The Integrated RNA Landscape of Renal Preconditioning against Ischemia-Reperfusion Injury

Abstract

BackgroundAlthough AKI lacks effective therapeutic approaches, preventive strategies using preconditioning protocols, including caloric restriction and hypoxic preconditioning, have been shown to prevent injury in animal models. A better understanding of the molecular mechanisms that underlie the enhanced resistance to AKI conferred by such approaches is needed to facilitate clinical use. We hypothesized that these preconditioning strategies use similar pathways to augment cellular stress resistance.MethodsTo identify genes and pathways shared by caloric restriction and hypoxic preconditioning, we used RNA-sequencing transcriptome profiling to compare the transcriptional response with both modes of preconditioning in mice before and after renal ischemia-reperfusion injury.ResultsThe gene expression signatures induced by both preconditioning strategies involve distinct common genes and pathways that overlap significantly with the transcriptional changes observed after ischemia-reperfusion injury. These changes primarily affect oxidation-reduction processes and have a major effect on mitochondrial processes. We found that 16 of the genes differentially regulated by both modes of preconditioning were strongly correlated with clinical outcome; most of these genes had not previously been directly linked to AKI.ConclusionsThis comparative analysis of the gene expression signatures in preconditioning strategies shows overlapping patterns in caloric restriction and hypoxic preconditioning, pointing toward common molecular mechanisms. Our analysis identified a limited set of target genes not previously known to be associated with AKI; further study of their potential to provide the basis for novel preventive strategies is warranted. To allow for optimal interactive usability of the data by the kidney research community, we provide an online interface for user-defined interrogation of the gene expression datasets (http://shiny.cecad.uni-koeln.de:3838/IRaP/).

Modulation of Endocannabinoids by Caloric Restriction Is Conserved in Mice but Is Not Required for Protection from Acute Kidney Injury

“…CR-mediated preconditioning has been shown to be extremely effective in the prevention of AKI in rodents [ 17 , 19 , 22 , 37 ]. In C. elegans CR is a classical longevity intervention increasing lifespan and metabolic heath.…”

“…As previously described [ 17 , 22 , 37 ], calorically restricted mice were provided with 66% (3 g per day per mouse) daily in the morning on the last 28 days prior to surgery. Before initiation of dietary preconditioning, CR-mice were set individually in new cages.…”

“…To maintain the body temperature, surgery was performed on a temperature-controlled heating pad (Havard apparatus, Holliston, MA, USA). As described before [ 22 , 37 ], following midline abdominal incision, the vessels of the right kidney were ligated with sutures and the kidney was removed afterward. Following this, the left renal artery and vein underwent unilateral clamping for 40 min with an atraumatic micro-vascular clamp and subsequent removal of the clamp for reperfusion, which was controlled visually.…”

“…These preconditioning strategies enhance cellular stress resistance before exposure to the injurious stimulus. Caloric restriction (CR) is one of the most potent preconditioning protocols and has been shown to increase stress resistance and increase lifespan in a multitude of species ranging from the nematode Caenorhabditis elegans ( C. elegans) to non-human primates [ 19 , 20 , 21 , 22 , 23 ]. However, the effect of CR in humans on stress resistance is less clear.…”

CALINCA—A Novel Pipeline for the Identification of lncRNAs in Podocyte Disease

“…Wildtype whole kidney and FACS-sorted podocyte RNA-seq datasets were used as previously published by our groups [ 37 , 42 ]. Briefly, separate libraries were prepared both after polyA-RNA enrichment and ribosomal RNA depletion and sequenced on an HiSeq4000 sequencer (Illumina, San Diego, CA, USA) with PE75 read length.…”