Expression quantitative trait Loci for extreme host response to influenza a in pre-collaborative cross mice

Abstract

Outbreaks of influenza occur on a yearly basis, causing a wide range of symptoms across the human population. Although evidence exists that the host response to influenza infection is influenced by genetic differences in the host, this has not been studied in a system with genetic diversity mirroring that of the human population. Here we used mice from 44 influenza-infected pre-Collaborative Cross lines determined to have extreme phenotypes with regard to the host response to influenza A virus infection. Global transcriptome profiling identified 2671 transcripts that were significantly differentially expressed between mice that showed a severe ("high") and mild ("low") response to infection. Expression quantitative trait loci mapping was performed on those transcripts that were differentially expressed because of differences in host response phenotype to identify putative regulatory regions potentially controlling their expression. Twenty-one significant expression quantitative trait loci were identified, which allowed direct examination of genes associated with regulation of host response to infection. To perform initial validation of our findings, quantitative polymerase chain reaction was performed in the infected founder strains, and we were able to confirm or partially confirm more than 70% of those tested. In addition, we explored putative causal and reactive (downstream) relationships between the significantly regulated genes and others in the high or low response groups using structural equation modeling. By using systems approaches and a genetically diverse population, we were able to develop a novel framework for identifying the underlying biological subnetworks under host genetic control during influenza virus infection.

Keywords: Mouse Collaborative Cross; Mouse Genetic Resource; SEM; collaborative cross; eQTL; host response; influenza.

Figure 1

Phenotypic distribution of pre-CC lines used for categorization Two groups (red boxes) correspond to mice that displayed HRI or LRI. The y-axis displays the percent change in weight at 4 DPI, relative to a baseline. The x-axis displays an IHC score (see Materials and Methods) that was an indicator of infection severity.

Figure 2

Ifi27l2a is a significantly cis-regulated gene with expression differences driven mainly by the PWK/PhJ allele. (A) A significant eQTL is located in distal Chr 12 (LOD = 18.7; 170.030−170.720 Mb). (B) The allele effects for the markers in the support interval indicate pre-CC mice with an allele inherited from the PWK/PhJ founder strain expressed Ifi27I2a at a lower level than the rest of the population. (C) The same pattern of allele effects was confirmed by qPCR in three animals from each of the eight founder strains, as we expect from a cis-regulated eQTL.