Host genetic variation has a major impact on infectious disease susceptibility. The study of pathogen resistance genes, largely aided by mouse models, has significantly advanced our understanding of infectious disease pathogenesis. The Collaborative Cross (CC), a newly developed multi-parental mouse genetic reference population, serves as a tractable model system to study how pathogens interact with genetically diverse populations. In this review, we summarize progress utilizing the CC as a platform to develop improved models of pathogen-induced disease and to map polymorphic host response loci associated with variation in susceptibility to pathogens.

Highlights d Humoral response to influenza A virus varies across genetically diverse mice d Distinct genetic loci are important for different aspects of the humoral response d Loci that regulate antibody to influenza are also important for other pathogens d Comparison across datasets informs rational selection of candidate genes

Objective To assess the effectiveness of L-cystine dimethyl ester (CDME), an inhibitor of cystine crystal growth, for the treatment of cystine urolithiasis in a Slc3a1 knockout mouse model of cystinuria. Methods CDME (200 μg per mouse) or water was delivered by gavage daily for four weeks. Higher doses by gavage or in the water supply were administered to assess organ toxicity. Urinary amino acids and cystine stones were analyzed to assess drug efficacy using several analytical methods. Results Treatment with CDME led to a significant decrease in stone size compared with the water group (p = 0.0002), but the number of stones was greater (p = 0.005). The change in stone size distribution between the two groups was evident by micro computed tomography. Overall, cystine excretion in urine was the same between the two groups (p = 0.23), indicating that CDME did not interfere with cystine metabolism. SEM analysis of cystine stones from the CDME group demonstrated a change in crystal habit, with numerous small crystals. L-cysteine methyl ester was detected by UPLC-MS in stones from the CDME group only, indicating that a CDME metabolite was incorporated into the crystal structure. No pathological changes were observed at the doses tested. Conclusions These data demonstrate that CDME promotes formation of small stones but does not prevent stone formation, consistent with the hypothesis that CDME inhibits cystine crystal growth. Combined with the lack of observed adverse effects, our findings support the use of CDME as a viable treatment for cystine urolithiasis.

Influenza A virus (IAV) is a respiratory pathogen that causes substantial morbidity and mortality during both seasonal and pandemic outbreaks. Infection outcomes in unexposed populations are affected by host genetics, but the host genetic architecture is not well understood. Here, we obtain a broad view of how heritable factors affect a mouse model of response to IAV infection using an 8 × 8 diallel of the eight inbred founder strains of the Collaborative Cross (CC). Expanding on a prior statistical framework for modeling treatment response in diallels, we explore how a range of heritable effects modify acute host response to IAV through 4 d postinfection. Heritable effects in aggregate explained ∼57% of the variance in IAV-induced weight loss. Much of this was attributable to a pattern of additive effects that became more prominent through day 4 postinfection and was consistent with previous reports of antiinfluenza myxovirus resistance 1 (Mx1) polymorphisms segregating between these strains; these additive effects largely recapitulated haplotype effects observed at the Mx1 locus in a previous study of the incipient CC, and are also replicated here in a CC recombinant intercross population. Genetic dominance of protective Mx1 haplotypes was observed to differ by subspecies of origin: relative to the domesticus null Mx1 allele, musculus acts dominantly whereas castaneus acts additively. After controlling for Mx1, heritable effects, though less distinct, accounted for ∼34% of the phenotypic variance. Implications for future mapping studies are discussed.

Influenza A virus (IAV) is a respiratory pathogen that causes substantial morbidity and mortality during both seasonal and pandemic 1 outbreaks. Infection outcomes in unexposed populations are affected by host genetics, but this host genetic architecture is not well 2 understood. Here we obtain a broad view of how heritable factors affect a mouse model of response to IAV infection using an 8×8 diallel 3 of the eight inbred founder strains of the Collaborative Cross (CC). Expanding on a prior statistical framework for modeling treatment 4 response in diallels, we explore how a range of heritable effects modify acute host response to IAV through 4 days post-infection. Heritable 5 effects in aggregate explained about 57% of the variance in IAV-induced weight loss. Much of this was attributable to a pattern of additive 6 effects that became more prominent through day 4 post-infection and was consistent with previous reports of anti-influenza myxovirus 7 resistance 1 (Mx1) polymorphisms segregating between these strains; the additive effects largely recapitulated haplotype effects observed 8 at the Mx1 locus in a previous study of the incipient CC (pre-CC), and are also replicated here in a CC recombinant intercross (CC-RIX) 9 population. Genetic dominance of protective Mx1 haplotypes was observed to differ by subspecies origin: relative to the domesticus null 10 Mx1 allele, musculus acts dominantly whereas castaneus acts additively. After controlling for Mx1, heritable effects, though less distinct, 11 accounted for about 34% of the phenotypic variance. Implications for future mapping studies are discussed. 12Keywords: treatment response, multiparental population, causal effect, Bayesian model, multiple imputation ARTICLE SUMMARY 14Seasonal and pandemic influenza viruses comprise an important public health burden, but the architecture of host genetic resistance to 15 viruses is poorly understood. We conducted an influenza challenge in a diallel cross of eight inbred mouse strains. Roughly 60% of variation 16 in disease at 4 days post-infection was explained by genetic and non-genetic diallel effects, with about 34% of variation independent of the 17 host resistance factor, Mx1. The dominance of Mx1 resistance was highly dependent on subspecies Mx1 allelic origin, and similar Mx1 18 effect patterns were found in the related Collaborative Cross strains, motivating integrated infection studies in these populations.