| Summary: | <p>Abstract</p> <p>Background</p> <p>The lung is critical in surveillance and initial defense against pathogens. In humans, as in mice, individual genetic differences strongly modulate pulmonary responses to infectious agents, severity of lung disease, and potential allergic reactions. In a first step towards understanding genetic predisposition and pulmonary molecular networks that underlie individual differences in disease vulnerability, we performed a global analysis of normative lung gene expression levels in inbred mouse strains and a large family of BXD strains that are widely used for systems genetics. Our goal is to provide a key community resource on the genetics of the normative lung transcriptome that can serve as a foundation for experimental analysis and allow predicting genetic predisposition and response to pathogens, allergens, and xenobiotics.</p> <p><b>Methods</b></p> <p>Steady-state polyA+ mRNA levels were assayed across a diverse and fully genotyped panel of 57 isogenic strains using the Affymetrix M430 2.0 array. Correlations of expression levels between genes were determined. Global expression QTL (eQTL) analysis and network covariance analysis was performed using tools and resources in GeneNetwork <url>http://www.genenetwork.org</url>.</p> <p><b>Results</b></p> <p>Expression values were highly variable across strains and in many cases exhibited a high heri-tability factor. Several genes which showed a restricted expression to lung tissue were identified. Using correlations between gene expression values across all strains, we defined and extended memberships of several important molecular networks in the lung. Furthermore, we were able to extract signatures of immune cell subpopulations and characterize co-variation and shared genetic modulation. Known QTL regions for respiratory infection susceptibility were investigated and several <it>cis</it>-eQTL genes were identified. Numerous <it>cis</it>- and <it>trans-</it>regulated <it>trans</it>cripts and chromosomal intervals with strong regulatory activity were mapped. The <it>Cyp1a1 </it>P450 <it>trans</it>cript had a strong <it>trans</it>-acting eQTL (LOD 11.8) on Chr 12 at 36 ± 1 Mb. This interval contains the <it>trans</it>cription factor <it>Ahr </it>that has a critical mis-sense allele in the <it>DBA/2J </it>haplotype and evidently modulates transcriptional activation by AhR.</p> <p><b>Conclusions</b></p> <p>Large-scale gene expression analyses in genetic reference populations revealed lung-specific and immune-cell gene expression profiles and suggested specific gene regulatory interactions.</p>
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