Ischemic and nephrotoxic acute renal failure are distinguished by their broad transcriptomic responses

Abstract

Acute renal failure (ARF) has a high morbidity and mortality. In animal ARF models, effective treatments must be administered before or shortly after the insult, limiting their clinical potential. We used microarrays to identify early biomarkers that distinguish ischemic from nephrotoxic ARF or biomarkers that detect both injury types. We compared rat kidney transcriptomes at 2 and 8 h after ischemia/reperfusion and after mercuric chloride. Quality control and statistical analyses were necessary to normalize microarrays from different lots, eliminate outliers, and exclude unaltered genes. Principal component analysis revealed distinct ischemic and nephrotoxic trajectories and clear array groupings. Therefore, we used supervised analysis, t-tests, and fold changes to compile gene lists for each group, exclusive or nonexclusive, alone or in combination. There was little network connectivity, even in the largest group. Some microarray-identified genes were validated by TaqMan assay, ruling out artifacts. Western blotting confirmed that heme oxygenase-1 (HO-1) and activating transcription factor-3 (ATF3) proteins were upregulated; however, unexpectedly, their localization changed within the kidney. HO-1 staining shifted from cortical (early) to outer stripe of the outer medulla (late), primarily in detaching cells, after mercuric chloride but not ischemia/reperfusion. ATF3 staining was similar, but with additional early transient expression in the outer stripe after ischemia/reperfusion. We conclude that microarray-identified genes must be evaluated not only for protein levels but also for anatomical distribution among different zones, nephron segments, or cell types. Although protein detection reagents are limited, microarray data lay a rich foundation to explore biomarkers, therapeutics, and the pathophysiology of ARF.

Identification of genes involved in gentamicin-induced nephrotoxicity in rats – A toxicogenomic investigation

“…(activating transcription factor 3), Lipocalin (LCN2) and TIMP1 (TIMP metallopeptidase inhibitor 1) (Hai et al, 1999, Thukral et al, 2005, Yuen et al, 2006, Sieber et al, 2009) which were described to be affected after kidney injury were found to be strongly up-regulated on mRNA level in our study. The finding of the EGF (epidermal growth factor) down-regulation was in line with the report of Verstrepen et al (1993) and was of interest as EGF downregulation is frequently observed after acute renal failure (Perco et al, 2006).…”

Effects of Mercuric Chloride on Gene Expression in NRK-52E Cells

“…Up-regulation of ATF3 mRNA was also reported previously to be induced by gentamycin treatment and after ischemic and nephrotoxic acute renal failure (Ozaki et al, 2009, Yuen et al, 2006. We detected 21 known genes common in all 3 concentration treatment group.…”

Cell-specific translational profiling in acute kidney injury

“…To date, broad molecular characterization of AKI models has largely focused on transcriptional profiling of organ-wide signatures (10)(11)(12)(13)(14)(15). Several promising biomarkers have emerged from these studies (16,17).…”