Bulk RNA-sequencing (bcRNA-SEQ) of human blood leucocytes during the onset of bacterial meningitis (BM)
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PROVIDER: PRJNA685177 | ENA |
REPOSITORIES: ENA
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Project description:Bulk RNA-sequencing (bcRNA-SEQ) of human cerebrospinal fluid (CSF) cells during the onset of bacterial meningitis (BM)
| PRJNA685176 | ENA
Project description:Purpose: Profiling the bulk transcriptomes of PBLs in sepsis-developed BM progression. Methods: The total RNA of PBLs from BM patients were extracted, and constructed into cDNA library. Raw data of mRNA profiles were sequenced by paired-end strategy. Gene-counts were generated through handling sequencing data with the combined workflow of UMI-tools, STAR, Subread package and Samtools. Results: Successfully acquirng multiple bulk-transcriptomic profiles of PBLs from BM patients in different sepsis conditions.
2020-12-15 | GSE163196 | GEO
Project description:Purpose: Profiling the bulk transcriptomes of CSF cells in sepsis-developed BM progression. Methods: The total RNA of CSF cells from BM patients were extracted, and constructed into cDNA library. Raw data of mRNA profiles were sequenced by paired-end strategy. Gene-counts were generated through handling sequencing data with the combined workflow of UMI-tools, STAR, Subread package and Samtools. Results: Successfully acquirng multiple bulk-transcriptomic profiles of CSF cells from BM patients in different sepsis conditions.
2020-12-15 | GSE163195 | GEO
Project description:Objectives: Central nervous system (CNS) infections are common causes of morbidity and mortality worldwide. We aimed to discover protein biomarkers that could rapidly and accurately identify the likely cause of the infections, essential for clinical management and improving outcome. Methods: We applied liquid chromatography tandem mass-spectrometry on 45 cerebrospinal fluid (CSF) samples from a cohort of adults with/without CNS infections to discover potential diagnostic biomarkers. We then validated the diagnostic performance of a selected biomarker candidate in an independent cohort of 364 consecutively treated adults with CNS infections admitted to a referral hospital in Vietnam. Results: In the discovery cohort, we identified lipocalin 2 (LCN2) as a potential biomarker of bacterial meningitis (BM) other than tuberculous meningitis. The analysis of the validation cohort showed that LCN2 could discriminate BM from other CNS infections (including tuberculous meningitis, cryptococcal meningitis and viral/antibody-mediated encephalitis), with the sensitivity: 0.88 (95% confident interval (CI): 0.77-0.94), the specificity: 0.91 (95%CI: 0.88-0.94) and the diagnostic odd ratio: 73.8 (95%CI: 31.8-171.4)). LCN2 outperformed other CSF markers (leukocytes, glucose, protein and lactate) commonly used in routine care worldwide. The combination of LCN2, CSF leukocytes, glucose, protein and lactate resulted in the highest diagnostic performance for BM (area under receiver-operating-characteristic-curve 0.96; 95%CI: 0.93-0.99). Conclusions: Our results suggest that LCN2 is a sensitive and specific biomarker for discriminating BM from a broad spectrum of other CNS infections. A prospective study is needed to assess the diagnostic utility of LCN2 in the diagnosis and management of CNS infections..
2020-08-20 | PXD020510 | Pride
Project description:The aim of present study was to describe the genetic pathways activated during the community acquired bacterial meningitis (BM) by using genome-wide RNA expression profiling combined with functional annotation of transcriptional changes. We included 21 patients with BM hospitalized in 2008. The control group consisted of 18 healthy subjects. The RNA was extracted from whole blood, globin mRNA was depleted and gene expression profiling was performed with GeneChip Human Gene 1.0 ST Arrays enabling the analysis of 28,869 genes. Gene expression profile data were analyzed using Bioconductor packages and Bayesian modeling. Functional annotation of the enriched gene sets was used to define changed genetic networks. We also analyzed if the gene expression profile depends on the clinical course and outcome. In order to verify the genechip results, we chose ten functionally relevant genes with high statistical significance (CD177, IL1R2, IL18R1, IL18RAP, OLFM4, TLR5, CPA3, FCER1A, IL5RA, IL7R) and performed quantitative real-time (qRT) PCR.We identified the significant differences at p values of <0.05 in 8569 genes and after False Discovery Rate (FDR) correction, total of 5500 genes remained significant at p value of <0.01. Quantitative RT-PCR confirmed differential expression for selected genes. Functional annotation and network analysis indicated that most of the genes were related to activation of humoral and cellular immune responses (enrichment score 43). Those changes were found in adults and in children with BM compared to the healthy controls. Gene expression profile didn’t depend on the clinical outcome, but there was very strong influence by the type of the pathogen. This study demonstrates a strong functional genomic evidence of the over-active immune response during bacterial meningitis. This hyperactive response possibly explains the complicated clinical course of this disease.
2012-09-05 | GSE40586 | GEO
Project description:The aim of present study was to describe the genetic pathways activated during the community acquired bacterial meningitis (BM) by using genome-wide RNA expression profiling combined with functional annotation of transcriptional changes. We included 21 patients with BM hospitalized in 2008. The control group consisted of 18 healthy subjects. The RNA was extracted from whole blood, globin mRNA was depleted and gene expression profiling was performed with GeneChip Human Gene 1.0 ST Arrays enabling the analysis of 28,869 genes. Gene expression profile data were analyzed using Bioconductor packages and Bayesian modeling. Functional annotation of the enriched gene sets was used to define changed genetic networks. We also analyzed if the gene expression profile depends on the clinical course and outcome. In order to verify the genechip results, we chose ten functionally relevant genes with high statistical significance (CD177, IL1R2, IL18R1, IL18RAP, OLFM4, TLR5, CPA3, FCER1A, IL5RA, IL7R) and performed quantitative real-time (qRT) PCR.We identified the significant differences at p values of <0.05 in 8569 genes and after False Discovery Rate (FDR) correction, total of 5500 genes remained significant at p value of <0.01. Quantitative RT-PCR confirmed differential expression for selected genes. Functional annotation and network analysis indicated that most of the genes were related to activation of humoral and cellular immune responses (enrichment score 43). Those changes were found in adults and in children with BM compared to the healthy controls. Gene expression profile didn’t depend on the clinical outcome, but there was very strong influence by the type of the pathogen. This study demonstrates a strong functional genomic evidence of the over-active immune response during bacterial meningitis. This hyperactive response possibly explains the complicated clinical course of this disease. 22 bacterial meningitis patients and 18 healthy controls
2012-09-05 | E-GEOD-40586 | biostudies-arrayexpress
Project description:In this study, we performed label-free based CSF quantitative proteomics to identify and analyze the differentially expressed proteins among bacterial meningitis, viral meningitis and hospital controls (children with benign intracranial hypertension). Compared with viral meningitis and hospital controls, we screened 135 differentially expressed proteins to distinguish bacterial meningitis from viral meningitis and controls. Among of them, 69 proteins as potential biomarkers for the diagnosis of bacterial meningitis, including both novel and previously reported candidate protein markers.
2022-05-20 | PXD026663 | Pride
Project description:Meningitis is a complex disease which can be caused by infection with either viral or bacterial pathogens. Viral meningitis is usually a sterile self-limiting disease with a good clinical prognosis, while bacterial meningitis is a potentially more serious disease with a higher mortality rate. Early diagnosis of bacterial meningitis is of paramount importance, as intervention with antimicrobial therapy increases the likelihood of a favourable clinical outcome. Routine diagnosis in many laboratories is still dependent to some degree on traditional methods e.g. culture, though molecular methods have been developed which can give a shorter time to diagnosis. However, there is not as yet a single test format that can detect all bacterial pathogens capable of causing meningitis. In addition, many tests e.g. real-time PCR have a finite limit for multiplexing and do not provide additional information such as strain or serogroup which is useful during outbreaks and for retrospective epidemiological surveillance. To this end we have developed a microarray probe set for detection of meningitis-associated bacterial pathogens including those in the N. meningitidis serogroups. Here we demonstrate utility of this array in specific detection of represented bacterial species and strains and in detection of pathogen signals in cerebrospinal fluid samples from patients with suspected bacterial meningitis. This method shows promise for development as a diagnostic tool; however, we discuss the technical issues encountered and suggest mechanisms to improve resolution of pathogen-specific signals in complex clinical samples.
2011-07-20 | GSE30794 | GEO
Project description:Single-cell RNA-sequencing (scRNA-SEQ) of cells in cerebrospinal fluid (CSF) from patients with bacterial meningitis (BM)
| PRJNA685175 | ENA
Project description:Meningitis is a complex disease which can be caused by infection with either viral or bacterial pathogens. Viral meningitis is usually a sterile self-limiting disease with a good clinical prognosis, while bacterial meningitis is a potentially more serious disease with a higher mortality rate. Early diagnosis of bacterial meningitis is of paramount importance, as intervention with antimicrobial therapy increases the likelihood of a favourable clinical outcome. Routine diagnosis in many laboratories is still dependent to some degree on traditional methods e.g. culture, though molecular methods have been developed which can give a shorter time to diagnosis. However, there is not as yet a single test format that can detect all bacterial pathogens capable of causing meningitis. In addition, many tests e.g. real-time PCR have a finite limit for multiplexing and do not provide additional information such as strain or serogroup which is useful during outbreaks and for retrospective epidemiological surveillance. To this end we have developed a microarray probe set for detection of meningitis-associated bacterial pathogens including those in the N. meningitidis serogroups. Here we demonstrate utility of this array in specific detection of represented bacterial species and strains and in detection of pathogen signals in cerebrospinal fluid samples from patients with suspected bacterial meningitis. This method shows promise for development as a diagnostic tool; however, we discuss the technical issues encountered and suggest mechanisms to improve resolution of pathogen-specific signals in complex clinical samples. We designed as part of a larger pan-pathogen microarray a sub-set of probes to meningitis-associated bacterial pathogens. We present here data confirming the pathogen-specificity of many of these probes and their potential use in clinical diagnosis through testing on a small number of patient clinical samples using human DNA and no added nucleic acid controls. These data are from single channel Cy3-labelled nucleic acids. Four technical replicates for each feature are included on the array.
2011-07-19 | E-GEOD-30794 | biostudies-arrayexpress