Indoleamine 2, 3-Dioxygenase Inhibition Shifts Gene Expression From Coding to Non-Coding Sequences Following Ischemia-Reperfusion Injury of the Kidney.

Abstract

Background: Indoleamine 2,3 dioxygenase (IDO) minimizes rejection in rat renal transplantation. Ischemia-reperfusion injury (IRI) is unavoidable in renal transplantation and correlates with graft loss. Despite its effects on rejection, IDO may facilitate renal IRI. To address this paradox, we queried for shifts in the gene expression signatures of renal IRI with and without IDO blockade. Methods: Male SD rats (N=5/group) underwent IRI (30 min ischemia, 60 min recovery) or sham surgery (SHA). To test IDO blockade, pretreatment with 1-methyl-D-tryptophan (1MT) or vehicle (VEH) was given. Expression of the renal cortical transcriptome was determined using the GeneChip®Rat Gene 1.0 ST Array (Affymetrix). Gene annotations were provided by Affymetrix. DAVID v6.7 was used for functional annotation clustering. Two comparisons (CMP) were made: IRI vs SHA with VEH (CMP1) and 1MT vs VEH in IRI (CMP2). CMP1 is a positive control for IRI, and CMP2 assessed the effect of IDO blockade in IRI. Results: The array contains over 27,000 gene-level probe sets, of which 8711 exhibited an interquartile range of 0.25, and were thus included in the analysis. Coding sequences altered: CMP1=108, CMP2=18, no overlap. Non-coding sequences altered: CMP1=3, CMP2=66, no overlap. The coding sequences changed in CMP1 (number of transcripts from various categories) included genes most commonly from apoptosis (17), cell biosynthesis (20-23), RNA associated processes (17-26) and transcriptional processes (17-29), none of which were altered with 1MT pre-treatment. The non-coding sequences changed in CMP2 were predominantly snoRNA (50). Conclusions: Blocking IDO in IRI induces a shift in gene expression from coding to non-coding transcripts. Loss of apoptosis activating coding sequences and/or activation of non-coding snoRnA sequences may contribute to improved recovery from renal IRI in 1MT treated rats.