomic biomarkers from urine cells indicate a unique metabolomic difference between sepsis and sterile inflammation (discovery cohort)

ABSTRACT: Genomic biomarkers from urine cells indicate a unique metabolomic difference between sepsis and sterile inflammation (discovery cohort)

PROVIDER: PRJNA707447 | ENA |

REPOSITORIES: ENA

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Genomic biomarkers from urine cells indicate a unique metabolomic difference between sepsis and sterile inflammation

Project description:Genomic biomarkers from urine cells indicate a unique metabolomic difference between sepsis and sterile inflammation

| PRJNA707442 | ENA

Genomic biomarkers from urine cells indicate a unique metabolomic difference between sepsis and sterile inflammation (validation cohort)

Project description:Genomic biomarkers from urine cells indicate a unique metabolomic difference between sepsis and sterile inflammation (validation cohort)

| PRJNA707444 | ENA

Genomic biomarkers from urine cells indicate a unique metabolomic difference between sepsis and sterile inflammation (discovery cohort)

Project description:Sepsis is a time-sensitive condition associated with significant mortality, morbidity, and healthcare costs, especially when the diagnosis is delayed. Clinicians often fail to accurately differentiate between sepsis and a sterile systemic inflammatory response syndrome (SIRS) among patients who incur sterile tissue damage from major surgery. Sepsis is driven by a dysregulated host response to pathogens; SIRS is driven by tissue damage. Transcriptomic profiling of whole blood or of specific cellular components of blood have been utilized for discovering underlying etiological differences between sepsis and uninfected SIRS. Blood-based gene microarrays have demonstrated efficacy in differentiating sepsis from SIRS. Urine is often collected from critically ill patients as standard clinical care, but the diagnostic utility of urine sepsis biomarkers is unknown. In this study we used single-center prospective cohorts of SIRS and sepsis patients, we tested the hypothesis that machine learning feature selection from whole genome transcriptomic urinary RNA signatures can identify gene expression patterns that differentiate between sepsis and sterile SIRS within twelve hours of sepsis onset.

2021-07-12 | GSE168442 | GEO

Genomic biomarkers from urine cells indicate a unique metabolomic difference between sepsis and sterile inflammation (validation cohort)

2021-07-12 | GSE168440 | GEO

Genomic biomarkers from urine cells indicate a unique metabolomic difference between sepsis and sterile inflammation

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-07-12 | GSE168443 | GEO

Global expression profile difference of hiPSCs between hESCs and human Urine-Derived Cells

Project description:Compare difference Global expression profile of hiPSCs between hESCs and human Somatic cells, showing that hiPSCs and hESCs is consistent in lineages and indicated that the induce method is safe and reliable. There are three groups of samples, each group has two repeated samples, hiPSCs respectively compared with hESCs and human Urine-Derived Cells.

2016-08-23 | E-GEOD-85885 | biostudies-arrayexpress

Urine Metabolomics and Colorectal Cancer Screening

Project description:This is a prospective, multi-centered study to assess whether urine metabolomics can play a role in the screening of colorectal cancer (CRC). Urine samples will be collected from 1000 patients going through an established CRC screening program, and from a further 500 patients who already have a diagnosis of CRC. Using nuclear magnetic resonance (NMR) spectroscopy, the 1H NMR spectrum of urine samples will be analyzed for specific metabolites, and establish the metabolomic signature of colorectal cancer. The results from metabolomic urinalysis of this screening cohort will be compared with results from colonoscopy, histological descriptions, fecal occult blood testing (FOBT), and fecal immune testing (FIT) to assess the accuracy of urine metabolomics in identifying patients with polyps and malignancies. The urine metabolomic results from the colorectal cancer group will be correlated with operative, histological and clinical staging to define the role of urine metabolomics in assessing colorectal cancer type, location and stage. Additionally approximately 300 urine samples from breast cancer patients and 300 from prostate cancer patients will be collected to validate that the colorectal cancer signature is unique.

| 2116822 | ecrin-mdr-crc

A benzimidazole inhibitor attenuates sterile inflammation induced in a model of systemic autoinflammation

Project description:Sterile stimuli can trigger inflammatory responses, and in some cases can lead to a variety of acute or chronic diseases. In this study, we hypothesize that a benzimidazole inhibitor may be used as a therapeutic in the treatment of sterile inflammation. In vitro, this inhibitor blocks TLR signalling and inflammatory responses. The benzimidazole inhibitor does not prevent mouse macrophage activation after stimulation with 2, 6, 10, 14-tetramethylpentadecane (TMPD, also known as pristane), a hydrocarbon oil that mimics features of sterile inflammation when injected in vivo. However, C57BL/6 female mice treated with the benzimidazole inhibitor exhibited a significant reduction of pristane-dependent induction of splenocyte number and weight. Conversely, no significant difference was observed in males. Using mass spectrometry, we found that the urine of pristane-injected mice contained increased levels of putative markers for several inflammatory diseases, which were reduced by the benzimidazole inhibitor. To study the mechanism, we showed that pristane-injected mice had increased cell free DNA in serum, which was not impacted by inhibitor treatment. However, chemokine release (e.g. MCP-1, RANTES and TARC) was significantly reduced in inhibitor-treated mice. Thus, the benzimidazole inhibitor might be used as a new drug to block the recruitment of immune cells during sterile inflammatory diseases in humans.

2020-07-27 | PXD017492 | Pride

Investigating the comprehensive health effects of municipal effluents on mice using transcriptomic and metabolomic approaches

Project description:Transcriptomic, metabolomic and metagenomic approaches were performed to investigate the multifaceted health effects of municipal effluents (ME) on mice. After chronic exposure for 90 days, alterations in liver gene expression, serum and urine metabolic profiles. A total of 4446 differentially expressed genes (DEGs) were identified, which related to 107 KEGG pathways. Metabolomics identified 8 and 10 differential altered metabolites (DAMs) in serum and urine, respectively. Moreover, the ME exposure also induced some perturbations of the gut microbiota, which related to co-metabolism and immune responses. Nine mice in each group were selected and the livers of every three mice were homogenized together to obtain a total RNA sample. Three RNA samples in the treated or control group were hybridized separately onto three arrays to compare the genomic expression between the two groups.

2016-05-31 | E-GEOD-48467 | biostudies-arrayexpress

Investigating the comprehensive health effects of municipal effluents on mice using transcriptomic and metabolomic approaches

2016-05-31 | GSE48467 | GEO