Mapping of a Chromosome 12 Region Associated with Airway Hyperresponsiveness in a Recombinant Congenic Mouse Strain and Selection of Potential Candidate Genes by Expression and Sequence Variation Analyses

In a previous study we determined that BcA86 mice, a strain belonging to a panel of AcB/BcA recombinant congenic strains, have an airway responsiveness phenotype resembling mice from the airway hyperresponsive A/J strain. The majority of the BcA86 genome is however from the hyporesponsive C57BL/6J strain. The aim of this study was to identify candidate regions and genes associated with airway hyperresponsiveness (AHR) by quantitative trait locus (QTL) analysis using the BcA86 strain. Airway responsiveness of 205 F2 mice generated from backcrossing BcA86 strain to C57BL/6J strain was measured and used for QTL analysis to identify genomic regions in linkage with AHR. Consomic mice for the QTL containing chromosomes were phenotyped to study the contribution of each chromosome to lung responsiveness. Candidate genes within the QTL were selected based on expression differences in mRNA from whole lungs, and the presence of coding non-synonymous mutations that were predicted to have a functional effect by amino acid substitution prediction tools. One QTL for AHR was identified on Chromosome 12 with its 95% confidence interval ranging from 54.6 to 82.6 Mbp and a maximum LOD score of 5.11 (p = 3.68×10−3). We confirmed that the genotype of mouse Chromosome 12 is an important determinant of lung responsiveness using a Chromosome 12 substitution strain. Mice with an A/J Chromosome 12 on a C57BL/6J background have an AHR phenotype similar to hyperresponsive strains A/J and BcA86. Within the QTL, genes with deleterious coding variants, such as Foxa1, and genes with expression differences, such as Mettl21d and Snapc1, were selected as possible candidates for the AHR phenotype. Overall, through QTL analysis of a recombinant congenic strain, microarray analysis and coding variant analysis we identified Chromosome 12 and three potential candidate genes to be in linkage with airway responsiveness.

既往研究中，我们明确了BcA86小鼠——属于AcB/BcA重组同类系（recombinant congenic strains）品系集合中的一个品系——其气道反应性（airway responsiveness）表型与气道高反应性（airway hyperresponsive）A/J品系小鼠相似。但BcA86小鼠的大部分基因组来自低反应性C57BL/6J品系。本研究旨在通过以BcA86品系为实验对象的数量性状位点（quantitative trait locus, QTL）分析，筛选与气道高反应性（airway hyperresponsiveness, AHR）相关的候选区域与基因。我们对将BcA86品系与C57BL/6J品系回交获得的205只F2小鼠的气道反应性进行了检测，并将其用于QTL分析，以筛选与AHR连锁的基因组区域。针对携带该QTL的染色体构建的替换系小鼠（consomic mice），我们对其进行了表型分析，以探究每条染色体对肺部反应性的贡献。我们基于全肺组织mRNA的表达差异，以及经氨基酸替换预测工具（amino acid substitution prediction tools）预判具有功能影响的编码区非同义突变（coding non-synonymous mutations）的存在情况，筛选了该QTL内的候选基因。我们在12号染色体上定位到一个与AHR相关的QTL，其95%置信区间为54.6至82.6 Mbp，最大对数似然比分值（LOD score）为5.11（p=3.68×10⁻³）。我们借助12号染色体替换品系，证实小鼠12号染色体的基因型是肺部反应性的重要决定因素。在C57BL/6J遗传背景下携带A/J品系12号染色体的小鼠，其AHR表型与高反应性品系A/J及BcA86相似。在该QTL内，我们将携带有害编码变异的Foxa1等基因，以及存在表达差异的Mettl21d、Snapc1等基因，选为AHR表型的潜在候选基因。综上，通过对重组同类系小鼠开展QTL分析、基因芯片分析（microarray analysis）及编码变异分析，我们确定12号染色体与3个潜在候选基因与气道反应性存在连锁关联。