Correction to: Detect tissue heterogeneity in gene expression data with BioQC.

After the publication of this work [1], a mistake was noticed in the Eq. 1. Given an m × n expression matrix with m genes and samples of n tissues, the correct definition of the Gini index for gene i is.

Detect tissue heterogeneity in gene expression data with BioQC.

BACKGROUND: Gene expression data can be compromised by cells originating from other tissues than the target tissue of profiling. Failures in detecting such tissue heterogeneity have profound implications on data interpretation and reproducibility. A computational tool explicitly addressing the issue is warranted. RESULTS: We introduce BioQC, a R/Bioconductor software package to detect tissue heterogeneity in gene expression data. To this end BioQC implements a computationally efficient Wilcoxon-Mann-Whitney test and provides more than 150 signatures of tissue-enriched genes derived from large-scale transcriptomics studies. Simulation experiments show that BioQC is both fast and sensitive in detecting tissue heterogeneity. In a case study with whole-organ profiling data, BioQC predicted contamination events that are confirmed by quantitative RT-PCR. Applied to transcriptomics data of the Genotype-Tissue Expression (GTEx) project, BioQC reveals clustering of samples and suggests that some samples likely suffer from tissue heterogeneity. CONCLUSIONS: Our experience with gene expression data indicates a prevalence of tissue heterogeneity that often goes unnoticed. BioQC addresses the issue by integrating prior knowledge with a scalable algorithm. We propose BioQC as a first-line tool to ensure quality and reproducibility of gene expression data.

New renal drug development to face chronic renal disease.

INTRODUCTION: For the first time in 2012, chronic kidney diseases were added to WHO disease list because of their impact on morbidity/mortality and their substantial impact on the cost to the health care system. Although representing a clear unmet medical need and a huge business case for the pharmaceutical industry, its clinical treatment still mainly relies on drugs invented in the 1980s used for controlling blood pressure. AREAS COVERED: In this review, the authors aim to elucidate why renal drug development is feasible today. The article provides a particular focus on the treatments that target the pathways involved in inflammation, fibrosis and the core mechanisms driving the vicious cycle responsible for disease progression and organ function loss. EXPERT OPINION: Currently, it is plausible to develop effective therapeutics for renal diseases with a plethora of approaches available for their development at a preclinical and clinical level. Furthermore, the relevance of biomarkers and the use of surrogate rare disease indications as proof of mechanism for faster and/or smaller clinical development are now possible; and these developments could revolutionize the way we treat renal disease in the future.

Epithelial cells as active player in fibrosis: findings from an in vitro model.

Kidney fibrosis, a scarring of the tubulo-interstitial space, is due to activation of interstitial myofibroblasts recruited locally or systemically with consecutive extracellular matrix deposition. Newly published clinical studies correlating acute kidney injury (AKI) to chronic kidney disease (CKD) challenge this pathological concept putting tubular epithelial cells into the spotlight. In this work we investigated the role of epithelial cells in fibrosis using a simple controlled in vitro system. An epithelial/mesenchymal 3D cell culture model composed of human proximal renal tubular cells and fibroblasts was challenged with toxic doses of Cisplatin, thus injuring epithelial cells. RT-PCR for classical fibrotic markers was performed on fibroblasts to assess their modulation toward an activated myofibroblast phenotype in presence or absence of that stimulus. Epithelial cell lesion triggered a phenotypical modulation of fibroblasts toward activated myofibroblasts as assessed by main fibrotic marker analysis. Uninjured 3D cell culture as well as fibroblasts alone treated with toxic stimulus in the absence of epithelial cells were used as control. Our results, with the caveats due to the limited, but highly controllable and reproducible in vitro approach, suggest that epithelial cells can control and regulate fibroblast phenotype. Therefore they emerge as relevant target cells for the development of new preventive anti-fibrotic therapeutic approaches.

Targeting the epithelial cells in fibrosis: a new concept for an old disease.

Fibrosis, which affects millions of individuals worldwide, is a leading cause of organ failure. For 40 years myofibroblasts have been recognized to be the key cellular players in fibrosis. Currently, several pharmaceutical targets are under investigation that may contribute to the activation of myofibroblasts. Recent preclinical and clinical evidence suggests that other components in the fibrotic microenvironment can trigger myofibroblast activation, providing new targets for pharmaceutical intervention. Epithelial cells may represent the most promising cellular phenotype that could be exploited in the design of new anti-fibrotic medicines through their paracrine action on myofibroblasts. The present review briefly highlights this hypothesis and discusses some interesting related pharmacological targets.

From acute injury to chronic disease: pathophysiological hypothesis of an epithelial/mesenchymal crosstalk alteration in CKD.

Observational clinical studies link acute kidney injury to chronic kidney disease (CKD) progression. The pathophysiological mechanisms that underlie this process are currently unknown but recently published papers suggest that tubular epithelial cells and interstitial mesenchymal cells emerge as a single unit, and their integrity alteration as a whole might lead to renal fibrosis and CKD. The present article reviews the biological findings supporting the hypothesis of an altered epithelial/mesenchymal crosstalk in fibrosis development and progression toward CKD.

Current drug development challenges in chronic kidney disease (CKD)--identification of individualized determinants of renal progression and premature cardiovascular disease (CVD).

Chronic kidney disease (CKD) and end-stage renal disease (ESRD) are currently considered as major health burdens. Notably, CKD can be regarded as an interesting clinical model of accelerated cardiovascular disease (CVD) and ageing, which offers exciting new perspectives and challenges for pharmaceutical drug development. However, during the last decades, therapeutic advances to slow down the progression of CKD and reduce CVD risk have largely failed due to several possible reasons including (i) the lack of profound understanding of the pathophysiology of chronic renal damage and its associated CVD; (ii) an inadequate characterization of molecular mechanisms of currently approved therapies such as renin-angiotensin-aldosterone-system (RAAS) blockade; (iii) the unclear biochemical property needs required for novel therapeutic approaches; (iv) the missing quantity and quality of clinical trials in the nephrology field; and, most importantly, (v) the absence of prognostic renal biomarkers that reflect the severity of the structural organ damage and predict ESRD as well as CVD mortality. There is clearly an insufficient understanding of why a significant proportion of CKD patients progress to ESRD and/or die from CVD whereas others rather remain stable. In this article, we urge renal researchers to develop novel experimental and clinical tools for rational and translational drug discovery. Identification of individualized determinants of CKD progression and/or premature CVD will enable personalized medicine and lead to novel innovative nephro- and/or cardioprotective pharmacological treatment in these high-risk patients.

Epithelial-mesenchymal crosstalk alteration in kidney fibrosis.

The incidence of chronic kidney diseases (CKD) is constantly rising, reaching epidemic proportions in the western world and leading to an enormous threat, even to modern health-care systems, in industrialized countries. Therapies of CKD have greatly improved following the introduction of drugs targeting the renin-angiotensin system (RAAS) but even this refined pharmacological approach has failed to stop progression to end-stage renal disease (ESRD) in many individuals. In vitro historical data and recent new findings have suggested that progression of renal fibrosis might occur as a result of an altered tubulo-interstitial microenvironment and, more specifically, as a result of an altered epithelial-mesenchymal crosstalk. Here we the review biological findings that support the hypothesis of an altered cellular crosstalk in an injured local tubulo-interstitial microenvironment leading to renal disease progression. Copyright © 2012 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

The kidney as a target organ in pharmaceutical research.

Kidney diseases are a major source of morbidity and mortality in humans. In developed countries, mortality owing to chronic kidney disease (CKD) terminating in end-stage renal failure is comparable with that associated with cancer. A full understanding of the mechanisms implicated in the progression of CKD is needed to achieve its prevention and to delay the need for support strategies based on dialysis and transplantation. Renal fibrosis is the unifying feature of progressive renal alterations. In this review, we discuss the current status of possible mechanisms, tools and targets in CKD. Pathophysiological compound identification, biomarker discovery and accurate selection of clinical validation criteria appear to be three key elements needed to develop a successful innovative pharmaceutical approach to treating kidney diseases.

Discovery of novel cyanodihydropyridines as potent mineralocorticoid receptor antagonists.

A new 1,4-dihydropyridine 5a, containing a cyano group at the C3 position, was recently reported to possess excellent mineralocorticoid receptor (MR) antagonist in vitro potency and no calcium channel-blocker (CCB) activity. In the present study, we report the structure-activity relationships of this novel series of cyano ester dihydropyridines that resulted in R6 substituted analogues with improved metabolic stability while maintaining excellent MR antagonist activity and selectivity against other nuclear receptors. Further structure optimization with the introduction of five-membered ring heterocycles at R6 resulted in compounds with excellent MR antagonist potency and a suitable pharmacokinetic profile. In vivo studies of a promising tool compound in the Dahl salt-sensitive rat model of hypertension showed similar blood pressure (BP) reduction as the steroidal MR antagonist eplerenone, providing proof-of-concept (POC) for a nonsteroidal, orally efficacious MR antagonist.

Acute impairment of rat renal function by L -NAME as measured using dynamic MRI.

OBJECTIVE: To assess the feasibility of utilizing dynamic contrast enhanced (DCE)-MRI for depicting the effects of N (G)-nitro-L -arginine methylester (L -NAME), a nitric oxide synthase (NOS) inhibitor, on glomerular filtration rate (GFR) in rats. Since Gd-DTPA is mainly cleared through the kidneys, a first-order kinetic model was used to estimate GFR based on a clearance index (k ( cl )) that describes the tracer transport rate from the renal cortex to the outer medulla. MATERIALS AND METHODS: Normotensive Sprague-Dawley rats were infused with either vehicle (0.9% NaCl) or one of three doses of L -NAME (1, 3 or 10 mg/kg) for 30 min prior to imaging. In a separate set of animals, systolic blood pressure (SBP) was measured for all treatment groups. RESULTS: L -NAME caused a significant increase in SBP at all doses when compared to pre-dose values and at the two highest doses, post-infusion, when compared to vehicle. Administration of L -NAME also led to dose-dependent changes in the rate of Gd-DTPA uptake and tracer concentrations reached in selected regions of the kidney. The k ( cl ) measurements indicated a significant impairment of GFR following NOS blockade at the highest dose of L -NAME. CONCLUSION: DCE-MRI method detected changes in GFR in response to NO inhibition with L -NAME. This non-invasive technique could be used in longitudinal studies in preclinical and clinical settings offering a rapid assessment of single-kidney function.

5,6-epoxyeicosatrienoic acid mediates the enhanced renal vasodilation to arachidonic acid in the SHR.

We have shown a cytochrome P450-dependent renal vasodilator effect of arachidonic acid in response to inhibition of cyclooxygenase and elevation of perfusion pressure, which was enhanced in the spontaneously hypertensive rat (SHR) and linked to increased production of and/or responsiveness to epoxyeicosatrienoic acids (EETs). In the SHR, vasodilation elicited by low doses of arachidonic acid was attenuated by the nitric oxide synthase inhibitor Nw-nitro-L-arginine (50 micromol/L), whereas the responses to high doses were unaffected. Inhibition of epoxygenases with miconazole (0.3 micromol/L) in the presence of Nw-nitro-L-arginine greatly reduced the renal vasodilator response to all doses of arachidonic acid. Tetraethylammonium (10 mmol/L), a nonselective K+ channel blocker, abolished the nitric oxide-independent renal vasodilator effect of arachidonic acid as well as the vasodilator effect of 5,6-EET, confirming that EET-dependent vasodilation involves activation of K+ channels. Under conditions of elevated perfusion pressure (200 mm Hg) and cyclooxygenase inhibition, 5,6-EET, 8, 9-EET, and 11,12-EET caused renal vasodilatation in both SHR and Wistar-Kyoto rats (WKY), whereas 14,15-EET produced vasoconstriction. 5,6-EET was the most potent renal vasodilator of the EET regioisomers in the SHR by a factor of 4 or more. In the SHR, 5,6-EET- and 11,12-EET-induced renal vasodilatation was >2-fold greater than that registered in WKY. Thus, the augmented vasodilator responses to arachidonic acid in the SHR is through activation of K+ channels, and 5,6-EET is the most likely mediator.