Lung pathology in select preCC mice.

<p>(A). OR63f51—normal parenchyma. (B). OR181f61—airway debris and cuffing and edema surrounding the associated vasculature. (C) OR220f57—denuded airway blocked with debris. (D) OR380f64 –perivascular cuffing including eosinophilia. (E) OR941f69 –alveolitis including hyaline membrane formation, arrows point to hyaline membranes. (F) OR5030f128 –normal airway and associated vasculature.</p

Phenotypic relationships.

<p>Heat map of the relationships between lung pathology, titer and weight loss in the preCC. Yellow indicates positive correlation and blue indicates negative correlation.</p

PreCC and founder strain phenotypes.

<p>(A) Weight loss is shown as percent of starting weight at day four post infection, individual preCC mice are shown in open diamonds and mean values for founders are shown in color. All CAST/EiJ mice died or were humanely euthanized before day four post infection. (B) Log transformed lung titer at day four post infection in individual preCC mice and founders, dashed line indicates the limit of detection at 100 PFU per lung. Individual preCC mice are shown in open diamonds, mean values for the founders are color coded by strain. (C) Lung titer vs. weight loss at day four post infection. Individual preCC mice are indicated in open diamonds, mean values for the founder strains are shown in color. The dashed line indicates the limit of detection at 100 PFU per lung.</p

Transcriptional analysis.

<p>(A) A heat map showing a comparison of functionally enriched biological pathways between <i>Trim55</i>^<i>-/-</i> and C57BL/6J mice at days two and four post infection based on RNA expression levels in the lung. Three mice used per condition, per timepoint. Experiment performed once. Relative expression of all DE genes (log2 FC of 1 or greater and FDR < .05, Trim55^-/- vs C57BL/6J) involved in granulocyte adhesion and diapedesis at day two (B) or four (C) post infection.</p

SARS QTL details.

<p>The four SARS-CoV susceptibility QTLs with genome region, LOD score, significance and percent of phenotypic variation.</p

Modeling Host Genetic Regulation of Influenza Pathogenesis in the Collaborative Cross

<div><p>Genetic variation contributes to host responses and outcomes following infection by influenza A virus or other viral infections. Yet narrow windows of disease symptoms and confounding environmental factors have made it difficult to identify polymorphic genes that contribute to differential disease outcomes in human populations. Therefore, to control for these confounding environmental variables in a system that models the levels of genetic diversity found in outbred populations such as humans, we used incipient lines of the highly genetically diverse Collaborative Cross (CC) recombinant inbred (RI) panel (the pre-CC population) to study how genetic variation impacts influenza associated disease across a genetically diverse population. A wide range of variation in influenza disease related phenotypes including virus replication, virus-induced inflammation, and weight loss was observed. Many of the disease associated phenotypes were correlated, with viral replication and virus-induced inflammation being predictors of virus-induced weight loss. Despite these correlations, pre-CC mice with unique and novel disease phenotype combinations were observed. We also identified sets of transcripts (modules) that were correlated with aspects of disease. In order to identify how host genetic polymorphisms contribute to the observed variation in disease, we conducted quantitative trait loci (QTL) mapping. We identified several QTL contributing to specific aspects of the host response including virus-induced weight loss, titer, pulmonary edema, neutrophil recruitment to the airways, and transcriptional expression. Existing whole-genome sequence data was applied to identify high priority candidate genes within QTL regions. A key host response QTL was located at the site of the known anti-influenza <i>Mx1</i> gene. We sequenced the coding regions of <i>Mx1</i> in the eight CC founder strains, and identified a novel <i>Mx1</i> allele that showed reduced ability to inhibit viral replication, while maintaining protection from weight loss.</p> </div

Candidate genes within QTL regions.

<p>For <i>HrI2</i>, (A) refers to genes with a private A/J SNP, (C) refers to genes with a private 129S1/SvImJ SNP. Unmarked genes had both A/J and 129S1/SvImJ SNPs.</p

A novel <i>Mx1</i> allele differentially impacts host response to influenza.

<p>The founder strain alleles at <i>Mx1</i> were grouped based on their phenotypic effects into three functionally distinct classes corresponding to <i>domesticus</i> (<i>dom</i>: A/J, C57BL6/J, 129s1/SvImJ, NOD/HiLtJ and WSB/EiJ), <i>castaneus</i> (<i>cast</i>: CAST/EiJ) and <i>musculus</i> (<i>mus</i>: PWK/PhJ and NZO/ShILtJ). Points shown are individual pre-CC animals with these haplotypes, mean bars are shown for each class. These functionally distinct classes were separable based upon differences in (A) D4 weight and (B) Log titer, with the heterozygous classes showing intermediate phenotypes. Across the pre-CC population, homozygous <i>dom</i> animals had severe weight loss and high titers. Homozygous <i>mus</i> animals showed little weight loss and low titers. Homozygous <i>cast</i> animals showed little weight loss, but had intermediate viral titers. Brackets between groups represent significant differences (* = p<0.05, ** = p<0.003) based on Tukey's HSD. We found no difference by qPCR (C) in expression of <i>Mx1</i> at 2 days post-infection following influenza infection in a strain from each of these three functional classes. By sequencing <i>Mx1</i> (D), we were able to identify five haplotypes across the eight founder strains (Haplotype 1 = A/J, C57BL/6J, 129S1/SvImJ, NOD/HiLtJ; Haplotype 2 = WSB/EiJ; Haplotype 3 = PWK/PhJ; Haplotype 4 = NZO/HiLtJ; Haplotype 5 = CAST/EiJ). Arrows indicate locations of polymorphisms, with small arrows indicating non-coding changes, and large arrows indicating coding changes. Colors correspond to the founder strains having those polymorphisms (brown = multiple strains possess mutation). Grey exons indicate those not transcribed due to either deletion and frameshift, or insertion and early stop codon.</p

QTL identified in the pre-CC population.

<p>QTL identified in the pre-CC population.</p

Phenotypes measured in the pre-CC and founder strains.

<p>Phenotypes measured in the pre-CC and founder strains.</p