Bioinformatics analysis of immune response to group A streptococcal sepsis integrating quantitative trait loci mapping with genome-wide expression studies

Abstract

Individuals infected with genetically identical group Astreptococcal (GAS) strains develop starkly different dis-ease progression and outcome [1]. We reported that HLAclass II allelic variation contributes to differences in sys-temic disease severity by modulating host responses tostreptococcal superantigens [2]. Inasmuch as the bacteriaproduce additional virulence factors, we sought to iden-tify additional host gene networks modulating GAS sep-sis. Accordingly, we used two parallel approaches todefine these gene networks, quantitative trait loci (QTL)mapping and genome-wide transcriptome analyses. Tomap QTLs modulating response to severe GAS sepsis, weused advanced recombinant inbred (ARI) strains, whichare genetically diverse strains that have common ancestralparents [3]. We chose to use BXD strains of ARI mice, asparental strains C57Bl/6J (B6) and DBA/2J (D2) show dif-ferential response to GAS sepsis and BXD strains are heav-ily genotyped at 13377 SNPs and microsatellite markers.BXD strains, derived from B6 and D2 parental strains, arehomozygous inbred lines, each of which is genetically dis-tinct. Using 30 different BXD strains (n = 5–26 mice perstrain), we identified significant QTLs on chromosome 2that strongly modulate disease severity [4]. To narrowdown these mapped QTLs, we applied bioinformaticstools including: linkage, interval specific haplotype analy-ses, and gene ontology and we identified multiple candi-date gene networks modulating immune response tosepsis.As a parallel approach, we performed genome-wide tran-scriptome analyses comparing resistant and susceptiblestrains. This comparison revealed 93 genes that were dif-ferentially regulated in mice spleens 36 h post-infection.These genes belonged to gene networks involvingimmune response to sepsis; particularly notable exampleswere prostaglandin (Ptges) and interleukin1 (IL-1) familypathways. Quantitative expression analyses, using realtime PCR, of prostaglandin E synthase (