Isabelle Rivals

Classification of Human Chromosome 21 Gene-Expression Variations in Down Syndrome: Impact on Disease Phenotypes

Down syndrome caused by chromosome 21 trisomy is the most common genetic cause of mental retardation in humans. Disruption of the phenotype is thought to be the result of gene-dosage imbalance. Variations in chromosome 21 gene expression in Down syndrome were analyzed in lymphoblastoid cells derived from patients and control individuals. Of the 359 genes and predictions displayed on a specifically designed high-content chromosome 21 microarray, one-third were expressed in lymphoblastoid cells. We performed a mixed-model analysis of variance to find genes that are differentially expressed in Down syndrome independent of sex and interindividual variations. In addition, we identified genes with variations between Down syndrome and control samples that were significantly different from the gene-dosage effect (1.5). Microarray data were validated by quantitative polymerase chain reaction. We found that 29% of the expressed chromosome 21 transcripts are overexpressed in Down syndrome and correspond to either genes or open reading frames. Among these, 22% are increased proportional to the gene-dosage effect, and 7% are amplified. The other 71% of expressed sequences are either compensated (56%, with a large proportion of predicted genes and antisense transcripts) or highly variable among individuals (15%). Thus, most of the chromosome 21 transcripts are compensated for the gene-dosage effect. Overexpressed genes are likely to be involved in the Down syndrome phenotype, in contrast to the compensated genes. Highly variable genes could account for phenotypic variations observed in patients. Finally, we show that alternative transcripts belonging to the same gene are similarly regulated in Down syndrome but sense and antisense transcripts are not.

Training wavelet networks for nonlinear dynamic input–output modeling

Abstract In the framework of nonlinear process modeling, we propose training algorithms for feedback wavelet networks used as nonlinear dynamic models. An original initialization procedure is presented that takes the locality of the wavelet functions into account. Results obtained for the modeling of several processes are presented; a comparison with networks of neurons with sigmoidal functions is performed.

Nonlinear internal model control using neural networks: application to processes with delay and design issues

We propose a design procedure of neural internal model control systems for stable processes with delay. We show that the design of such nonadaptive indirect control systems necessitates only the training of the inverse of the model deprived from its delay, and that the presence of the delay thus does not increase the order of the inverse. The controller is then obtained by cascading this inverse with a rallying model which imposes the regulation dynamic behavior and ensures the robustness of the stability. A change in the desired regulation dynamic behavior, or an improvement of the stability, can be obtained by simply tuning the rallying model, without retraining the whole model reference controller. The robustness properties of internal model control systems being obtained when the inverse is perfect, we detail the precautions which must be taken for the training of the inverse so that it is accurate in the whole space visited during operation with the process. In the same spirit, we make an emphasis on neural models affine in the control input, whose perfect inverse is derived without training. The control of simulated processes illustrates the proposed design procedure and the properties of the neural internal model control system for processes without and with delay.

Green Tea Polyphenols Rescue of Brain Defects Induced by Overexpression of DYRK1A

Individuals with partial HSA21 trisomies and mice with partial MMU16 trisomies containing an extra copy of the DYRK1A gene present various alterations in brain morphogenesis. They present also learning impairments modeling those encountered in Down syndrome. Previous MRI and histological analyses of a transgenic mice generated using a human YAC construct that contains five genes including DYRK1A reveal that DYRK1A is involved, during development, in the control of brain volume and cell density of specific brain regions. Gene dosage correction induces a rescue of the brain volume alterations. DYRK1A is also involved in the control of synaptic plasticity and memory consolidation. Increased gene dosage results in brain morphogenesis defects, low BDNF levels and mnemonic deficits in these mice. Epigallocatechin gallate (EGCG) — a member of a natural polyphenols family, found in great amount in green tea leaves — is a specific and safe DYRK1A inhibitor. We maintained control and transgenic mice overexpressing DYRK1A on two different polyphenol-based diets, from gestation to adulthood. The major features of the transgenic phenotype were rescued in these mice.

Neural-network construction and selection in nonlinear modeling

We study how statistical tools which are commonly used independently can advantageously be exploited together in order to improve neural network estimation and selection in nonlinear static modeling. The tools we consider are the analysis of the numerical conditioning of the neural network candidates, statistical hypothesis tests, and cross validation. We present and analyze each of these tools in order to justify at what stage of a construction and selection procedure they can be most useful. On the basis of this analysis, we then propose a novel and systematic construction and selection procedure for neural modeling. We finally illustrate its efficiency through large-scale simulations experiments and real-world modeling problems.

Construction of confidence intervals for neural networks based on least squares estimation

We present the theoretical results about the construction of confidence intervals for a nonlinear regression based on least squares estimation and using the linear Taylor expansion of the nonlinear model output. We stress the assumptions on which these results are based, in order to derive an appropriate methodology for neural black-box modeling; the latter is then analyzed and illustrated on simulated and real processes. We show that the linear Taylor expansion of a nonlinear model output also gives a tool to detect the possible ill-conditioning of neural network candidates, and to estimate their performance. Finally, we show that the least squares and linear Taylor expansion based approach compares favorably with other analytic approaches, and that it is an efficient and economic alternative to the nonanalytic and computationally intensive bootstrap methods.

On cross validation for model selection

In response to Zhu and Rower (1996), a recent communication (Goutte, 1997) established that leave-one-out cross validation is not subject to the no-free-lunch criticism. Despite this optimistic conclusion, we show here that cross validation has very poor performances for the selection of linear models as compared to classic statistical tests. We conclude that the statistical tests are preferable to cross validation for linear as well as for nonlinear model selection.

Trisomy for Synaptojanin1 in Down syndrome is functionally linked to the enlargement of early endosomes

Enlarged early endosomes have been observed in neurons and fibroblasts in Down syndrome (DS). These endosome abnormalities have been implicated in the early development of Alzheimers disease (AD) pathology in these subjects. Here, we show the presence of enlarged endosomes in blood mononuclear cells and lymphoblastoid cell lines (LCLs) from individuals with DS using immunofluorescence and confocal microscopy. Genotype-phenotype correlations in LCLs carrying partial trisomies 21 revealed that triplication of a 2.56 Mb locus in 21q22.11 is associated with the endosomal abnormalities. This locus contains the gene encoding the phosphoinositide phosphatase synaptojanin 1 (SYNJ1), a key regulator of the signalling phospholipid phosphatidylinositol-4,5-biphosphate that has been shown to regulate clathrin-mediated endocytosis. We found that SYNJ1 transcripts are increased in LCLs from individuals with DS and that overexpression of SYNJ1 in a neuroblastoma cell line as well as in transgenic mice leads to enlarged endosomes. Moreover, the proportion of enlarged endosomes in fibroblasts from an individual with DS was reduced after silencing SYNJ1 expression with RNA interference. In LCLs carrying amyloid precursor protein (APP) microduplications causing autosomal dominant early-onset AD, enlarged endosomes were absent, suggesting that APP overexpression alone is not involved in the modification of early endosomes in this cell type. These findings provide new insights into the contribution of SYNJ1 overexpression to the endosomal changes observed in DS and suggest an attractive new target for rescuing endocytic dysfunction and lipid metabolism in DS and in AD.

Gene expression signature of cerebellar hypoplasia in a mouse model of Down syndrome during postnatal development

BackgroundDown syndrome is a chromosomal disorder caused by the presence of three copies of chromosome 21. The mechanisms by which this aneuploidy produces the complex and variable phenotype observed in people with Down syndrome are still under discussion. Recent studies have demonstrated an increased transcript level of the three-copy genes with some dosage compensation or amplification for a subset of them. The impact of this gene dosage effect on the whole transcriptome is still debated and longitudinal studies assessing the variability among samples, tissues and developmental stages are needed.ResultsWe thus designed a large scale gene expression study in mice (the Ts1Cje Down syndrome mouse model) in which we could measure the effects of trisomy 21 on a large number of samples (74 in total) in a tissue that is affected in Down syndrome (the cerebellum) and where we could quantify the defect during postnatal development in order to correlate gene expression changes to the phenotype observed. Statistical analysis of microarray data revealed a major gene dosage effect: for the three-copy genes as well as for a 2 Mb segment from mouse chromosome 12 that we show for the first time as being deleted in the Ts1Cje mice. This gene dosage effect impacts moderately on the expression of euploid genes (2.4 to 7.5% differentially expressed). Only 13 genes were significantly dysregulated in Ts1Cje mice at all four postnatal development stages studied from birth to 10 days after birth, and among them are 6 three-copy genes. The decrease in granule cell proliferation demonstrated in newborn Ts1Cje cerebellum was correlated with a major gene dosage effect on the transcriptome in dissected cerebellar external granule cell layer.ConclusionHigh throughput gene expression analysis in the cerebellum of a large number of samples of Ts1Cje and euploid mice has revealed a prevailing gene dosage effect on triplicated genes. Moreover using an enriched cell population that is thought responsible for the cerebellar hypoplasia in Down syndrome, a global destabilization of gene expression was not detected. Altogether these results strongly suggest that the three-copy genes are directly responsible for the phenotype present in cerebellum. We provide here a short list of candidate genes.

Transcriptional disruptions in Down syndrome: A case study in the Ts1Cje mouse cerebellum during post-natal development

To understand the aetiology and the phenotypic severity of Down syndrome, we searched for transcriptional signatures in a substructure of the brain (cerebellum) during post‐natal development in a segmental trisomy 16 model, the Ts1Cje mouse. The goal of this study was to investigate the effects of trisomy on changes in gene expression across development time. The primary gene‐dosage effect on triplicated genes (∼1.5) was observed at birth [post‐natal day 0 (P0)], at P15 and P30. About 5% of the non‐triplicated genes were significantly differentially expressed between trisomic and control cerebellum, while 25% of the transcriptome was modified during post‐natal development of the cerebellum. Indeed, only 165, 171 and 115 genes were dysregulated in trisomic cerebellum at P0, P15 and P30, respectively. Surprisingly, there were only three genes dysregulated in development and in trisomic animals in a similar or opposite direction. These three genes (Dscr1, Son and Hmg14) were, quite unexpectedly, triplicated in the Ts1Cje model and should be candidate genes for understanding the aetiology of the phenotype observed in the cerebellum.