Background: Huntington's disease (HD) is a devastating brain disorder with no effective treatment or cure available. The scarcity of brain tissue makes it hard to study changes in the brain and... Show moreBackground: Huntington's disease (HD) is a devastating brain disorder with no effective treatment or cure available. The scarcity of brain tissue makes it hard to study changes in the brain and impossible to perform longitudinal studies. However, peripheral pathology in HD suggests that it is possible to study the disease using peripheral tissue as a monitoring tool for disease progression and/or efficacy of novel therapies. In this study, we investigated if blood can be used to monitor disease severity and progression in brain. Since previous attempts using only gene expression proved unsuccessful, we compared blood and brain Huntington's disease signatures in a functional context.Methods: Microarray HD gene expression profiles from three brain regions were compared to the transcriptome of HD blood generated by next generation sequencing. The comparison was performed with a combination of weighted gene co-expression network analysis and literature based functional analysis (Concept Profile Analysis). Uniquely, our comparison of blood and brain datasets was not based on (the very limited) gene overlap but on the similarity between the gene annotations in four different semantic categories: "biological process", "cellular component", "molecular function" and "disease or syndrome".Results: We identified signatures in HD blood reflecting a broad pathophysiological spectrum, including alterations in the immune response, sphingolipid biosynthetic processes, lipid transport, cell signaling, protein modification, spliceosome, RNA splicing, vesicle transport, cell signaling and synaptic transmission. Part of this spectrum was reminiscent of the brain pathology. The HD signatures in caudate nucleus and BA4 exhibited the highest similarity with blood, irrespective of the category of semantic annotations used. BA9 exhibited an intermediate similarity, while cerebellum had the least similarity. We present two signatures that were shared between blood and brain: immune response and spinocerebellar ataxias.Conclusions: Our results demonstrate that HD blood exhibits dysregulation that is similar to brain at a functional level, but not necessarily at the level of individual genes. We report two common signatures that can be used to monitor the pathology in brain of HD patients in a non-invasive manner. Our results are an exemplar of how signals in blood data can be used to represent brain disorders. Our methodology can be used to study disease specific signatures in diseases where heterogeneous tissues are involved in the pathology. Show less
Mina, E.; Roon-Mom, W. van; Hettne, K.; Zwet, E. van; Goeman, J.; Neri, C.; ... ; Roos, M. 2016
The approval and differentiation of new compounds in clinical development often demands non-inferiority trials, in which the test drug is compared against a reference treatment. However, non... Show moreThe approval and differentiation of new compounds in clinical development often demands non-inferiority trials, in which the test drug is compared against a reference treatment. However, non-inferiority trials impose major operational burden with serious ethical and scientific implications for the development of new medicines. Traditional approaches make limited use of historical information on placebo and neglect inter-trial variability, relying on the constancy assumption that the control-to-placebo effect size is maintained across trials. We propose a model-based approach that overcomes such limitations and may be used as a tool to explore differentiation during clinical development. Parameter distributions are introduced which reflect the heterogeneity of trials. The method is illustrated using data from impetigo trials. Based on simulation scenarios, this Bayesian technique yields a definitive, consistent increase in the statistical power over two accepted statistical methods, allowing lower sample size requirements for the assessment of non-inferiority. Show less
Santen, G.; Zwet, E. van; Bettica, P.; Gomeni, R.A.; Danhof, M.; Pasqua, O. della 2011
Clinical trials with antidepressant drugs often fail to detect drug effect, even with drugs that are known to be efficacious. In a previous publication, we showed that a model-based approach is... Show moreClinical trials with antidepressant drugs often fail to detect drug effect, even with drugs that are known to be efficacious. In a previous publication, we showed that a model-based approach is required to address some of the existing challenges in the design of clinical trial protocols. Here, we illustrate how the implementation of an interim analysis (IA) may help to identify studies that are headed for failure, early in the trial before completion of treatment. In contrast to traditional IA procedures, an adaptive Bayesian approach is proposed to optimize the timing of analysis and decision criteria for futility and efficacy, taking into account enrollment rate and treatment response at intermediate visits in the trial. Validation procedures involving re-enrollment of patients confirmed the performance of the method. Our findings reveal that optimization of the timing and decision criteria at the interim stage is critical for the accuracy of the conclusions about treatment efficacy or futility. Show less
