Experiment
The aim of this study was to identify the best gene candidates within the Gdac1 locus contributing to the murine colitis phenotype.
In a previous study, J:171572, the authors reported that the GPX-deficiency associated colitis 1 locus, Gdac1, containing the C57BL/6J allele, confers resistance to colitis in the 129/SvImJ background. In that study Gdac1 mapped to Chr2:119-133 Mbp and appeared to overlap the cytokine-deficiency induced colitis susceptibility locus, Cdcs3.
Cdcs3 was localized based on mapping in a resistant B6 IL10-KO vs sensitive C3H/HeJBir (C3H) IL10-KO mice.
By increasing the sample size of the original mapping population (Gpx1 and Gpx2 double knockout mice (GPX1/2-DKO, homozygous for Gpx1tm1Ysh and Gpx2tm2Coh) on a mixed C57BL/6J (B6) and 129S1/SvImJ (129) background (F1 hybrid and N5-N10 on 129)) to 155 additional mice and the SNP density throughout the Gdac1 region the original boundaries of the QTL were refined. The phenotypes measured were disease activity index, colon length, colon pathology score, and E. coli overgrowth. R/QTL calculated LOD ranged from ~11-21 within the 95% confidence interval which was refined to 118-125 Mbp on Chr 2. The region contained 128 well-annotated protein coding genes.
Using in silico analysis based on published colon expression data , the relevance of pathways to colitis, gene mutations, presence of non synonymous SNPs and whether the SNPs were predicted to have an impact on protein function or expression; and analysis for expression-quantitative-trait loci; two genes, Pla2g4f and Duox2, were identified as the most likely colitis gene candidates. [Fig 5.]
Gdca1 was determined to lie adjacent to colitis susceptibility loci Cdcs3 and Dssc2. Gdac1 was also conserved in humans at Chr.15q:38-49 Mbp.
Analysis Tools