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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression changes induced by MV130 (BactekÂ®) in human monocytes-derived dendritic cells.

ABSTRACT: MV130 is a commercially polyvalent bacterial preparation, which has shown to reduce the the rate of respiratory infections in patients suffering from recurrent respiratory tract infections. However, the immunological mechanisms associated to this clinical benefit remain unknown. We wanted to identify immunological mechanisms in human monocytes-derived dendritic cells (hmoDCs) from 4 healthy donors treated with MV130 compared to control. Global comparative transcription by DNA technology, allows us to detect genes, pathways and clusters that are differentially expressed with the treatment (MV130) respect to control.

ORGANISM(S): Homo sapiens

SUBMITTER: Cristina Cirauqui ArmendÃ¡riz

PROVIDER: E-MTAB-5259 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Sublingual therapeutic immunization with a polyvalent bacterial preparation in patients with recurrent respiratory infections: immunomodulatory effect on antigen-specific memory CD4+ T cells and impact on clinical outcome.

Alecsandru D D Valor L L Sánchez-Ramón S S Gil J J Carbone J J Navarro J J Rodríguez J J Rodríguez-Sainz C C Fernández-Cruz E E

Clinical and experimental immunology 20110401 1

Recurrent respiratory tract infections (RRTIs) are common clinical conditions in individuals with alterations of the immune function. A prospective open pilot study in a cohort of patients with RRTIs has been performed to assess whether sublingual immunization with a polyvalent bacterial vaccine could exert an immunomodulatory effect on the antigen-specific immunological responses and have an impact on the clinical outcome. Seventeen patients with RRTIs were recruited. An oral polyvalent bacteri ...[more]

PMID: 21391984

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RNA-seq-based analysis of the physiologic cold shock-induced changes in Moraxella catarrhalis gene expression

Project description:Background: Moraxella catarrhalis, a major nasopharyngeal pathogen of the human respiratory tract, is exposed to rapid downshifts of environmental temperature when humans breathe cold air. The prevalence of pharyngeal colonization and respiratory tract infections caused by M. catarrhalis is greatest in winter. We investigated how M. catarrhalis uses the physiologic exposure to cold air to regulate pivotal survival systems that may contribute to M. catarrhalis virulence. Results: In this study we used the RNA-seq techniques to quantitatively catalogue the transcriptome of M. catarrhalis exposed to a 26Â°C cold shock or to continuous growth at 37Â°C. Validation of RNA-seq data using quantitative RT-PCR analysis demonstrated the RNA-seq results to be highly reliable. We observed that a 26Â°C cold shock induces the expression of genes that in other bacteria have been related to virulence: a strong induction was observed for genes involved in high affinity phosphate transport and iron acquisition, indicating that M. catarrhalis makes a better use of both phosphate and iron resources after exposure to cold shock. We detected the induction of genes involved in nitrogen metabolism, as well as several outer membrane proteins, including ompA, m35-like porin and multidrug efflux pump (acrAB) indicating that M. catarrhalis remodels its membrane components in response to downshift of temperature. Furthermore, we demonstrate that a 26Â°C cold shock enhances the induction of genes encoding the type IV pili that are essential for natural transformation, and increases the genetic competence of M. catarrhalis, which may facilitate the rapid spread and acquisition of novel virulence-associated genes. mRNA profiles of Moraxella catarrhalis were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.

2013-07-22 | E-GEOD-46256 | biostudies-arrayexpress

Characterization of the molecular interplay between Moraxella catarrhalis and human respiratory tract epithelial cells: Expression Moraxella catarrhalis strain BBH18 during adherence to human phanryngeal epithelial Detroit 562 cells

Project description:During the course of infection, respiratory pathogens like Moraxella catarrhalis needs to adhere to epithelial cells of different host niches such as the nasopharynx and lungs. Consequently, efficient adhesion to epithelial cells is considered an important virulence trait of M. catarrhalis. We examined the interaction between human pharyngeal epithelial Detroit 562 cells and M. catarrhalis BBH18 during adherence using a combination of Tn-seq, a genome-wide negative selection screenings technology, and expression profiling of both host and pathogen. The results described in this study are further discussed in Stefan P.W. de Vries, Marc J. Eleveld, Peter W.M. Hermans, Hester J. Bootsma: Characterization of the molecular interplay between Moraxella catarrhalis and human respiratory tract epithelial cells, submitted. After 1 hour adherence to Detroit 562 cells, RNA was isolated from adherent (n = 4) and non-adherent (planktonic) (n = 4) M. catarrhalis BBH18 as well as from bacteria incubated in the infection medium alone (n = 3). RNA obtained from the adherent fraction was enriched for bacterial RNA using the MICROBEnrich kit (Ambion). Total RNA was labeled according to standard Nimblegen gene expression array protocols and hybridized to a 4x72K Nimblegen M. catarrhalis expression array for read-out.

2013-06-27 | E-GEOD-47870 | biostudies-arrayexpress

Identification of genes essential for Moraxella catarrhalis growth under iron-limiting conditions using Genomic Array Footprinting (GAF): Expression analysis of directed gene deletion mutants.

Project description:Iron-sequestration by the human host is a first line defense against respiratory pathogens like Moraxella catarrhalis, which consequently experiences a period of iron-starvation during colonization and infection. We determined the genetic requirements for M. catarrhalis growth during iron-starvation using the high-throughput genome-wide screening technology genomic array footprinting (GAF). To further characterize the functional consequences of the gene deletions (GAF identified genes), we determined transcriptome profiles of the wild-type and directed mutant strains during exponential growth in BHI medium. The results described in this study are further discussed in Stefan P.W. de Vries, Peter Burghout, Jeroen D. Langereis, Aldert Zomer, Peter W.M. Hermans, Hester J. Bootsma: Genetic requirements for Moraxella catarrhalis growth under iron-limiting conditions, Molecular Microbiology. M. catarrhalis BBH18 directed mutants (n = 3) and their parental wild-type BBH18 strain (n = 4) were expanded to mid-log phase (OD620nm, 1.2 to 1.4) and RNA was isolated as previously described (de Vries et al., 2010 J Bacteriol 192: 3574-3583). Total RNA was labeled according to standard Nimblegen gene expression array protocols and hybridized to 4x72K custom design Nimblegen arrays for read-out.

2013-06-06 | E-GEOD-41547 | biostudies-arrayexpress

Expression profiling of Moraxella catarrhalis RH4 during in vitro growth in brain heart infusion (BHI) medium

Project description:Transcriptome analysis of M. catarrhalis RH4 predicted coding sequences and clustered regularly interspaced short palindromic repeats (CRISPRs) regions. The results described in this study are further discussed in De Vries, S.P.W., van Hijum, S.A.F.T., Schueler, W., Riesbeck, K., Hays, J.P., Hermans, P.W.M., Bootsma, H.J.; Genome analysis of Moraxella catarrhalis strain RH4: a human respiratory tract pathogen; Journal of Bacteriology Total RNA from lag phase (OD620 = 0.2-0.3), exponential phase (OD620 = 1.2-1.4), or stationary phase (OD620 = 2.0-2.2) bacteria grown in triplicate in BHI medium, and hybridized in duplicate on 4x72K custom design Nimblegen arrays

2010-05-07 | E-GEOD-21632 | biostudies-arrayexpress

Deciphering the genetic basis of Moraxella catarrhalis complement resistance: Gene expression analysis of Moraxella catarrhalis BBH18 upon exposure to normal human serum.

Project description:The complement system is an important part of the innate defense against invading pathogens. The ability to resist complement-mediated killing is considered to be an important virulence trait for the human-restricted respiratory tract pathogen M. catarrhalis, as most disease-associated M. catarrhalis isolates are complement-resistant. Here we studied the molecular basis of M. catarrhalis complement-resistance by transcriptome profiling upon exposure to 10% normal human serum (NHS). After 1h exposure of M. catarrhalis BBH18 to 10% NHS (n = 5) or the NHS dilution buffer alone (control, n = 5), total RNA was isolated and labeled cDNA was generated according to standard Nimblegen gene expression array protocols and hybridized to 4x72K Nimblegen M. catarrhalis expression arrays for read-out.

2014-06-23 | E-GEOD-52552 | biostudies-arrayexpress

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Expression data of Pseudomonas aeruginosa isolates from Cystic Fibrosis patients in Denmark

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2011-08-05 | E-GEOD-31227 | biostudies-arrayexpress

The rhinobiome of exacerbated preschool wheezers & asthmatics: insights from a German pediatric exacerbation network

Project description:Although the nose, as a gateway for organism-environment interactions, may have a key role in asthmatic exacerbation, the rhinobiome of exacerbated children with asthma was widely neglected to date. Deep nasopharyngeal swab specimens, nasal epithelial spheroid cultures (NAEsp), and blood samples of acute exacerbated wheezers (WH), asthmatics (AB), and healthy controls (HC) were used for culture (n=146), 16 S-rRNA gene amplicon sequencing (n=64), proteomic and cytokine analyses. Interestingly, Proteobacteria were over-represented in WH (WH to AB: p=0.005; WH to HC: p=0.021), whereas Firmicutes and Bacterioidetes were associated with AB. In contrast, Actinobacteria commonly colonized HCs (PermANOVA p=0.005). Moreover, Staphylococcaceae (p<0.05), Enterobacteriaceae (p<0.05), Burkholderiaceae (p<0.05), Xanthobacteraceae (p<0.05), and Sphingomonadaceae (p<0.05) were significantly more abundant in AB compared to WH and HC. The α‐diversity analyses demonstrated an increase of bacterial abundance levels in atopic AB and a decrease in WH samples. Microbiome profiles of atopic WH differed significantly from atopic AB. The NAEsp bacterial exposure with M. catarrhalis, S. aureus and H. influenzae experiments provided a disrupted epithelial cell integrity, a cytokine release and cohort specific proteomic differences especially for M. catarrhalis cultures. Our comprehensive dataset contributes to a deeper insight into the poorly understood plasticity of the nasal microbiota, and, in particular, may enforce our understanding in the pathogenesis of asthma exacerbation in childhood.

2021-05-27 | PXD024694 | Pride

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Project description:This series includes 278 microarrays used to detect respiratory viruses in a set of nasopharyngeal lavage specimens from children with respiratory tract infections Objective: To assess the utility of a pan-viral DNA microarray platform (Virochip) in the detection of viruses associated with pediatric respiratory tract infections. Study Design: The Virochip was compared to conventional clinical direct fluorescent antibody (DFA) and PCR-based testing for the detection of respiratory viruses in 278 consecutive nasopharyngeal aspirate samples from 222 children. Results: The Virochip was superior in performance to DFA, showing a 19% increase in the detection of 7 respiratory viruses included in standard DFA panels, and was similar to virus-specific PCR (sensitivity 85-90%, specificity 99%, PPV 94-96%, NPV 97-98%) in the detection of respiratory syncytial virus, influenza A, and rhino-/enteroviruses. The Virochip also detected viruses not routinely tested for or missed by DFA and PCR, as well as double infections and infections in critically ill patients that DFA failed to detect. Conclusions: Given its favorable sensitivity and specificity profile and greatly expanded spectrum of detection, microarray-based viral testing holds promise for clinical diagnosis of pediatric respiratory tract infections. Keywords: viral detection The series includes 278 clinical specimens

2010-05-26 | E-GEOD-10294 | biostudies-arrayexpress

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