Identification of novel neuroprotective loci modulating ischemic stroke volume in a cross between wild-derived inbred mouse strains

To identify genes involved in cerebral infarction we have employed a forward genetic approach using quantitative trait locus (QTL) mapping for cerebral infarct volume after middle cerebral artery occlusion, using common inbred mouse strains. This work has demonstrated that infarct volume is inversely correlated with cerebral collateral vessel density, since the collateral circulation provides a compensatory shunt for reperfusion of the ischemic territory. To overcome the limited genetic diversity among domesticated inbred mouse strains, we have expanded the pool of allelic variation by utilizing the eight parental strains of the Collaborative Cross. We found that one wild-derived strain, WSB/EiJ, breaks general rule that collateral vessel density inversely correlates with infarct volume. WSB/EiJ and another wild-derived strain, CAST/EiJ, show the highest collateral vessel densities of any inbred strain, but infarct volume of WSB/EiJ is 8.7-fold larger than CAST/EiJ. QTL mapping between these strains identified 4 new neuroprotective loci modulating cerebral infarct volume while not affecting collateral vessel phenotypes. To identify causative variants in genes within the loci, we surveyed non-synonymous coding SNPs between the strains and also performed RNA sequencing of brain tissue to determine strain-specific gene expression differences. Combining the lists of genes harboring coding SNPs predicted to be damaging with genes showing strain-specific expression differences leaves only 15 genes mapping in any of the four intervals. The identification of the genes underlying these neuroprotective loci will provide new understanding of genetic risk factors of ischemic stroke which may provide novel targets for future therapeutic intervention of human ischemic stroke.