ECMO-biofilms and sepsis risks
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ABSTRACT:
PROVIDER: PRJEB93957 | ENA |
REPOSITORIES: ENA
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Project description:Escherichia coli strain:EcMO Genome sequencing and assembly
| PRJNA382712 | ENA
Project description:The temporal evolution of sepsis was monitored by transcriptional profiling of five critically ill children with meningococcal sepsis and sepsis-induced multiple organ failure. Blood was sampled at 6 time points during the first 48 hours of their admission to pediatric intensive care, where the children received standard clinical treatment including organ support and antimicrobial therapy. Striking transcript instability was observed over the 48 hours, with increasing numbers of regulated genes over time. Most notably, proposed biomarkers for sepsis risk stratification also showed expression instability, with varied expression levels over 48 hours. This study demonstrates the extent of the complexity of temporal changes in gene expression that occur during the evolution of sepsis-induced multiple organ failure. Importantly, stratification tools that propose expression of biomarkers must take into account the temporal changes, over the use of single snapshots that may be less informative.
2013-04-03 | E-MEXP-3850 | biostudies-arrayexpress
Project description:The mortality risk from cancer-associated sepsis is differentially affected by individual cancer sites and host responses to sepsis are heterogenous. Native Hawaiians have a 2-fold higher mortality risk from cancer-associated sepsis than Whites and also higher mortality risk from colorectal cancer (CRC). We investigated this disparity by examining ethnic variation in the transcriptome of patients with CRC-associated sepsis and its relation to survival and genetic diversity. We conducted transcriptomic profiling of CRC tumors and adjacent non-tumor tissue obtained from adult patients of Native Hawaiian and Japanese ethnicity who died from cancer-associated sepsis. We examined differential gene expression in relation to patient survival and sepsis disease etiology.
2022-09-01 | GSE198103 | GEO
Project description:The present study aims to characterise proteins bound to circuits collected from children on extracorporeal membrane oxygenation (ECMO). ECMO circuits were collected from 6 patients. Quantification of concentrations for proteins bound to the ECMO circuit samples was performed using bicinchoninic acid (BCA) protein assay, whilst characterisation of the bound proteome was performed using Data-independent acquisition Mass Spectrometry (DIA-MS). Reactome Over-representation Pathway Analyses tool was used to identify functional pathways corresponding to the common proteins bound to circuits across all patients.
2024-10-07 | PXD045889 | Pride
Project description:Extracorporeal membrane oxygenation (ECMO) has been increasingly applied to both adult and paediatric patients worldwide. However, continuous contact between blood and foreign surface of the ECMO circuit may contribute to haemostatic, inflammatory and other physiological disturbances during ECMO. Although previous studies have extensively investigated blood samples from patients on ECMO, the protein and cellular binding to the ECMO circuit has largely been overlooked as an additional factor that could contribute to differences in clinical outcomes. The detailed protocol described in this paper enables the comprehensive characterisation of protein and cellular binding in paediatric ECMO circuits, which could extend our knowledge of the pathophysiology of circuit binding and provide guidance for improved ECMO circuit design.
2024-10-07 | PXD046085 | Pride
Project description:1364 plasma proteome samples taken at time-of-admission to the emergency department from patients suspected of sepsis.
Used initially with the following abstract:
Sepsis is one of the leading causes of mortality in the world. Currently, the heterogeneity of sepsis makes it challenging to determine the molecular mechanisms that define the syndrome. Here, we leverage population scale proteomics to analyze a well-defined cohort of 1364 blood samples taken at time-of-admission to the emergency department from patients suspected of sepsis. We identified panels of proteins using explainable artificial intelligence that predict clinical outcomes and applied these panels to reduce high-dimensional proteomics data to a low-dimensional interpretable latent space (ILS). Using the ILS, we constructed an adaptive digital twin model that accurately predicted organ dysfunction, mortality, and early-mortality-risk patients using only data available at time-of-admission. In addition to being highly effective for investigating sepsis, this approach supports the flexible incorporation of new data and can generalize to other diseases to aid in translational research and the development of precision medicine.
2024-04-08 | MSV000094486 | MassIVE
Project description:Background: Sepsis, a leading cause of morbidity and mortality, is not a homogeneous disease but rather a syndrome encompassing many heterogeneous pathophysiologies. Patient factors including genetics predispose to poor outcomes, though current clinical characterizations fail to identify those at greatest risk of progression and mortality. Results: The Community Acquired Pneumonia and Sepsis Outcome Diagnostic study enrolled 1,152 subjects with suspected sepsis. We sequenced peripheral blood RNA of 129 representative subjects with systemic inflammatory response syndrome (SIRS) or sepsis (infection with SIRS), including 78 sepsis survivors and 28 sepsis nonsurvivors, who had previously undergone plasma proteomic and metabolomic profiling. The expression of 338 genes differed between subjects with SIRS and those with sepsis, primarily reflective of immune activation in sepsis. The expression of 1,238 genes differed with sepsis outcome: Nonsurvivors had lower expression of many immune function-related genes. Functional genetic variants associated with sepsis mortality were sought based on a common disease â rare variant hypothesis. VPS9D1, whose expression was increased in sepsis survivors, had a higher burden of missense variants in sepsis survivors, and these were associated with altered expression of 3,799 genes, primarily reflecting Golgi and endosome biology. Conclusions: Host response in sepsis survivors â activation of immune response-related genes â was muted in sepsis nonsurvivors. The association of sepsis survival with robust immune response and presence of missense variants in VPS9D1 warrants replication and further functional studies. We sequenced peripheral blood RNA of 129 representative subjects with systemic inflammatory response syndrome (SIRS, n=23) or sepsis (infection with SIRS), including 78 sepsis survivors and 28 sepsis nonsurvivors, who had previously undergone plasma proteomic and metabolomic profiling.
2015-01-01 | E-GEOD-63042 | biostudies-arrayexpress