The transcriptome of a complete episode of acute otitis media

Abstract

BackgroundOtitis media is the most common disease of childhood, and represents an important health challenge to the 10-15% of children who experience chronic/recurrent middle ear infections. The middle ear undergoes extensive modifications during otitis media, potentially involving changes in the expression of many genes. Expression profiling offers an opportunity to discover novel genes and pathways involved in this common childhood disease.The middle ears of 320 WBxB6 F1 hybrid mice were inoculated with non-typeable Haemophilus influenzae (NTHi) or PBS (sham control). Two independent samples were generated for each time point and condition, from initiation of infection to resolution. RNA was profiled on Affymetrix mouse 430 2.0 whole-genome microarrays.ResultsApproximately 8% of the sampled transcripts defined the signature of acute NTHi-induced otitis media across time. Hierarchical clustering of signal intensities revealed several temporal gene clusters. Network and pathway enrichment analysis of these clusters identified sets of genes involved in activation of the innate immune response, negative regulation of immune response, changes in epithelial and stromal cell markers, and the recruitment/function of neutrophils and macrophages. We also identified key transcriptional regulators related to events in otitis media, which likely determine the expression of these gene clusters. A list of otitis media susceptibility genes, derived from genome-wide association and candidate gene studies, was significantly enriched during the early induction phase and the middle re-modeling phase of otitis but not in the resolution phase. Our results further indicate that positive versus negative regulation of inflammatory processes occur with highly similar kinetics during otitis media, underscoring the importance of anti-inflammatory responses in controlling pathogenesis.ConclusionsThe results characterize the global gene response during otitis media and identify key signaling and transcription factor networks that control the defense of the middle ear against infection. These networks deserve further attention, as dysregulated immune defense and inflammatory responses may contribute to recurrent or chronic otitis in children.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1475-7) contains supplementary material, which is available to authorized users.

Panel 8: Report on Recent Advances in Molecular and Cellular Biochemistry

“…Nonetheless, neither TLRs nor their signaling molecules appear to be singularly essential for the initial expression of nontypeable H influenzae-mediated inflammation in the middle ear, implicating multiple innate immune receptors and signaling networks alternative to TLRs in the middle ear, such as NOD-like receptors (NLRs) as well as bacterial DNA receptors, plus others. 15,16 Expression of members of the NLR family of inflammasome receptors was significantly upregulated early in OM 9 and cholesteatoma, 17 potentially activating specific downstream regulatory cascades that contribute to the proliferative inflammatory response observed during OM. Activation of the pyrin domain containing NLRs (NLRPs) results in the formation of inflammasome, a large multimolecular signaling platform consisting of an active NLRP, the bipartite adaptor protein ASC, and caspase 1.…”

“…The active NF-kB subunits p65 and p50 translocate into the nucleus, where they can induce the expression of specific genes that have DNA-binding sites for NF-kB in their promoters. During middle ear infection, activation of the NF-kB signaling pathway occurs in the early phase 16 and leads to the increase in the gene expression levels of IFN-b/TNF-a/IL-8 and mucin MUC5AC, among other inflammatory-related genes. 26 …”

Panel 5: Immunology

“…TLR genes and their signaling molecules were generally upregulated in OM in murine studies. 22 Of interest was TLR-9 with NTHi and DNA sensing in OM pathogenesis and recovery 32 and the deletion of c-Jun N-terminal kinase 1 in delaying recovery from OM while c-Jun N-terminal kinase 2 deficiency prevented recovery 33 ( Table 2). Demonstration that deletion of virtually any innate immune receptor, signaling molecule, or major effector delays OM recovery suggests that an intact innate immune signaling system is critical to the resolution of bacterial OM.…”

“…From the onset of infection through to its complete resolution, advances have been made via gene arrays. 21,22 Genes involved in innate and adaptive immunity-including innate immune receptors, downstream signaling molecules and effectors, pro-and antiinflammatory genes, and antimicrobial compounds (especially cathelicidins)-change throughout AOM.…”

“…The expression profiles from the MEs of hybrid mice infected with live NTHi showed that approximately 8% of the sampled transcripts profiled defined the signature of acute NTHi-induced OM over infection time. 22 The earliest wave of gene expression, peaking 3 to 6 hours after infection, included genes related to immune and defense responding to biotic stimulus, interleukin, TLR and TNFR signaling, and NFkB and neutrophil activation. A cluster peaking at 6 and 48 hours was enriched for STAT1/2 and IRF1/7/8 targets, with enriched pathways for interferon and JAK/STAT signaling, antiviral responses, the inflammasome, and leukocyte chemotaxis.…”