3D MDS analysis view 2

Three-dimensional MDS analysis of riBAQ values for DIA samples, fractional normalization and log transformation, view 2

3D MDS analysis view 1

Three-dimensional MDS analysis of riBAQ values for DIA samples, fractional normalization and log transformation, view 1

Otitis Media Impacts Hundreds of Mouse Middle and Inner Ear Genes

<div><p>Objective</p><p>Otitis media is known to alter expression of cytokine and other genes in the mouse middle ear and inner ear. However, whole mouse genome studies of gene expression in otitis media have not previously been undertaken. Ninety-nine percent of mouse genes are shared in the human, so these studies are relevant to the human condition.</p><p>Methods</p><p>To assess inflammation-driven processes in the mouse ear, gene chip analyses were conducted on mice treated with trans-tympanic heat-killed <i>Hemophilus influenza</i> using untreated mice as controls. Middle and inner ear tissues were separately harvested at 6 hours, RNA extracted, and samples for each treatment processed on the Affymetrix 430 2.0 Gene Chip for expression of its 34,000 genes.</p><p>Results</p><p>Statistical analysis of gene expression compared to control mice showed significant alteration of gene expression in 2,355 genes, 11% of the genes tested and 8% of the mouse genome. Significant middle and inner ear <i>up</i>regulation (fold change >1.5, p<0.05) was seen in 1,081 and 599 genes respectively. Significant middle and inner ear <i>down</i>regulation (fold change <0.67, p<0.05) was seen in 978 and 287 genes respectively. While otitis media is widely believed to be an exclusively middle ear process with little impact on the inner ear, the inner ear changes noted in this study were numerous and discrete from the middle ear responses. This suggests that the inner ear does indeed respond to otitis media and that its response is a distinctive process. Numerous new genes, previously not studied, are found to be affected by inflammation in the ear.</p><p>Conclusion</p><p>Whole genome analysis via gene chip allows simultaneous examination of expression of hundreds of gene families influenced by inflammation in the middle ear. Discovery of new gene families affected by inflammation may lead to new approaches to the study and treatment of otitis media.</p></div

IL-17 pathway fold change values.

<p>IL-17 pathway fold change values.</p

IL-1 Pathway Map.

<p>IL-1 Pathway Map, showing all genes in theIL-1 gene pathway and the amount of upregulation seen in our dataset by the histogram bars (Cox-2, IL-6, iNOS, endothelin-1, Pal1, STAT1, IRF1, NF-kB p50/p65, TNFα, Myd88, IL-1Rl, IL1RAP, IL-1α, IL-1β). Highest fold change activity seen in IL-6 for both ME and IE. (Data summary from Genego.)</p

IL-17 pathway map.

<p>IL-17 pathway map, showing all genes in the IL-1 gene pathway and the amount of upregulation seen in our dataset by the histogram bars (G-CSF, GM, CSF, c-FOS, CCL2 and 7, iNOS, GRO-1, IL-2, IL-1, IL-8, RANKL, Stromelysin, JAK2, C/EPbeta). Highest fold change activity seen in IL-6 for both ME and IE. (Data summary from Genego.)</p

Middle and inner ear genes affected by acute inner ear inflammation.

<p>Middle and inner ear genes affected by acute inner ear inflammation, >1.5× upregulation or <1.5× downregulation. Note that while there is overlap between the shared inner and middle ear genes up- or downregulated, there is a high percentage of unique genes in both categories.</p

Interactome Analysis of ME and IE Genes.

<p>Interactome analysis: performed with limiting the dataset to named genes and protein/gene interactions <i>in our data set</i>, fold change >1.5× upregulation and <1.5× downregulation and p<0.05.</p

IL-1 pathway fold change values.

<p>IL-1 pathway fold change values.</p

Cross comparison of cytokine gene expression measured by Affymetrix Gene Chip and qRT-PCR.

<p>Middle ear fold change analyses (top) showed a significant correlation between the two methods (p = 0.0098). Inner ear analyses (bottom) showed a similar pattern of cytokine expression that also was significantly correlated between the two methods (p = 0.0241).</p