Reference
The Collaborative Cross (CC) is a large (~1,000 line) panel of recombinant inbred (RI) mouse strains being developed through a community effort (Churchill et al. 2004). The CC combines the genomes of eight genetically diverse founder strains - A/J, C57BL/6J, 129S1/SvImJ, NOD/ShiLtJ, NZO/HlLtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ - to capture nearly 90% of the known variation present in laboratory mice. CC strains are derived using a unique funnel breeding scheme. Once inbred, the RI CC lines can be used to generate thousands of potential 'outbred' but completely reproducible genomes through the generation of recombinant inbred crosses (RIX). The designation 'PreCC' is used to describe a mapping population of CC mice that is still at incipient stages of inbreeding.
CTC (2004), Churchill, G. A., et al.. The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nat Genet. 36, 1133-7.
Experiment
Mouse IgE and mast cell (MC) functions have been studied primarily using inbred strains. Here, the authors (a) identified effects of genetic background on mouse IgE and MC phenotypes, (b) defined the suitability of various strains for studying IgE and MC functions, and (c) began to study potentially novel genes involved in such functions.
The authors screened 47 Collaborative Cross (CC#/Unc) strains, as well as C57BL/6J and BALB/cJ mice, for strength of passive cutaneous anaphylaxis (PCA) and responses to the intestinal parasite Strongyloides venezuelensis (S.v.). For screening using CC mice, the authors prepared 3 or 5 mice per genotype. Some mice died before the beginning of the screening or after the authors performed PCA. Therefore, n = 3 or 5 for most of the data, but some are n = 2 or 1. The screening was performed as 8 independent experiments, and the data were pooled. To validate the accuracy of the screening, the authors performed a second round of screening using a small number of strains (4 CC strains plus C57BL/6J and BALB/cJ mice). For this, the authors prepared n = 4 for CC027/Unc and n = 6 for other strains. The second-round screening was performed as 3 independent experiments, and the data were pooled.
CC#/Unc mice exhibited a diversity in PCA strength and S.v. responses. Among strains tested, C57BL/6J and CC027/Unc mice showed, respectively, moderate and uniquely potent MC activity.
QTL analysis was performed for each of the following quantitative traits: PCA MAX, shorter duration of S.v. infection, and the magnitude of the IgE fold change. The authors used DOQTL v1.19.0 Bioconductor package (70) for QTL mapping. Genotype markers and haplotype probabilities for the CC#/Unc mice were obtained from the Systems Genetics Core Facility at the UNC (http://csbio.unc.edu/CCstatus/index.py).
One significant QTL was identified (genome coordinates relative to GRCm38/mm10):
Pcam1 (passive cutaneous anaphylaxis max 1) maps to Chr 1: 81.7 - 92.9 Mb with a peak p-value of 0.0031. The NOD/ShiLtJ allele contributes high trait values at Pcam1, while the PWK/PhJ allele contibutes low trait values.
The duration of S.v. infection and IgE fold change did not show any significant peaks, but the authors found a weak contribution of Pcam1 to the two traits, and the causal founder haplotype variant for both traits was also of the NOD/ShiLtJ strain.
The authors also explored potential QTL negatively affecting MC functions. This revealed that chromosome 10 in the interval of 79.4 - 94.0 Mb from the NZO/HlLtJ strain contributed to a lower PCA MAX, a longer duration of S.v. infection, and lower IgE fold change. The authors found 231 protein-coding genes within 79.4 - 94.0 Mb on chromosome 10. A search of the ENCODE database revealed that 4 genes - Zbtb7a, Polr3b, Cfap54, and Usp44 - had NZO/HlLtJ strain-specific protein-changing SNPs (missense variants or in-frame insertion).
QTL analysis and RNA sequencing of M-derived cultured MCs (BMCMCs) from CC027/Unc mice suggested Sp140 as a candidate gene for MC activation.
siRNA-mediated knock-down of Sp140 in BMCMCs decreased IgE-dependent histamine release and cytokine production.
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