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
CD8 T cells play an important role in mediating protection against cancer and bacterial, viral, and parasitic infections, and hosts containing memory CD8 T cells are often better protected against tumors or pathogenic re-infection. Here, the authors advance the utility of the Collaborative Cross (CC) mapping population as a tool to analyze the immune response to viral infection. They describe variability in resting immune cell composition and adaptive immune responses generated among CC strains following systemic virus infection and reveal QTL responsible for generation of CD62L+ memory CD8 T cells.
To corroborate previous studies and to document steady-state immune composition for the 47 CC strains utilized in this study, the authors bled all mice prior to infection and stained peripheral blood leukocytes (PBLs) using 5 flow cytometry panels to identify CD4 and CD8 T cells, Foxp3+ regulatory CD4 T cells, B220+/CD3- B cells, NKp46+/CD3- natural killer (NK) cells, and SSC(hi)/CD11b(hi) granulocytes or SSC(lo)/CD11b(hi) monocytes. They also analyzed commonly used inbred C57BL/6 and BALB/c strains for comparison. In agreement with previous studies, the authors found wide variation in representation of immune cell subsets, including CD4 T cells, CD8 T cells, Foxp3+ CD4 T cells, B cells, NK cells, granulocytes, and monocytes, and ratio of CD4 to CD8 T cells at steady state among CC strains examined in this study.
The authors infected C57BL/6, BALB/c, and CC strains with Armstrong strain of LCMV (LCMV Arm), as the immune response following acute infection with this virus has been well described in C57BL/6 and BALB/c mice (Zhou et al., 2012; Laposova et al., 2013). Following infection, the authors analyzed inflammatory cytokines present in serum at day 3 (d3) as a measure of the innate response, weight loss at d8 following infection, and CD4 and CD8 effector responses (CD4 T(eff) and CD8 T(eff)) at d8 as a measure of the adaptive response.
In an attempt to identify gene regions associated with quantitative measurements of the CD8 T cell response to infection, the authors performed QTL mapping on size of the CD8 T(eff) response and size of the CD8 T(M) pool generated. For QTL scans, 1,000 permutations were run, and log of the odds ratio (LOD) scores above the 95th percentile of the distribution were selected as significant QTL. QTL intervals were then identified based on the LOD scores and effect of founder alleles in Diversity Outbred (DO) mice strains observed at those regions (Gatti et al., 2014). The authors did not find significant QTL associated with size of the CD8 T(eff) or T(M) pool.
The authors also performed QTL mapping to show the contribution of each of the founder alleles and identify genes associated with generation of qualitatively distinct memory CD8 T cells based on expression of CD8 T(M) phenotypic markers and CD8 T(M) subset representation. Here, they did find significant QTL associated with development of CD62L+ CD8 T(M) cells with LOD scores corresponding to p < 0.05:
Cdtm1 (CD62L+ CD8 TM cells 1) maps to Chr 18: 60 - 80 Mb. NOD/ShiLtJ, CAST/EiJ, and WSB/EiJ contribut high alleles at Cdtm1, while A/J and PWK/PhJ contribute low alleles. Mbd2 and Dcc are identified as putative candidate genes for Cdtm1.
Cdtm2 (CD62L+ CD8 TM cells 2) maps to Chr 19: 10 - 20 Mb. 129S1/SvImJ and NZO/HlLtJ contribute high alleles at Cdtm2, while A/J, CAST/EiJ, and PWK/PhJ contribute low alleles. Ms4a3, Patl1, Gm22272, Olfr235, Olfr1434, Olfr1436, and Pfpl are identified as putative candidate genes for Cdtm2.
Cdtm1 and Cdtm2 together explain 61% of variance for generation of CD62L+ CD8 T(M) cells.
The authors found a trending QTL associated with development of Tcm cells at the same region within Cdtm1 that accounted for 50% of variance for generation of Tcm cells, providing further evidence that this chromosomal region is associated with the development of qualitatively distinct Tcm CD8 T cells.
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