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Host transcription profile in nasal epithelium and blood of hospitalized children under two years old with Respiratory Syncitial Virus infection [nasopharyngeal swaps]

ABSTRACT: Analysis of transcriptional profiles in whole blood and nasopharyngeal swaps from children hospitalized with lower respiratory tract infections at their admission and their discharge, and diagnosed with either RSV or rhinovirus infections. The hypothesis is that this information will contribute to better understand the viral specific immunity and host responses to RSV infection and may suggest leads for the develoment of vaccines and specific treatment.

ORGANISM(S): Homo sapiens

PROVIDER: GSE97742 | GEO | 2017/04/14

SECONDARY ACCESSION(S): PRJNA382800

REPOSITORIES: GEO

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Host transcription profile in nasal epithelium and blood of hospitalized children under two years old with Respiratory Syncitial Virus infection [whole blood]

Project description:Analysis of transcriptional profiles in whole blood and nasopharyngeal swaps from children hospitalized with lower respiratory tract infections at their admission and their discharge, and diagnosed with either RSV or rhinovirus infections. The hypothesis is that this information will contribute to better understand the viral specific immunity and host responses to RSV infection and may suggest leads for the develoment of vaccines and specific treatment.

2017-04-14 | GSE97741 | GEO

Respiratory Syncytial Virus Genotypes and Disease Severity in Young Children Hospitalized with Bronchiolitis

Project description:Background: There is limited data on how different RSV genotypes and associated viral loads influence disease phenotypes. We characterized the genetic variability of RSV strains during five non-consecutive respiratory seasons, and evaluated the role of RSV subtypes, genotypes and viral loads on clinical disease severity. Methods: Healthy infants hospitalized with RSV bronchiolitis were prospectively enrolled and nasopharyngeal samples obtained within 24h of hospitalization for RSV load quantitation by PCR, typing and genotyping. Parameters of disease severity were assessed, and multivariate models constructed to identify virologic and clinical factors predictive of clinical outcomes. Results: From March 2004 to April 2011, we enrolled 253 patients (56.5 % males; median age 2.1 (1.1-4.0) months). RSV A infections predominated over RSV B (69% vs. 31%; p<0.001) and showed greater genotype variability. The most common genotypes were RSV A/GA2, A/GA5 and RSV B/BA. Infants infected with RSV GA5 had higher viral loads compared with GA2 or BA infection (p<0.01), independent of duration of symptoms. After adjusting for other covariates, RSV A/GA5 infections were associated with longer hospital stay. Conclusions: RSV A infections were more frequent than RSV B infections and displayed greater genetic variability. Infections with GA5 were independently associated with clinical disease severity.

2018-03-21 | GSE103842 | GEO

High expression of oleoyl-ACP-hydrolase predicts mortality in patients hospitalized with avian A(H7N9) influenza

Project description:Although respiratory viral infections cause significant morbidity and mortality, it is still not fully clear why some individuals succumb to severe disease. In patients hospitalized with avian A(H7N9) influenza, we investigated early drivers underpinning hypercytokinemia and fatal disease. Our transcriptomics studies identified differential expression of 10 early host genes, defined by 16 probe sets, between patients who recovered and died. Seven probe sets were specific for the same host gene encoding for a key enzyme mediating free fatty acid production, oleoyl-ACP-hydrolase (OLAH). High olah transcript levels in fatal A(H7N9) patients were detected early after hospital admission and persisted until patients died. Conversely, patients who recovered had minimal olah transcript expression throughout their hospital stays.

2024-09-02 | GSE268303 | GEO

Genome-wide analysis of whole blood transcriptional response to Respiratory Syncytial Virus, Influenza and Rhinovirus lower respiratory tract infection (LRTI) in children

Project description:Analysis of transcriptional profiles in whole blood from children < 2 years of age (and healthy matched controls) with RSV, rhinovirus and influenza infection. The hypothesis tested is that transcriptional profile heterogeneity will reflect patient clinical heterogeneity and that RSV infection induces a distinct host response compared with influenza and rhinovirus infection Total RNA extracted from whole blood (lysed in Tempus tubes) drawn from individual pediatric patients with acute RSV, influenza and Rhinovirus lower respiratory tract infection. A total of 241 samples are analyzed: 135 with acute RSV LRTI, 30 with Rhinovirus LRTI, 16 with influenza LRTI, 39 age-sex matched healthy controls and 21 samples obtained one month after the acute hospitalization in children with RSV. Samples GSM1226237-GSM1226272, which were hybridized to Platform GPL10558, were normalized separately from the other Samples in this Series, which were hybridized to Platform GPL6884. 'GSE38900_non-normalized_GSM1226237-GSM1226272.txt.gz' includes the non-normalized data for Samples GSM1226237-GSM1226272; 'GSE38900_non-normalized.txt.gz' includes the non-normalized data for the other Samples.

2013-11-12 | E-GEOD-38900 | biostudies-arrayexpress

Distinct peripheral blood mononuclear cells transcriptional modules in the response to human respiratory syncytial virus or human rhinovirus in hospitalized infants with bronchiolitis

Project description:Human respiratory syncytial virus (HRSV) is the main cause of bronchiolitis during the first year of life, but other viruses such as rhinovirus also occur and are clinically indistinguishable. In hospitalized infants with bronchiolitis, the analysis of the peripheral blood mononuclear cells (PBMC) gene expression might be useful for identification the etiologies caused by HRSV and human rhinovirus (HRV) and to the development of future tests, as well as to elucidate the pathogenic mechanisms triggered by different viral agents and new therapeutic possibilities. In this study, we conducted a comparative global gene expression analysis of infants with acute viral bronchiolitis infected by HRSV (HRSV group) or HRV (HRV group).

2019-03-19 | GSE124124 | GEO

Transcriptional profile of PBMCs in patients with acute RSV or Influenza infection

Project description:To study the transcriptional profile of patients with acute RSV or Influenza infection,children of median age 2.4 months (range 1.5-8.6) hospitalized with acute RSV and influenza virus infection were offered study enrollment after microbiologic confirmation of the diagnosis. Blood samples were collected from them within 42-72 hours of hospitalization. We excluded children with suspected or proven polymicrobial infections, with underlying chronic medical conditions (i.e congenital heart disease, renal insufficiency), with immunodeficiency, or those who received systemic steroids or other immunomodulatory therapies. The RSV cohort consisted of 51 patients with median age of 2 months (range 1.5-3.9) and the influenza cohort had 28 patients with median age of 5.5 months (range 1.4-21). Control samples were obtained from healthy children undergoing elective surgical procedures or at outpatient clinic visits. To exclude viral co-infections we performed nasopharyngeal viral cultures of all subjects. We recruited 10 control patients for the RSV cohort with median age of 6.7 months (range 5-10), and 12 control patients for the influenza cohort with median age of18.5 months (range 10.5-26). We used microarrays to obtain the transcriptional profile of PBMCs from patients with acute RSV or Influenza infection and compared these signatures with the transcriptional profile of primary airway epithelial cells infected with RSV or Influenza.

2012-03-12 | E-GEOD-34205 | biostudies-arrayexpress

Blood mRNA profiling to support prognosis of disease severity in respiratory syncytial virus infected infants

Project description:In this study we investigated whether there exists a genomic signature that can accurately predict the course of a respiratory syncytial virus (RSV) infection in hospitalized young infants. We used early blood microarray transcriptome profiles from 39 infants that were followed until recovery and of which the level of disease severity was determined retrospectively. Applying support vector machine learning on age by sex standardized transcriptomic data, an 84 gene signature was identified that discriminated hospitalized infants with eventually less severe RSV infection from infants that suffered from most severe RSV disease.

2016-11-11 | E-MTAB-5195 | biostudies-arrayexpress

Genome-wide analysis of whole blood transcriptional response to Respiratory Syncytial Virus, Influenza and Rhinovirus lower respiratory tract infection (LRTI) in children

2013-11-12 | GSE38900 | GEO

Multiomic chromatin accessibility and gene expression in peripheral blood predicts future decompensation in hospitalized adults with COVID-19

Project description:To elucidate host response elements that define impending decompensation during SARS-CoV-2 infection, we enrolled subjects hospitalized with COVID-19 who were matched for disease severity and comorbidities at the time of admission and initial sampling. We then performed combined single-cell RNA sequencing (scRNA-seq) and single cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) on peripheral blood mononuclear cells (PBMCs) from the time of admission and compared subjects who improved from their initial low-level oxygen requirement (no change from initial WHO Ordinal category 4/5) to those who later clinically decompensated and required invasive mechanical ventilation or died (WHO Ordinal score 7/8). Chromatin accessibility and transcriptomic immune profiles were markedly altered at admission in patients who will go on to develop critical illness. The greatest immunologic signals were seen in CD4+ T cells, inflammatory T cells, dendritic cells, and NK cell subsets, where an aggregate multiomic signature score calculated at admission offered strong prediction of future clinical deterioration (area under the receiver operating characteristic curve (auROC) 0.91). Epigenetic and transcriptional changes in PBMCs reveal unique, early, and conserved aspects of the immune response before typical clinical signals of decompensation are apparent and thus provide novel biomarkers that can predict future disease severity.

2023-10-17 | GSE215915 | GEO

Proteomic Characterization of Acute Kidney Injury in Patients Hospitalized with SARS-CoV2 Infection

Project description:Background: Acute kidney injury (AKI) is a known complication of COVID-19 and is associated with an increased risk of in-hospital mortality. Unbiased proteomics using biological specimens can lead to improved risk stratification and discover pathophysiological mechanisms. Methods: Using measurements of ~4000 plasma proteins in two cohorts of patients hospitalized with COVID-19, we discovered and validated markers of COVID-associated AKI (stage 2 or 3) and long-term kidney dysfunction. In the discovery cohort (N= 437), we identified 413 higher plasma abundances of protein targets and 40 lower plasma abundances of protein targets associated with COVID-AKI (adjusted p <0.05). Of these, 62 proteins were validated in an external cohort (p <0.05, N =261). Results: We demonstrate that COVID-AKI is associated with increased markers of tubular injury (NGAL) and myocardial injury. Using estimated glomerular filtration (eGFR) measurements taken after discharge, we also find that 25 of the 62 AKI-associated proteins are significantly associated with decreased post-discharge eGFR (adjusted p <0.05). Proteins most strongly associated with decreased post-discharge eGFR included desmocollin-2, trefoil factor 3, transmembrane emp24 domain-containing protein 10, and cystatin-C indicating tubular dysfunction and injury. Conclusions: Using clinical and proteomic data, our results suggest that while both acute and long-term COVID-associated kidney dysfunction are associated with markers of tubular dysfunction, AKI is driven by a largely multifactorial process involving hemodynamic instability and myocardial damage.

2023-12-01 | GSE225349 | GEO

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