During the last 3 years, a number of approaches for the normalization of RNA sequencing data have emerged in the literature, differing both in the type of bias adjustment and in the statistical strategy adopted. However, as data continue to accumulate, there has been no clear consensus on the appropriate normalization method to be used or the impact of a chosen method on the downstream analysis. In this work, we focus on a comprehensive comparison of seven recently proposed normalization methods for the differential analysis of RNA-seq data, with an emphasis on the use of varied real and simulated datasets involving different species and experimental designs to represent data characteristics commonly observed in practice. Based on this comparison study, we propose practical recommendations on the appropriate normalization method to be used and its impact on the differential analysis of RNA-seq data.
The first large genome-wide association (GWA) study of systemic sclerosis (SSc) recently included 2296 SSc patients and 5014 healthy controls from four case–control series of Caucasian individuals and involved the analysis of about 280 000 single nucleotide polymorphisms (SNPs).1 Outside the HLA region, SNPs mapping to the known TNPO3 - IRF5 and STAT4 regions showed the strongest association but three other loci reached genome-wide significance (namely CD247 locus in 1q22–23, CDH7 in 18q22 and EXOC2 - IRF4 near 6p25) although only one ( CD247 ) could be replicated in the second set of samples. Given the major challenge of separating the many false-positive associations from the few true-positive associations with disease in GWA studies, resulting in a stratification bias, a critical strategy is replication of results in independent samples.2 Therefore, we herein provide an attempt of …
Background The effects of α and ß adrenergic receptor modulation on the risk of developing heart failure (HF) remains uncertain due to a lack of randomized controlled trials. This study aimed to estimate the effects of α and ß adrenergic receptors modulation on the risk of HF and to provide proof of principle for genetic target validation studies in HF. Methods Genetic variants within the cis regions encoding the adrenergic receptors α1A, α2B, ß1, and ß2 associated with blood pressure in a 757,601-participant genome-wide association study (GWAS) were selected as instruments to perform a drug target Mendelian randomization study. Effects of these variants on HF risk were derived from the HERMES GWAS (542,362 controls; 40,805 HF cases). Results Lower α1A or ß1 activity was associated with reduced HF risk: odds ratio (OR) 0.83 (95% CI 0.74–0.93, P = 0.001) and 0.95 (95% CI 0.93–0.97, P = 8 × 10 −6 ). Conversely, lower α2B activity was associated with increased HF risk: OR 1.09 (95% CI 1.05–1.12, P = 3 × 10 −7 ). No evidence of an effect of lower ß2 activity on HF risk was found: OR 0.99 (95% CI 0.92–1.07, P = 0.95). Complementary analyses showed that these effects were consistent with those on left ventricular dimensions and acted independently of any potential effect on coronary artery disease. Conclusions This study provides genetic evidence that α1A or ß1 receptor inhibition will likely decrease HF risk, while lower α2B activity may increase this risk. Genetic variant analysis can assist with drug development for HF prevention.
Background: Human diseases are multi-factorial biological phenomena resulting from perturbations of numerous functional networks. The complex nature of human diseases explains frequently observed marginal or transitory efficacy of mono-therapeutic interventions. For this reason, combination therapy is being increasingly evaluated as a biologically plausible strategy for reversing disease state, fostering the development of dedicated methodological and experimental approaches. In parallel, genome-wide association studies (GWAS) provide a prominent opportunity for disclosing human-specific therapeutic targets and rational drug repurposing. Objective: In this context, our objective was to elaborate an integrated computational platform to accelerate discovery and experimental validation of synergistic combinations of repurposed drugs for treatment of common human diseases. Methods: The proposed approach combines adapted statistical analysis of GWAS data, pathway-based functional annotation of genetic findings using gene set enrichment technique, computational reconstruction of signaling networks enriched in disease-associated genes, selection of candidate repurposed drugs and proof-of-concept combinational experimental screening. Results: It enables robust identification of signaling pathways enriched in disease susceptibility loci. Therapeutic targeting of the disease-associated signaling networks provides a reliable way for rational drug repurposing and rapid development of synergistic drug combinations for common human diseases. Conclusion: Here we demonstrate the feasibility and efficacy of the proposed approach with an experiment application to Alzheimer’s disease.
Abstract Objective Pulmonary arterial hypertension (PAH) has emerged as a leading cause of death in systemic sclerosis (SSc). The genetic basis of PAH has been unraveled in recent years, with a major role played by transforming growth factor β receptors; however, some other candidate genes have also been advocated, including potassium voltage‐gated channel, shaker‐related subfamily, member 5 ( KCNA5 ). We undertook this study to determine whether KCNA5 polymorphisms confer susceptibility to SSc and its vascular phenotype, including PAH. Methods Four KCNA5 single‐nucleotide polymorphisms (SNPs), rs10744676, rs1860420, rs3741930, and rs2284136, were genotyped in a discovery set of 638 SSc patients and 469 controls. In addition, rs10744676 was genotyped in an independent replication sample (938 SSc patients and 564 controls) and in a cohort of 168 patients with different PAH subtypes. Results The KCNA5 rs10744676 variant was found to be associated with SSc in the discovery sample, with an odds ratio (OR) of 0.62 (95% confidence interval [95% CI] 0.48–0.79, adjusted P = 0.0003) in comparison with controls (C allele frequency 11.4% versus 17.2%). When subphenotypes were investigated, an association was found solely for PAH associated with SSc (OR 0.31 [95% CI 0.13–0.71], adjusted P = 0.04). The other KCNA5 SNPs tested were not associated with any SSc subset. The above association with PAH associated with SSc was replicated in the second set. In the combined population, rs10744676 was strongly associated with PAH associated with SSc in comparison with controls (OR 0.36 [95% CI 0.21–0.63], P = 0.0002). In the independent cohort of patients with PAH, after investigating PAH subtypes, only rs10744676 showed an association with PAH associated with SSc. Conclusion Our results provide the first evidence for an association between the KCNA5 rs10744676 variant and PAH associated with SSc.
Enhancing the efficacy of drugs targeting cognitive decline in Alzheimer disease (AD), together with improving their safety, has been a long-term goal of therapeutic development. Currently approved standards of care (SOCs) exhibit transient efficacy and their use is accompanied by undesirable side effects. Thus, drug combination therapies, particularly those applying low doses, may represent next generation therapies for AD. We previously demonstrated the synergistic effectiveness of a combination therapy (known as PXT864) consisting of two repurposed drugs – acamprosate and baclofen – in AD models. As patients are usually treated with a SOC, we investigated whether the efficacy of these SOCs at inactive doses is improved by combining them with low or inactive doses of PXT864. To this end, we assessed the efficacy of PXT864 combined with the SOCs, donepezil or memantine, on different cellular and behavioral endpoints in an in vitro neuronal primary culture model intoxicated with oligomeric β-amyloid peptides (Aβ), and an in vivo intracebroventricular Aβ-injection mouse model. We found that tri-therapy with PXT864+donepezil or PXT864+memantine synergistically protected neuronal cells against Aβ toxicity with a higher protective effect than the individual drugs alone. In AD model animals, doses of individual drugs selected for their inactivity, and binary combinations of such doses of individual drugs, were totally ineffective whereas the tri-therapeutic combination synergistically alleviated cognitive deficits. These findings highlight the value of using repurposed drugs combined with low doses of existing SOC therapeutics, and emphasize the value of network pharmacology approach that allows to discover combinations with new mechanisms of action.
Objective. Identification of an association between IRF5 rs2004640 and systemic sclerosis (SSc) has highlighted a key role for type 1 interferon (IFN). Additional functional IRF5 variants have been identified as autoimmune susceptibility factors. Our aim was to investigate whether IRF5 haplotypes confer susceptibility to SSc, and to perform genotype haplotype-phenotype correlation analyses. Methods. We genotyped IRF5 rs377385, rs2004640, and rs10954213 in 1623 individuals of French European Caucasian origin. SSc patient subphenotypes were analyzed according to cutaneous subsets and for SSc-related pulmonary fibrosis. Results. Case-control studies of single markers revealed an association between IRF5 rs3757385, rs2004640, and rs10954213 variants and SSc. We identified an IRF5 risk haplotype “R” (p adj = 0.024, OR 1.23, 95% CI 1.07–1.40) and a mirrored protective haplotype “P” (p adj = 8.8 × 10 −3 , OR 0.78, 95% CI 0.68–0.90) for SSc susceptibility. Genotype-phenotype correlation analyses failed to detect any association with a single marker. By contrast, phenotype-haplotype correlation analysis was able to detect intra-cohort association and to discriminate SSc patients with from those without the following clinical traits: “R” and/or “P” haplotypes identified diffuse cutaneous SSc (p = 0.0081) and fibrosing alveolitis (p = 0.018). Conclusion. IRF5 haplotypes are more informative than single markers, suggesting that they could be helpful for risk stratification of SSc patients. Our study provides further evidence of a key role of IRF5 in SSc severity.
11040 Background: Loss-of-function variants in the melanocortin 1 receptor gene (MC1R) are low penetrant melanoma predisposing alleles. Methods: A cohort comprising 1,019 patients affected by melanoma (MelanCohort) and 1,466 Caucasian controls skin cancer-free were studied. Ten polymorphisms, including five functional MC1R alleles (R151C, R160W, D294H, R142H, D84E), two non-synonymous SLC45A2 variants (L374F and E272K), and three intronic OCA2 variants previously shown to be strongly associated with eye color (rs7495174, rs4778241 and rs4778138) were genotyped. Genotype, allele, haplotype and diplotype frequencies were compared in the two groups using Fisher’s exact test and odds ratio calculations Results: As expected, MC1R variants were closely associated with melanoma risk (P-value < 2.20×10-16). Interestingly, the SLC45A2 variants L374F and E272K were also significantly and strongly associated with melanoma (respectively, P-value × 2.12×10-15, OR × 0.35 [0.26–0.46], and P-value = 1.10×10-6 OR × 0.40 [0.27–0.59]). MC1R and SLC45A2 variants had additive effects on melanoma risk, and after adjusting for clinical risk factors, the risk was persistent, even though both genes were strongly associated with pigmentation. Conclusions: Future studies may show whether genetic information could provide a useful complement to physical examination in predicting melanoma risk. No significant financial relationships to disclose.
The Charcot-Marie-Tooth Neuropathy Score (CMTNS) was developed as a main efficacy endpoint for application in clinical trials of Charcot-Marie-Tooth disease type 1A (CMT1A). However, the sensitivity of the CMTNS for measuring disease severity and progression in CMT1A patients has been questioned. Here, we applied a Rasch analysis in a French cohort of patients to evaluate the psychometrical properties of the CMTNS. Overall, our analysis supports the validity of the CMTNS for application to CMT1A patients though with some limitations such as certain items of the CMTNS being more suitable for moderate to severe forms of the disease, and some items being disordered. We suggest that additional items and/or categories be considered to better assess mild-to-moderate patients.
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