{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Edward Parkinson"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15687"],"description":["The purpose of this study was to investigate changes in host gene expression profiles of neonatal infants with sepsis prior to the initiation of and during vancomycin therapy, to identify treatment-responsive genes and signature pathways associated with recovery from neonatal sepsis. The study analyzed data from a subset of 35 infants recruited to the NeoVanc trial, a multi-center randomized open label phase IIb study which compared the efficacy, safety and pharmacokinetics of an optimized dosing to a standard dosing regimen of vancomycin in neonates and infants aged less than 90 days with late onset bacterial sepsis (ClinicalTrials.gov ID: NCT02790996). All infants selected had a positive blood culture for Staphylococcus epidermidis in addition to a clinical diagnosis of neonatal sepsis. Whole blood samples were collected for each infant at five time points between the time of randomization to the trial until a short term follow up visit, approximately 30 days after randomization."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - 50 µL samples of whole blood of were mixed with stabilizing reagent potassium amyl xanthate (PAX) in small volume PAXgene blood RNA tubes (Thermo Fisher Scientific) and stored at -80C. Total RNA quality and quantity was assessed using Agilent 4200 TapeStation and a High Sensitivity RNA kit (Agilent Technologies).","Labeling - 2-10 ng of total RNA with a RNA Integrity Number (RIN) value > 5 was amplified following a 2-cycle cDNA amplification protocol, fragmented and biotinylated using the GeneChip WT Pico labelling kit (Thermo Fisher Scientific) according to the manufacturer's instructions. Briefly, first strand complementary deoxyribonucleic acid (cDNA) was synthesized with a combination of Poly-dT and random primers containing a 5’-adaptor sequence. A 3’-adaptor was added to the single stranded cDNA followed by low-cycle polymerase chain reaction (PCR) amplification. The cDNA was used as template for in vitro transcription (IVT) that produces amplified amounts of antisense messenger RNA (cRNA). The cRNA was then used as input for a second round of first strand cDNA synthesis, producing single stranded sense cDNA, which was then enzymatically fragmented to short lengths (approx. 40-70 base pairs) and end-labelled with biotin using terminal deoxynucleotidyl transferase (TdT).","Hybridization - Single stranded sense cDNA was hybridized to the Affymetrix Clariom D human microarray assay according to the manufacturer’s instructions (Thermo Fisher Scientific).","Sample Collection - This study analyzed data from infants recruited to the NeoVanc trial, a multi-center randomized open label phase IIb study which compared the efficacy, safety and pharmacokinetics of an optimized dosing to a standard dosing regimen of vancomycin in neonates and infants aged less than 90 days with late onset bacterial sepsis (ClinicalTrials.gov ID: NCT02790996). NeoVanc and this biomarker sub-analysis were approved by the London–West London and Gene Therapy Advisory Committee (REC reference [16]/LO/1026) on July 18, 2016. Ethics committee and regulatory body approvals were obtained for each participating hospital. Written informed consent was obtained from all patients’ parents or guardians. The study was performed in accordance with the International Conference on Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use Good Clinical Practice guidelines, local regulations, and standard operating procedures. Infants were eligible for inclusion with a postnatal age ≥72 h and ≤90 days at randomization and either a diagnosis of clinical sepsis, defined by the presence of any three clinical or laboratory criteria taken from the adapted European Medicines Agency neonatal sepsis criteria (Hill et al. 2020) in the 24 h before randomization, or confirmed, significant bacterial sepsis as defined by positive culture with a Gram-positive bacterium from a normally sterile site and at least one clinical or one laboratory criterion in the 24 h before randomization. Exclusion criteria included the administration of any systemic antibiotic regimen for > 24 h before randomization, unless the change was driven by the apparent lack of efficacy of the original regimen, and treatment with vancomycin for ≥24h at any time within 7 days of randomization. Full details of the trial inclusion and exclusion criteria are provided in the trial protocol paper (Hill et al. 2020). The 35 infants analyzed in this substudy were selected on the basis of having microbiologically confirmed late onset sepsis with the pathogen identified as Staphylococcus epidermidis in all cases. The group comprised 18 male and 17 female patients and were selected from 11 of the recruiting tertiary neonatal ICUs across 5 European countries (Estonia, Greece, Italy, Spain and the UK). Infants whose therapy followed trial protocol were sampled 4 times in the optimized arm and 5 times in the standard arm. The biomarker sample numbers correspond to trial assessment visits as follows. Sample 1 was taken at visit 1a at the time of randomization. Sample 2 was taken at visit 3 that occurred 72 ± 8 h after initiation of study vancomycin. Sample 3 was taken at visit 4, that occurred 5±1 days after initiation of study vancomycin. Sample 4 was taken in the standard arm only at visit 5, that occured10±2 days after initiation of study vancomycin. Sample 5 was taken at visit 7, the short-term-follow-up visit that occurred 30±5 days after initiation of study vancomycin. Those infants whose vancomycin therapy ended earlier or later than outlined in the protocol were also sampled at the end of vancomycin therapy time point.","Scaning - GeneChips were imaged on the GeneTitan Multi- Channel Instrument according to the manufacturer’s instructions (Thermo Fisher Scientific)."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"data_protocol":["Data Transformation - Raw cell intensity file (CEL) data was read into R version 4.1.2 and analyzed for quality using the arrayQualityMetrics package. Potential outliers, in particular arrays with very low amounts of hybridization, were identified by visual inspection of box plots of raw expression values and calculating the value of the non-parametric Kolmogorov–Smirnov test statistic, comparing each sample with a reference of all samples. Outliers were identified for further investigation based on values greater than 1.5 times the interquartile range, and arrays deemed to exhibit poor hybridization were excluded from further analysis. Raw intensities were normalized with the robust multi-array average (RMA) method using the oligo package. Probeset IDs were annotated with a National Center for Biotechnology Information (NCBI) gene name using annotateEset() function from the affcoretools package with the Affymetrix clariomdhuman annotation data package clariomdhumantranscriptcluster.db version 8.8.0. Only probesets mapped to a NCBI gene name were retained, and maximum average intensities taken over replicate gene names. Potential outlier arrays following RMA normalization and probe summarization were again investigated using the arrayQualityMetrics package, and outliers identified based on the values of three comparative metrics: (i) the total L1 (Manhattan) distance of each sample’s counts from all other samples; (ii) the value of the non-parametric Kolmogorov–Smirnov test statistic, comparing each sample with a reference of all samples; and (iii) Hoeffding’s D statistic, a nonparametric measure of the independence of the log2 ratio and the log2 average of intensities between each sample and a reference of all samples. Outliers were identified based on values greater than 1.5 times the interquartile range in at least two out of these three tests and excluded from further analysis. Low intensity genes with a log2 transformed intensity of 3 or below in all samples were removed. The low intensity threshold was set based on visual inspection of a histogram of the distribution of log2 transformed intensities based. The resulting 117 samples were retained for analysis."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"pubmed_abstract":["<h4>Background</h4>Vancomycin has been used in clinical practice for over 50 years; however, validated, pharmacokinetic (PK) data relating clinical outcomes to different dosing regimens in neonates are lacking. Coagulase negative staphylococci (CoNS) are the most commonly isolated organisms in neonatal, late-onset sepsis (LOS). Optimised use to maximise efficacy while minimising toxicity and resistance selection is imperative to ensure vancomycin's continued efficacy.<h4>Methods</h4>NeoVanc is a European, open-label, Phase IIb, randomised, controlled, non-inferiority trial comparing an optimised vancomycin regimen to a standard vancomycin regimen when treating LOS known/suspected to be caused by Gram-positive organisms (excluding Staphylococcus aureus) in infants aged ≤ 90 days. Three hundred infants will be recruited and randomised in a 1:1 ratio. Infants can be recruited if they have culture confirmed (a positive culture from a normally sterile site and at least one clinical/laboratory criterion) or clinical sepsis (presence of any ≥ 3 clinical/laboratory criteria) in the 24 h before randomisation. The optimised regimen consists of a vancomycin loading dose (25 mg/kg) followed by 5 ± 1 days of 15 mg/kg q12h or q8h, dependent on postmenstrual age (PMA). The standard regimen is a 10 ± 2 day vancomycin course at 15 mg/kg q24h, q12h or q8h, dependent on PMA. The primary endpoint is a successful outcome at the test of cure visit (10 ± 1 days after the end of vancomycin therapy). A successful outcome consists of the patient being alive, having successfully completed study vancomycin therapy and having not had a clinical/microbiological relapse/new infection requiring treatment with vancomycin or other anti-staphylococcal antibiotic for > 24 h. Secondary endpoints include clinical/microbiological relapse/new infection at the short-term follow-up visit (30 ± 5 days after the initiation of vancomycin), evaluation of safety (renal/hearing), vancomycin PK and assessment of a host biomarker panel over the course of vancomycin therapy.<h4>Discussion</h4>Based on previous pre-clinical data and a large meta-analysis of neonatal, PK/pharmacodynamic data, NeoVanc was set up to provide evidence on whether a loading dose followed by a short vancomycin course is non-inferior, regarding efficacy, when compared to a standard, longer course. If non-inferiority is demonstrated, this would support adoption of the optimised regimen as a way of safely reducing vancomycin exposure when treating neonatal, Gram-positive LOS.<h4>Trial registration</h4>ClinicalTrials.gov, NCT02790996. Registered on 7 April 2016. EudraCT, 2015-000203-89. Entered on 18 July 2016.","Sepsis is a leading cause of mortality and morbidity in neonates yet remains difficult to diagnose. This leads to widespread empiric antibiotic therapy, which can facilitate the development of antimicrobial resistance. How the dysregulated host response to infection and sepsis evolves after antibiotic treatment is poorly understood. Temporal gene expression in neonates with microbiologically confirmed sepsis, treated with the antibiotic vancomycin as part of a randomized controlled trial, was profiled to reveal a treatment-responsive gene signature. The signature exhibited a rapid reversal of the septic state, observable within 24 hours of the initiation of therapy. Unexpectedly, response rates associated with the adaptive immune system were among the fastest, and these changes were reproduced in both pediatric and adult patients with sepsis, indicating conservation and reversibility of sepsis signatures across the life course. We demonstrated how these treatment-responsive genes could be translated into a prognostic clinical measure, exhibiting strong agreement with clinical assessments. Network modeling of sepsis-responsive genes identified a signature associated with treatment comprising an early transient elevation of antimicrobial defensive genes, suggesting an impaired bactericidal response in neonatal sepsis. These findings suggest that the host response is regulated in sepsis and offer insights into early prognostic approaches for reducing antibiotic overuse."],"study_type":["transcription profiling by array"],"species":["Homo sapiens"],"pubmed_title":["A rapid time-resolved host gene expression signature predicts responses to antibiotic treatment in neonatal bacterial sepsis","An optimised dosing regimen versus a standard dosing regimen of vancomycin for the treatment of late onset sepsis due to Gram-positive microorganisms in neonates and infants aged less than 90 days (NeoVanc): study protocol for a randomised controlled trial"],"pubmed_authors":["Edward C. Parkinson, W. John Watkins, Sarah Edkins, James E. McLaren, Michelle N. Clements, Robert Andrews, Federico Liberatore, Irja Lutsar, Mark A. Turner, Emmanuel Roilides, Paul T. Heath, Michael Sharland, Louise F. Hill, Peter Ghazal on behalf of the NeoVanc Consortium.","Louise Hill","Louise F. Hill, Mark A. Turner, Irja Lutsar, Paul T. Heath, Pollyanna Hardy, Louise Linsell, Evelyne Jacqz-Aigrain, Emmanuel Roilides, Mike Sharland on behalf of the NeoVanc Consortium.","James McLaren","Edward Parkinson"],"additional_accession":[]},"is_claimable":false,"name":"Whole blood mRNA transcription profiling of host immune changes in neonatal sepsis during vancomycin therapy","description":"The purpose of this study was to investigate changes in host gene expression profiles of neonatal infants with sepsis prior to the initiation of and during vancomycin therapy, to identify treatment-responsive genes and signature pathways associated with recovery from neonatal sepsis. The study analyzed data from a subset of 35 infants recruited to the NeoVanc trial, a multi-center randomized open label phase IIb study which compared the efficacy, safety and pharmacokinetics of an optimized dosing to a standard dosing regimen of vancomycin in neonates and infants aged less than 90 days with late onset bacterial sepsis (ClinicalTrials.gov ID: NCT02790996). All infants selected had a positive blood culture for Staphylococcus epidermidis in addition to a clinical diagnosis of neonatal sepsis. Whole blood samples were collected for each infant at five time points between the time of randomization to the trial until a short term follow up visit, approximately 30 days after randomization.","dates":{"release":"2025-11-25T00:00:00Z","modification":"2026-05-27T04:01:08.355Z","creation":"2025-10-09T16:15:33.885Z"},"accession":"E-MTAB-15687","cross_references":{"pubmed":["32293527"],"EFO":["EFO_0002768","EFO_0002944","EFO_0003814","EFO_0003813","EFO_0005518","EFO_0003816","EFO_0003815"],"doi":["10.1186/s13063-020-4184-8","10.1126/scitranslmed.adt1938"]}}