Selection of SNP subsets for association studies in candidate genes: comparison of the power of different strategies to detect single disease susceptibility locus effects

BACKGROUND: The recent advances in genotyping and molecular techniques have greatly increased the knowledge of the human genome structure. Millions of polymorphisms are reported and freely available in public databases. As a result, there is now a need to identify among all these data, the relevant markers for genetic association studies. Recently, several methods have been published to select subsets of markers, usually Single Nucleotide Polymorphisms (SNPs), that best represent genetic polymorphisms in the studied candidate gene or region. RESULTS: In this paper, we compared four of these selection methods, two based on haplotype information and two based on pairwise linkage disequilibrium (LD). The methods were applied to the genotype data on twenty genes with different patterns of LD and different numbers of SNPs. A measure of the efficiency of the different methods to select SNPs was obtained by comparing, for each gene and under several single disease susceptibility models, the power to detect an association that will be achieved with the selected SNP subsets. CONCLUSION: None of the four selection methods stands out systematically from the others. Methods based on pairwise LD information turn out to be the most interesting methods in a context of association study in candidate gene. In a context where the number of SNPs to be tested in a given region needs to be more limited, as in large-scale studies or wide genome scans, one of the two methods based on haplotype information, would be more suitable

Haploinsufficiency of Dmxl2, Encoding a Synaptic Protein, Causes Infertility Associated with a Loss of GnRH Neurons in Mouse

International audienceCharacterization of the genetic defects causing gonadotropic deficiency has made a major contribution to elucidation of the fundamental role of Kisspeptins and Neurokinin B in puberty onset and reproduction. The absence of puberty may also reveal neurodevelopmental disorders caused by molecular defects in various cellular pathways. Investigations of these neurodevelopmental disorders may provide information about the neuronal processes controlling puberty onset and reproductive capacity. We describe here a new syndrome observed in three brothers, which involves gonadotropic axis deficiency, central hypothyroidism, peripheral demyelinating sensorimotor polyneuropathy, mental retardation, and profound hypoglycemia, progressing to nonautoimmune insulin-dependent diabetes mellitus. High-throughput sequencing revealed a homozygous in-frame deletion of 15 nucleotides in DMXL2 in all three affected patients. This homozygous deletion was associated with lower DMXL2 mRNA levels in the blood lymphocytes of the patients. DMXL2 encodes the synaptic protein rabconnectin-3a, which has been identified as a putative scaffold protein for Rab3-GAP and Rab3-GEP, two regulators of the GTPase Rab3a. We found that rabconnectin-3a was expressed in exocytosis vesicles in gonadotropin-releasing hormone (GnRH) axonal extremities in the median eminence of the hypothalamus. It was also specifically expressed in cells expressing luteinizing hormone (LH) and follicle-stimulating hormone (FSH) within the pituitary. The conditional heterozygous deletion of Dmxl2 from mouse neurons delayed puberty and resulted in very low fertility. This reproductive phenotype was associated with a lower number of GnRH neurons in the hypothalamus of adult mice. Finally, Dmxl2 knockdown in an insulin-secreting cell line showed that rabconnectin-3a controlled the constitutive and glucose-induced secretion of insulin. In conclusion, this study shows that low levels of DMXL2 expression cause a complex neurological phenotype, with abnormal glucose metabolism and gonadotropic axis deficiency due to a loss of GnRH neurons. Our findings identify rabconectin-3a as a key controller of neuronal and endocrine homeostatic processes

Sensitive Skin: Lessons From Transcriptomic Studies

In 2016, a special interest group from the International Forum for the Study of Itch defined sensitive skin (SS) as a syndrome that manifests with the occurrence of unpleasant sensations (stinging, burning, pain, pruritus, and tingling sensations) after stimuli that should not cause a reaction, such as water, cold, heat, or other physical and/or chemical factors. The pathophysiology of sensitive skin is still poorly understood, but the symptoms described suggest inflammation and peripheral innervation. Only two publications have focused on sensitive skin transcriptomics. In the first study, the authors performed a microarray comparison of SS and non-sensitive skin (NSS) samples and showed differences in the expression of numerous genes in SS and NSS samples. Moreover, in the SS samples, two clusters of genes were identified, including upregulated and downregulated genes, compared to NSS samples. These results provide some interesting clues for the understanding of the pathophysiology of SS. The second study compared SS and NSS samples using RNA-seq assays. This method allowed the identification of long non-coding RNAs (lncRNAs) and differentially expressed mRNAs and provided a comprehensive profile in subjects with SS. The results showed that a wide range of genes may be involved in the pathogenesis of SS and suggested pathways that could be associated with them. In this paper, we discuss these two studies in detail and show how transcriptomic studies can help understand the pathophysiology of sensitive skin. We call for new transcriptomic studies on larger populations to be conducted before putative pathogenic mechanisms can be detected and analyzed to achieve a better understanding of this complex condition

A mitochondrial origin for frontotemporal dementia and amyotrophic lateral sclerosis through CHCHD10 involvement.

Mitochondrial DNA instability disorders are responsible for a large clinical spectrum, among which amyotrophic lateral sclerosis-like symptoms and frontotemporal dementia are extremely rare. We report a large family with a late-onset phenotype including motor neuron disease, cognitive decline resembling frontotemporal dementia, cerebellar ataxia and myopathy. In all patients, muscle biopsy showed ragged-red and cytochrome c oxidase-negative fibres with combined respiratory chain deficiency and abnormal assembly of complex V. The multiple mitochondrial DNA deletions found in skeletal muscle revealed a mitochondrial DNA instability disorder. Patient fibroblasts present with respiratory chain deficiency, mitochondrial ultrastructural alterations and fragmentation of the mitochondrial network. Interestingly, expression of matrix-targeted photoactivatable GFP showed that mitochondrial fusion was not inhibited in patient fibroblasts. Using whole-exome sequencing we identified a missense mutation (c.176C>T; p.Ser59Leu) in the CHCHD10 gene that encodes a coiled-coil helix coiled-coil helix protein, whose function is unknown. We show that CHCHD10 is a mitochondrial protein located in the intermembrane space and enriched at cristae junctions. Overexpression of a CHCHD10 mutant allele in HeLa cells led to fragmentation of the mitochondrial network and ultrastructural major abnormalities including loss, disorganization and dilatation of cristae. The observation of a frontotemporal dementia-amyotrophic lateral sclerosis phenotype in a mitochondrial disease led us to analyse CHCHD10 in a cohort of 21 families with pathologically proven frontotemporal dementia-amyotrophic lateral sclerosis. We identified the same missense p.Ser59Leu mutation in one of these families. This work opens a novel field to explore the pathogenesis of the frontotemporal dementia-amyotrophic lateral sclerosis clinical spectrum by showing that mitochondrial disease may be at the origin of some of these phenotypes

Exome sequencing identifies rare damaging variants in ATP8B4 and ABCA1 as novel risk factors for Alzheimers Disease

The genetic component of Alzheimer’s disease (AD) has been mainly assessed using Genome Wide Association Studies (GWAS), which do not capture the risk contributed by rare variants. Here, we compared the gene-based burden of rare damaging variants in exome sequencing data from 32,558 individuals —16,036 AD cases and 16,522 controls— in a two-stage analysis. Next to known genes TREM2, SORL1 and ABCA7, we observed a significant association of rare, predicted damaging variants in ATP8B4 and ABCA1 with AD risk, and a suggestive signal in ADAM10. Next to these genes, the rare variant burden in RIN3, CLU, ZCWPW1 and ACE highlighted these genes as potential driver genes in AD-GWAS loci. Rare damaging variants in these genes, and in particular loss-of-function variants, have a large effect on AD-risk, and they are enriched in early onset AD cases. The newly identified AD-associated genes provide additional evidence for a major role for APP-processing, Aβ-aggregation, lipid metabolism and microglial function in AD

Exome sequencing identifies rare damaging variants in ATP8B4 and ABCA1 as risk factors for Alzheimer’s disease

Alzheimer’s disease (AD), the leading cause of dementia, has an estimated heritability of approximately 70%1. The genetic component of AD has been mainly assessed using genome-wide association studies, which do not capture the risk contributed by rare variants2. Here, we compared the gene-based burden of rare damaging variants in exome sequencing data from 32,558 individuals—16,036 AD cases and 16,522 controls. Next to variants in TREM2, SORL1 and ABCA7, we observed a significant association of rare, predicted damaging variants in ATP8B4 and ABCA1 with AD risk, and a suggestive signal in ADAM10. Additionally, the rare-variant burden in RIN3, CLU, ZCWPW1 and ACE highlighted these genes as potential drivers of respective AD-genome-wide association study loci. Variants associated with the strongest effect on AD risk, in particular loss-of-function variants, are enriched in early-onset AD cases. Our results provide additional evidence for a major role for amyloid-β precursor protein processing, amyloid-β aggregation, lipid metabolism and microglial function in AD

Optimisation de l'utilisation des SNPs dans l'étude de la composante génétique des maladies complexes

LE KREMLIN-B.- PARIS 11-BU Méd (940432101) / SudocPARIS-BIUP (751062107) / SudocSudocFranceF

Lesinteractions gène-environnement dans les études génétiques des maladies complexes

LE KREMLIN-B.- PARIS 11-BU Méd (940432101) / SudocSudocFranceF

Influence et traitement des données manquantes dans les études d'association sur trios (application à des données sur la sclérose en plaques)

ORSAY-PARIS 11-BU Sciences (914712101) / SudocSudocFranceF

ABCD2, une cible thérapeutique pour l adrénoleucodystrophie liée au chromosome X (régulation par des thyromimétiques et caractérisation fonctionnelle)

L'adrénoleucodystrophie liée au chromosome X (X-ALD, OMIM 300100) est une maladie neurodégénérative associée au gène ABCD1 codant pour un hémi-transporteur ABC peroxysomal. ABCD1 est associé à l'entrée des acides gras à très longue chaîne dans le peroxysome, lieu unique de leur beta-oxydation. ABCD2, un autre hémi-transporteur peroxysomal, présente une redondance fonctionnelle partielle avec ABCD1. Une thérapie pharmacologique ciblée sur une augmentation de l'expression d'ABCD2 pourrait donc être envisagée pour compenser la déficience d'ABCD1. Nous avons ainsi évalué les effets, in vitro, de thyromimétiques (analogues pharmacologiques de la T3) comme inducteurs potentiels de l'expression d'ABCD2. Une nouvelle voie d'induction de l'expression d'ABCD2 par les thyromimétiques GC-1 et CGS 23425 a ainsi été mise en évidence dans des lignées cellulaires humaines. En parallèle, pour tenter de mieux comprendre le phénomène de redondance fonctionnelle entre les deux transporteurs, il est primordial de caractériser la fonction et la spécificité de substrat d'ABCD2. A l'aide de modèles cellulaires surexprimant une protéine de fusion ABCD2-EGFP fonctionnelle ou non fonctionnelle de manière contrôlée, nous avons confirmé la redondance fonctionnelle partielle entre ABCD1 et ABCD2 pour le transport du C26:0, du C24:0 et du C26:1 (n-9). De plus, ce travail nous a permis suggérer l'existence d'une hétérodimérisation entre les transporteurs ABCD2 et ABCD1, et surtout, un effet trans-dominant négatif d'ABCD2 muté sur ABCD1. Il devient donc primordial de poursuivre la recherche des substrats d'ABCD2 en relation avec l'étude de son statut dimérique.X-linked Adrenoleukodystrophy (X-ALD, OMIM 300100) is a neurodegenerative disease due to mutations in the ABCD1 gene. ABCD1 encodes for a half ABC transporter of the peroxisomal membrane, which seems to be associated with the entry of very-long chain fatty acids (VLCFA, C>22) in peroxisome. The ABCD2 gene, an other peroxisomal half-transporter, displays a partial functional redundancy with ABCD1. A pharmacological induction of ABCD2 expression could be envisaged to compensate for ABCD1 deficiency. We have investigated the effects, in vitro, of thyromimetics (pharmacological homologs of T3) on the expression of ABCD2. The thyromimetics, GC-1 and CGS 23425, trigger up-regulation of ABCD2 expression in human cell lines. Besides, in order to understand the partial functional redundancy between ABCD2 and ABCD1, it's crucial to characterize the function and the substrate specificity of ABCD2. To this end, with two stable cell clones overexpressing a functional or a non functional ABCD2-EGFP fusion protein in a controlled manner, we have confirmed the functional redundancy of ABCD1 and ABCD2 towards C26:0, C24:0 and C26:1 (n-9). Moreover, the results suggest heterodimerization between ABCD2 and ABCD1, and a trans-dominant negative effect of the mutated ABCD2-EGFP protein on ABCD1. It thus becomes essential to pursue the search for the substrates of ABCD2 in connection with the study of its dimeric status.DIJON-BU Sciences Economie (212312102) / SudocPARIS-BIUP (751062107) / SudocSudocFranceF