Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function.

In conducting genome-wide association studies (GWAS), analytical approaches leveraging biological information may further understanding of the pathophysiology of clinical traits. To discover novel associations with estimated glomerular filtration rate (eGFR), a measure of kidney function, we developed a strategy for integrating prior biological knowledge into the existing GWAS data for eGFR from the CKDGen Consortium. Our strategy focuses on single nucleotide polymorphism (SNPs) in genes that are connected by functional evidence, determined by literature mining and gene ontology (GO) hierarchies, to genes near previously validated eGFR associations. It then requires association thresholds consistent with multiple testing, and finally evaluates novel candidates by independent replication. Among the samples of European ancestry, we identified a genome-wide significant SNP in FBXL20 (P = 5.6 × 10(-9)) in meta-analysis of all available data, and additional SNPs at the INHBC, LRP2, PLEKHA1, SLC3A2 and SLC7A6 genes meeting multiple-testing corrected significance for replication and overall P-values of 4.5 × 10(-4)-2.2 × 10(-7). Neither the novel PLEKHA1 nor FBXL20 associations, both further supported by association with eGFR among African Americans and with transcript abundance, would have been implicated by eGFR candidate gene approaches. LRP2, encoding the megalin receptor, was identified through connection with the previously known eGFR gene DAB2 and extends understanding of the megalin system in kidney function. These findings highlight integration of existing genome-wide association data with independent biological knowledge to uncover novel candidate eGFR associations, including candidates lacking known connections to kidney-specific pathways. The strategy may also be applicable to other clinical phenotypes, although more testing will be needed to assess its potential for discovery in general.

Modular support for developing mobile ad hoc applications

Abstract This PhD thesis addresses the issue of alleviating the burden of developing ad hoc applications. Such applications have the particularity of running on mobile devices, communicating in a peer-to-peer manner and implement some proximity-based semantics. A typical example of such application can be a radar application where users see their avatar as well as the avatars of their friends on a map on their mobile phone. Such application become increasingly popular with the advent of the latest generation of mobile smart phones with their impressive computational power, their peer-to-peer communication capabilities and their location detection technology. Unfortunately, the existing programming support for such applications is limited, hence the need to address this issue in order to alleviate their development burden. This thesis specifically tackles this problem by providing several tools for application development support. First, it provides the location-based publish/subscribe service (LPSS), a communication abstraction, which elegantly captures recurrent communication issues and thus allows to dramatically reduce the code complexity. LPSS is implemented in a modular manner in order to be able to target two different network architectures. One pragmatic implementation is aimed at mainstream infrastructure-based mobile networks, where mobile devices can communicate through fixed antennas. The other fully decentralized implementation targets emerging mobile ad hoc networks (MANETs), where no fixed infrastructure is available and communication can only occur in a peer-to-peer fashion. For each of these architectures, various implementation strategies tailored for different application scenarios that can be parametrized at deployment time. Second, this thesis provides two location-based message diffusion protocols, namely 6Shot broadcast and 6Shot multicast, specifically aimed at MANETs and fine tuned to be used as building blocks for LPSS. Finally this thesis proposes Phomo, a phone motion testing tool that allows to test proximity semantics of ad hoc applications without having to move around with mobile devices. These different developing support tools have been packaged in a coherent middleware framework called Pervaho.

Anemia and chronic kidney disease are associated with poor outcomes in heart failure patients.

BACKGROUND: Chronic kidney disease (CKD) has been linked to higher heart failure (HF) risk. Anemia is a common consequence of CKD, and recent evidence suggests that anemia is a risk factor for HF. The purpose of this study was to examine among patients with HF, the association between CKD, anemia and inhospital mortality and early readmission. METHODS: We performed a retrospective cohort study in two Swiss university hospitals. Subjects were selected based the presence of ICD-10 HF codes in 1999. We recorded demographic characteristics and risk factors for HF. CKD was defined as a serum creatinine > or = 124 956;mol/L for women and > or = 133 micromol/L for men. The main outcome measures were inhospital mortality and thirty-day readmissions. RESULTS: Among 955 eligible patients hospitalized with heart failure, 23.0% had CKD. Twenty percent and 6.1% of individuals with and without CKD, respectively, died at the hospital (p < 0.0001). Overall, after adjustment for other patient factors, creatinine and hemoglobin were associated with an increased risk of death at the hospital, and hemoglobin was related to early readmission. CONCLUSION: Both CKD and anemia are frequent among older patients with heart failure and are predictors of adverse outcomes, independent of other known risk factors for heart failure.

Liver kidney microsomal type 1 antibodies reduce the CYP2D6 activity in patients with chronic hepatitis C virus infection.

Liver kidney microsomal type 1 (LKM-1) antibodies have been shown to decrease the CYP2D6 activity in vitro and are present in a minority of patients with chronic hepatitis C infection. We investigated whether LKM-1 antibodies might reduce the CYP2D6 activity in vivo. All patients enrolled in the Swiss Hepatitis C Cohort Study and tested for LKM-1 antibodies were assessed (n = 1723): 10 eligible patients were matched with patients without LKM-1 antibodies. Patients were genotyped for CYP2D6 variants to exclude individuals with a poor metabolizer genotype. CYP2D6 activity was measured by a specific substrate using the dextromethorphan/dextrorphan metabolic ratio to classify patients into four activity phenotypes. All patients had a CYP2D6 extensive metabolizer genotype. The observed phenotype was concordant with the CYP2D6 genotype in most LKM-negative patients, whereas only three LKM-1 positive patients had a concordant phenotype (six presented an intermediate and one a poor metabolizer phenotype). The median DEM/DOR ratio was sixfold higher in LKM-1 positive than in LKM-1 negative patients (0.096 vs. 0.016, P = 0.004), indicating that CYP2D6 metabolic function was significantly reduced in the presence of LKM-1 antibodies. In chronic hepatitis C patients with LKM-1 antibodies, the CYP2D6 metabolic activity was on average reduced by 80%. The impact of LKM-1 antibodies on CYP2D6-mediated drug metabolism pathways warrants further translational studies.

Ectopic pacing at physiological rate improves postanoxic recovery of the developing heart.

Recently, rapid and transient cardiac pacing was shown to induce preconditioning in animal models. Whether the electrical stimulation per se or the concomitant myocardial ischemia affords such a protection remains unknown. We tested the hypothesis that chronic pacing of a cardiac preparation maintained in a normoxic condition can induce protection. Hearts of 4-day-old chick embryos were electrically paced in ovo over a 12-h period using asynchronous and intermittent ventricular stimulation (5 min on-10 min off) at 110% of the intrinsic rate. Sham (n = 6) and paced hearts (n = 6) were then excised, mounted in vitro, and subjected successively to 30 min of normoxia (20% O(2)), 30 min of anoxia (0% O(2)), and 60 min of reoxygenation (20% O(2)). Electrocardiogram and atrial and ventricular contractions were simultaneously recorded throughout the experiment. Reoxygenation-induced chrono-, dromo-, and inotropic disturbances, incidence of arrhythmias, and changes in electromechanical delay (EMD) in atria and ventricle were systematically investigated in sham and paced hearts. Under normoxia, the isolated heart beat spontaneously and regularly, and all baseline functional parameters were similar in sham and paced groups (means +/- SD): heart rate (190 +/- 36 beats/min), P-R interval (104 +/- 25 ms), mechanical atrioventricular propagation (20 +/- 4 mm/s), ventricular shortening velocity (1.7 +/- 1 mm/s), atrial EMD (17 +/- 4 ms), and ventricular EMD (16 +/- 2 ms). Under anoxia, cardiac function progressively collapsed, and sinoatrial activity finally stopped after approximately 9 min in both groups. During reoxygenation, paced hearts showed 1) a lower incidence of arrhythmias than sham hearts, 2) an increased rate of recovery of ventricular contractility compared with sham hearts, and 3) a faster return of ventricular EMD to basal value than sham hearts. However, recovery of heart rate, atrioventricular conduction, and atrial EMD was not improved by pacing. Activity of all hearts was fully restored at the end of reoxygenation. These findings suggest that chronic electrical stimulation of the ventricle at a near-physiological rate selectively alters some cellular functions within the heart and constitutes a nonischemic means to increase myocardial tolerance to a subsequent hypoxia-reoxygenation.

Not all inflammatory markers are linked to kidney function: results from a population-based study.

BACKGROUND: Several studies have reported increased levels of inflammatory biomarkers in chronic kidney disease (CKD), but data from the general population are sparse. In this study, we assessed levels of the inflammatory markers C-reactive protein (hsCRP), tumor necrosis factor α (TNF-α), interleukin (IL)-1β and IL-6 across all ranges of renal function. METHODS: We conducted a cross-sectional study in a random sample of 6,184 Caucasian subjects aged 35-75 years in Lausanne, Switzerland. Serum levels of hsCRP, TNF-α, IL-6, and IL-1β were measured in 6,067 participants (98.1%); serum creatinine-based estimated glomerular filtration rate (eGFR(creat), CKD-EPI formula) was used to assess renal function, and albumin/creatinine ratio on spot morning urine to assess microalbuminuria (MAU). RESULTS: Higher serum levels of IL-6, TNF-α and hsCRP and lower levels of IL-1β were associated with a lower renal function, CKD (eGFR(creat) <60 ml/min/1.73 m(2); n = 283), and MAU (n = 583). In multivariate linear regression analysis adjusted for age, sex, hypertension, smoking, diabetes, body mass index, lipids, antihypertensive and hypolipemic therapy, only log-transformed TNF-α remained independently associated with lower renal function (β -0.54 ±0.19). In multivariate logistic regression analysis, higher TNF-α levels were associated with CKD (OR 1.17; 95% CI 1.01-1.35), whereas higher levels of IL-6 (OR 1.09; 95% CI 1.02-1.16) and hsCRP (OR 1.21; 95% CI 1.10-1.32) were associated with MAU. CONCLUSION: We did not confirm a significant association between renal function and IL-6, IL-1β and hsCRP in the general population. However, our results demonstrate a significant association between TNF-α and renal function, suggesting a potential link between inflammation and the development of CKD. These data also confirm the association between MAU and inflammation.

Is the obesity epidemic exaggerated? Clues from a developing country

Rapid response to: Patrick Basham and John Luik. Is the obesity epidemic exaggerated? Yes. BMJ 2008; 336: 244. doi: 10.1136/bmj.39458.495127.AD

Interpretation of needle biopsies of the kidney for investigation of renal masses.

The development of new therapeutic options for renal tumors has lead to the need of a pretherapeutic diagnosis for an increasing proportion of patients presenting with a renal mass. This need is particularly important for a small, incidentally discovered renal mass (less than 4 cm) as it can be a benign lesion in a significant percentage of cases. Recent studies have shown that needle biopsy is an accurate and safe method allowing for a precise histopathological diagnosis of the mass in most cases. The aims of the biopsy are (1) to assess the benign or malignant nature of the lesion, (2) to assess the primary or secondary nature of the lesion, and (3), in case of a primary malignancy, to determine histological prognostic factors, such as the tumor type. This review, based on the most recent literature and our own experience, is intended to provide a practical approach to the diagnosis, relying on appropriate morphologic assessment and the use of immunohistochemistry.

Drug adherence in chronic kidney diseases and dialysis.

Poor long-term adherence and persistence to drug therapy is universally recognized as one of the major clinical issues in the management of chronic diseases, and patients with renal diseases are also concerned by this important phenomenon. Chronic kidney disease (CKD) patients belong to the group of subjects with one of the highest burdens of daily pill intake with up to >20 pills per day depending on the severity of their disease. The purpose of the present review is to discuss the difficulties encountered by nephrologists in diagnosing and managing poor adherence and persistence in CKD patients including in patients receiving maintenance dialysis. Our review will also attempt to provide some clues and new perspectives on how drug adherence could actually be addressed and possibly improved. Working on drug adherence may look like a long and tedious path, but physicians and healthcare providers should always be aware that drug adherence is in general much lower than what they may think and that there are many ways to improve and support drug adherence and persistence so that renal patients obtain the full benefits of their treatments.

Ammonia-induced toxicity in developing brain cells and strategies for neuroprotection

RESUME L'hyperammonémie est particulièrement toxique pour le cerveau des jeunes patients et entraîne une atrophie corticale, un élargissement des ventricules et des défauts de myélinisation, responsables de retards mentaux et développementaux. Les traitements actuels se limitent à diminuer le plus rapidement possible le taux d'ammoniaque dans l'organisme. L'utilisation de traitements neuroprotecteurs pendant les crises d'hyperammonémie permettrait de contrecarrer les effets neurologiques de l'ammoniaque et de prévenir l'apparition des troubles neurologiques. Au cours de cette thèse, nous avons testé trois stratégies de neuroprotection sur des cultures de cellules en agrégats issues du cortex d'embryons de rats et traitées à l'ammoniaque. - Nous avons tout d'abord testé si l'inhibition de protéines intracellulaires impliquées dans le déclenchement de la mort cellulaire pouvait protéger les cellules de la toxicité de l'ammoniaque. Nous avons montré que L'exposition à l'ammoniaque altérait la viabilité des neurones et des oligodendrocytes, et activait les caspases, la calpaïne et la kinase-5 dépendante des cyclines (cdk5) associée à son activateur p25. Alors que l'inhibition pharmacologique des caspases et de la calpaïne n'a pas permis de protéger les cellules cérébrales, un inhibiteur de la cdk5, appelé roscovitine, a réduit significativement la mort neuronale. L'inhibition de la cdk5 semble donc être une stratégie thérapeutique prometteuse pour prévenir 1es effets toxiques de 1'ammoniaque sur les neurones. - Nous avons ensuite étudié les mécanismes neuroprotecteurs déclenchés par le cerveau en réponse à la toxicité de l'ammoniaque. Nous avons montré que l'ammoniaque induisait la synthèse du facteur neurotrophique ciliaire (CNTF) par les astrocytes, via l'activation de la protéine kinase (MIAPK) p38. D'autre part, l'ajout de CNTF a permis de protéger les oligodendrocytes mais pas les neurones des cultures exposées à l'ammoniaque, via les voies de signalisations JAK/STAT, SAPK/JNK et c-jun. - Dans une dernière partie, nous avons voulu contrecarrer, par l'ajout de créatine, le déficit énergétique cérébral induit par l'ammoniaque. La créatine a permis de protéger des cellules de type astrocytaire mais pas les cellules cérébrales en agrégats. Cette thèse amis en évidence que les stratégies de neuroprotection chez les patients hyperammonémiques nécessiteront de cibler plusieurs voies de signalisation afin de protéger tous les types cellulaires du cerveau. Summary : In pediatric patients, hyperammonemia is mainly caused by urea cycle disorders or other inborn errors of metabolism, and leads to neurological injury with cortical atrophy, ventricular enlargement and demyelination. Children rescued from neonatal hyperammonemia show significant risk of mental retardation and developmental disabilities. The mainstay of therapy is limited to ammonia lowering through dietary restriction and alternative pathway treatments. However, the possibility of using treatments in a neuroprotective goal may be useful to improve the neurological outcome of patients. Thus, the main objective of this work was to investigate intracellular and extracellular signaling pathways altered by ammonia tonicity, so as to identify new potential therapeutic targets. Experiments were conducted in reaggregated developing brain cell cultures exposed to ammonia, as a model for the developing CNS of hyperammonemic young patients. Theses strategies of neuroprotection were tested: - The first strategy consisted in inhibiting intracellular proteins triggering cell death. Our data indicated that ammonia exposure altered the viability of neurons and oligodendrocytes. Apoptosis and proteins involved in the trigger of apoptosis, such as caspases, calpain and cyclin-dependent kinase-5 (cdk5) with its activator p25, were activated by ammonia exposure. While caspases and calpain inhibitors exhibited no protective effects, roscovitine, a cdk5 inhibitor, reduced ammonia-induced neuronal death. This work revealed that inhibition of cdk5 seems a promising strategy to prevent the toxic effects of ammonia on neurons. - The second strategy consisted in mimicking, the endogenous protective mechanisms triggered by ammonia in the brain. Ammonia exposure caused an increase of the ciliary neurotrophic factor (CNTF) expression, through the activation of the p38 mitogen-activated protein kinase (MAPK) in astrocytes. Treatment of cultures exposed to ammonia with exogenous CNTF demonstrated strong protective effects on oligodendrocytes but not on neurons. These protective effects seemed to involve JAK/STAT, SAPK/JNK and c-jun proteins. - The third strategy consisted in preventing the ammonia-induced cerebral energy deficit with creatine. Creatine treatment protected the survival of astrocyte-like cells through MAPKs pathways. In contrast, it had no protective effects in reaggregated developing brain cell cultures exposed to ammonia. The present study suggests that neuroprotective strategies should optimally be directed at multiple targets to prevent ammonia-induced alterations of the different brain cell types.

Stress reaction of kidney epithelial cells to inorganic solid-core nanoparticles.

A route of accumulation and elimination of therapeutic engineered nanoparticles (NPs) may be the kidney. Therefore, the interactions of different solid-core inorganic NPs (titanium-, silica-, and iron oxide-based NPs) were studied in vitro with the MDCK and LLC-PK epithelial cells as representative cells of the renal epithelia. Following cell exposure to the NPs, observations include cytotoxicity for oleic acid-coated iron oxide NPs, the production of reactive oxygen species for titanium dioxide NPs, and cell depletion of thiols for uncoated iron oxide NPs, whereas for silica NPs an apparent rapid and short-lived increase of thiol levels in both cell lines was observed. Following cell exposure to metallic NPs, the expression of the tranferrin receptor/CD71 was decreased in both cells by iron oxide NPs, but only in MDCK cells by titanium dioxide NPs. The tight association, then subsequent release of NPs by MDCK and LLC-PK kidney epithelial cells, showed that following exposure to the NPs, only MDCK cells could release iron oxide NPs, whereas both cells released titanium dioxide NPs. No transfer of any solid-core NPs across the cell layers was observed.