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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.

Kanagaratham C, Marino R, Camateros P, Ren J, Houle D, Sladek R, Vidal SM, Radzioch D - PLoS ONE (2014)

Bottom Line: 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)).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.

View Article: PubMed Central - PubMed

Affiliation: Department of Human Genetics, McGill University, Montreal, Quebec, Canada.

ABSTRACT
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.

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Selection of candidate genes within quantitative trait locus with expression differences.(A, B, and C) Dot plots of candidate genes from microarray analysis. Expression of Eapp and Snapc1 was higher in hyporesponsive C57BL/6J strain than both hyperresponsive strains, CSS12 and BcA86. Conversely, the expression of Mettl21d was higher in CSS12 and BcA86 compared to C57BL/6J. (D, E, and F) Quantitative RT-PCR validates the microarray expression differences of Mettl21 and Snapc1, but not of Eapp. Data are presented as mean ± SEM and statistical significance was calculated by one-way ANOVA and Bonferroni correction. n = 3 per strain for microarray and n>5 per strain for PCR; * and *** represents p<0.05 and p<0.001 respectively.
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pone-0104234-g005: Selection of candidate genes within quantitative trait locus with expression differences.(A, B, and C) Dot plots of candidate genes from microarray analysis. Expression of Eapp and Snapc1 was higher in hyporesponsive C57BL/6J strain than both hyperresponsive strains, CSS12 and BcA86. Conversely, the expression of Mettl21d was higher in CSS12 and BcA86 compared to C57BL/6J. (D, E, and F) Quantitative RT-PCR validates the microarray expression differences of Mettl21 and Snapc1, but not of Eapp. Data are presented as mean ± SEM and statistical significance was calculated by one-way ANOVA and Bonferroni correction. n = 3 per strain for microarray and n>5 per strain for PCR; * and *** represents p<0.05 and p<0.001 respectively.

Mentions: From the microarray, Eapp, Mettl21d, and Snapc1 were differentially expressed between the hyporesponsive strains and hyperresponsive strains, and also annotated as “validated” in the Reference Sequence database (Figure 5A-C). The differences observed in Mettl21d and Snapc1, but not Eapp, were confirmed by quantitative RT-PCR (Figure 5D-F). Mettl21d was expressed at higher levels in hyperresponsive strains, while the opposite was observed for Snapc1.


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.

Kanagaratham C, Marino R, Camateros P, Ren J, Houle D, Sladek R, Vidal SM, Radzioch D - PLoS ONE (2014)

Selection of candidate genes within quantitative trait locus with expression differences.(A, B, and C) Dot plots of candidate genes from microarray analysis. Expression of Eapp and Snapc1 was higher in hyporesponsive C57BL/6J strain than both hyperresponsive strains, CSS12 and BcA86. Conversely, the expression of Mettl21d was higher in CSS12 and BcA86 compared to C57BL/6J. (D, E, and F) Quantitative RT-PCR validates the microarray expression differences of Mettl21 and Snapc1, but not of Eapp. Data are presented as mean ± SEM and statistical significance was calculated by one-way ANOVA and Bonferroni correction. n = 3 per strain for microarray and n>5 per strain for PCR; * and *** represents p<0.05 and p<0.001 respectively.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4128649&req=5

pone-0104234-g005: Selection of candidate genes within quantitative trait locus with expression differences.(A, B, and C) Dot plots of candidate genes from microarray analysis. Expression of Eapp and Snapc1 was higher in hyporesponsive C57BL/6J strain than both hyperresponsive strains, CSS12 and BcA86. Conversely, the expression of Mettl21d was higher in CSS12 and BcA86 compared to C57BL/6J. (D, E, and F) Quantitative RT-PCR validates the microarray expression differences of Mettl21 and Snapc1, but not of Eapp. Data are presented as mean ± SEM and statistical significance was calculated by one-way ANOVA and Bonferroni correction. n = 3 per strain for microarray and n>5 per strain for PCR; * and *** represents p<0.05 and p<0.001 respectively.
Mentions: From the microarray, Eapp, Mettl21d, and Snapc1 were differentially expressed between the hyporesponsive strains and hyperresponsive strains, and also annotated as “validated” in the Reference Sequence database (Figure 5A-C). The differences observed in Mettl21d and Snapc1, but not Eapp, were confirmed by quantitative RT-PCR (Figure 5D-F). Mettl21d was expressed at higher levels in hyperresponsive strains, while the opposite was observed for Snapc1.

Bottom Line: 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)).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.

View Article: PubMed Central - PubMed

Affiliation: Department of Human Genetics, McGill University, Montreal, Quebec, Canada.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus