Background: Non-coding RNAs (NCR) arise from the non-protein-coding portion of the genome and include microRNAs, small nucleolar RNAs (snoRNA) and ribosomal RNAs (rRNA). NCR are important in normal physiology and disease, including ischemia-reperfusion injury (IRI) of the kidney. Indoleamine 2,3-dioxygenase (IDO) is a heme containing enzyme shown to prevent rejection in rat kidney transplants. However, IDO may also facilitate IRI. We theorized that NCR may play a role in the regulation of IDO-mediated effects in IRI. To address this question, we used DNA microarrays to assess the effect of IDO inhibition on NCR expression from rats exposed to IRI.

Methods: Male SD rats (N=5/group) underwent IRI (30 min ischemia, 60 min recovery) or sham surgery (SHA), with or without pre-treatment with the IDO blocker 1-methyl-D-tryptophan (1MT). At sacrifice one kidney from each animal was snap frozen and the renal cortical transcriptome hybridized to the GeneChip®Rat Gene 1.0 ST Array (Affymetrix).

Results: 8711 probe sets from each chip were analyzed. Limma was used to test for differential gene expression in pair wise comparisons. IRI vs SHA was the positive control for IRI, and IRI vs MT-IRI tested the effect of 1MT in IRI. The table shows the effect of 1MT on transcripts previously altered by IRI.

The p value reflects whether the percent of transcripts not effected is the same as the per cent that were effected by 1MT. The data indicate that pretreatment with 1MT prior to IRI altered snoRNA and rRNA expression by 18 to 31 fold compared to IRI alone. mRNA was also significantly affected with an 11 fold change. cDNA expression in IRI was not affected by 1MT pre-treatment.

Conclusions: Blocking IDO in IRI induces a shift in differential gene expression in NCR with significant changes in rRNA and snoRNA, without effect on cDNA expression. The influence of IDO on NCR expression may affect renal recovery from IRI.

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