Identification of potential transcriptomic markers in developing pediatric sepsis: a weighted gene co-expression network analysis and a case–control validation study

Journal of Translational Medicine

Research

Fang Fang¹  Jian Wang¹  Yiping Li¹  Jian Pan¹  Yanhong Li²  Zhenjiang Bai³ 

[1] Institute of Pediatric Research, Children’s Hospital of Soochow University, Suzhou, China;Institute of Pediatric Research, Children’s Hospital of Soochow University, Suzhou, China;Department of Nephrology, Children’s Hospital of Soochow University, Suzhou, China;Pediatric Intensive Care Unit, Children’s Hospital of Soochow University, Suzhou, China;

关键词: Transcriptomic markers;    Co-expression modules;    Pediatric sepsis;    Diagnosis;    Hub genes;   

DOI  :  10.1186/s12967-017-1364-8

 received in 2017-10-17, accepted in 2017-12-08,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundSepsis represents a complex disease with the dysregulated inflammatory response and high mortality rate. The goal of this study was to identify potential transcriptomic markers in developing pediatric sepsis by a co-expression module analysis of the transcriptomic dataset.MethodsUsing the R software and Bioconductor packages, we performed a weighted gene co-expression network analysis to identify co-expression modules significantly associated with pediatric sepsis. Functional interpretation (gene ontology and pathway analysis) and enrichment analysis with known transcription factors and microRNAs of the identified candidate modules were then performed. In modules significantly associated with sepsis, the intramodular analysis was further performed and “hub genes” were identified and validated by quantitative real-time PCR (qPCR) in this study.Results15 co-expression modules in total were detected, and four modules (“midnight blue”, “cyan”, “brown”, and “tan”) were most significantly associated with pediatric sepsis and suggested as potential sepsis-associated modules. Gene ontology analysis and pathway analysis revealed that these four modules strongly associated with immune response. Three of the four sepsis-associated modules were also enriched with known transcription factors (false discovery rate-adjusted P < 0.05). Hub genes were identified in each of the four modules. Four of the identified hub genes (MYB proto-oncogene like 1, killer cell lectin like receptor G1, stomatin, and membrane spanning 4-domains A4A) were further validated to be differentially expressed between septic children and controls by qPCR.ConclusionsFour pediatric sepsis-associated co-expression modules were identified in this study. qPCR results suggest that hub genes in these modules are potential transcriptomic markers for pediatric sepsis diagnosis. These results provide novel insights into the pathogenesis of pediatric sepsis and promote the generation of diagnostic gene sets.

【 授权许可】

CC BY   
© The Author(s) 2017