Abstract
Purpose:
Gene expression and bioinformatic analyses were used to identify progressive gene expression profiles that define the IRBP knock out mouse over the first wave of abnormal retinal degeneration (postnatal days (p) 20-25).
Methods:
Retinas from IRBP knockout (KO) and wildtype control (WT) mice at P20, 21, 22, 23, 24, and 25 were isolated. For each condition 3 biological replicates were obtained. Total RNAs were used to screen Illumina bead chip mouse gene expression arrays. The relative levels of gene expression were measured using Illumina Genome/Bead Studio software, and quality confirmed and normalized using Lumi. Pairwise comparisons between conditions were performed using BioConductor Limma. Expression profiles were compared to P20 for WT and KO at each age. An adjusted p-value of 0.05 with a fold-change of at least 1.3 was used as the cut-off at which a transcript was considered statistically significantly differentially expressed. Additional informatic analyses of gene lists were performed with IPA software (Ingenuity Systems).
Results:
We identified more differential expressed genes in the combined KO p21-25 (x p20) profiles than in the WT p21-25 (x p20) profiles. Over the period of interest we identified 1766 differentially expressed genes in the KO animals (relative to KOp20), and 990 genes in the WT animals (relative to WTp20). There was an overlap of 550 genes between the KO comparison and the WT comparison, Overall there were very few differential genes identified at p21 and p22 relative to p20 in both KO and WT. There is a large increase in differential genes identified at p23xp20, p24xp20 and p25xp20 in KO than WT animals. An ontology analysis of the differential genes identified a surge in the number of apoptosis, anti-apoptosis, innate immune, and DNA damage associated genes at p24xp20 in KO animals over p24xp20 WT animals.
Conclusions:
Knocking out the IRBP gene results in a drastic change in the normal expression profile for the period of p20 to p25. This is the period that marks the first wave of abnormal retinal cell death in this model system. Overall we identified 488 putative IRBP inducible genes and 1264 IRBP repressed genes. Gene profiling results are consistent with a tissue undergoing active cell death and accented by changes in innate immune markers.