Clinical and molecular characterization of 17q21.31 microdeletion syndrome in 14 French patients with mental retardation.

International audienceChromosome 17q21.31 microdeletion was one of the first genomic disorders identified by chromosome microarrays. We report here the clinical and molecular characterization of a new series of 14 French patients with this microdeletion syndrome. The most frequent clinical features were hypotonia, developmental delay and facial dysmorphism, but scaphocephaly, prenatal ischemic infarction and perception deafness were also described. Genotyping of the parents showed that the parent from which the abnormality was inherited carried the H2 inversion polymorphism, confirming that the H2 allele is necessary, but not sufficient to generate the 17q21.31 microdeletion. Previously reported molecular analyses of patients with 17q21.31 microdeletion syndrome defined a 493 kb genomic fragment that was deleted in most patients after taking into account frequent copy number variations in normal controls, but the deleted interval was significantly smaller (205 kb) in one of our patients, encompassing only the MAPT, STH and KIAA1267 genes. As this patient presents the classical phenotype of 17q21.31 syndrome, these data make it possible to define a new minimal critical region of 160.8 kb, strengthening the evidence for involvement of the MAPT gene in this syndrome

Mutations involving the SRY-related gene SOX8 are associated with a spectrum of human reproductive anomalies.

© The Author(s) 2018. Published by Oxford University Press. All rights reserved. SOX8 is an HMG-box transcription factor closely related to SRY and SOX9. Deletion of the gene encoding Sox8 in mice causes reproductive dysfunction but the role of SOX8 in humans is unknown. Here, we show that SOX8 is expressed in the somatic cells of the early developing gonad in the human and influences human sex determination. We identified two individuals with 46, XY disorders/differences in sex development (DSD) and chromosomal rearrangements encompassing the SOX8 locus and a third individual with 46, XY DSD and a missense mutation in the HMG-box of SOX8. In vitro functional assays indicate that this mutation alters the biological activity of the protein. As an emerging body of evidence suggests that DSDs and infertility can have common etiologies, we also analysed SOX8 in a cohort of infertile men (n=274) and two independent cohorts of women with primary ovarian insufficiency (POI; n=153 and n=104). SOX8 mutations were found at increased frequency in oligozoospermic men (3.5%; P < 0.05) and POI (5.06%; P=4.5×10 -5 ) as compared with fertile/normospermic control populations (0.74%). The mutant proteins identified altered SOX8 biological activity as compared with the wild-type protein. These data demonstrate that SOX8 plays an important role in human reproduction and SOX8 mutations contribute to a spectrum of phenotypes including 46, XY DSD, male infertility and 46, XX POI.Link_to_subscribed_fulltex

Widening of the genetic and clinical spectrum of Lamb-Shaffer syndrome, a neurodevelopmental disorder due to SOX5 haploinsufficiency

Purpose Lamb-Shaffer syndrome (LAMSHF) is a neurodevelopmental disorder described in just over two dozen patients with heterozygous genetic alterations involving SOX5, a gene encoding a transcription factor regulating cell fate and differentiation in neurogenesis and other discrete developmental processes. The genetic alterations described so far are mainly microdeletions. The present study was aimed at increasing our understanding of LAMSHF, its clinical and genetic spectrum, and the pathophysiological mechanisms involved. Methods Clinical and genetic data were collected through GeneMatcher and clinical or genetic networks for 41 novel patients harboring various types ofSOX5 alterations. Functional consequences of selected substitutions were investigated. Results Microdeletions and truncating variants occurred throughout SOX5. In contrast, most missense variants clustered in the pivotal SOX-specific high-mobility-group domain. The latter variants prevented SOX5 from binding DNA and promoting transactivation in vitro, whereas missense variants located outside the high-mobility-group domain did not. Clinical manifestations and severity varied among patients. No clear genotype-phenotype correlations were found, except that missense variants outside the high-mobility-group domain were generally better tolerated. Conclusions This study extends the clinical and genetic spectrum associated with LAMSHF and consolidates evidence that SOX5 haploinsufficiency leads to variable degrees of intellectual disability, language delay, and other clinical features

Meta-analysis of SHANK Mutations in Autism Spectrum Disorders: A Gradient of Severity in Cognitive Impairments.

International audienceSHANK genes code for scaffold proteins located at the post-synaptic density of glutamatergic synapses. In neurons, SHANK2 and SHANK3 have a positive effect on the induction and maturation of dendritic spines, whereas SHANK1 induces the enlargement of spine heads. Mutations in SHANK genes have been associated with autism spectrum disorders (ASD), but their prevalence and clinical relevance remain to be determined. Here, we performed a new screen and a meta-analysis of SHANK copy-number and coding-sequence variants in ASD. Copy-number variants were analyzed in 5,657 patients and 19,163 controls, coding-sequence variants were ascertained in 760 to 2,147 patients and 492 to 1,090 controls (depending on the gene), and, individuals carrying de novo or truncating SHANK mutations underwent an extensive clinical investigation. Copy-number variants and truncating mutations in SHANK genes were present in ∼1% of patients with ASD: mutations in SHANK1 were rare (0.04%) and present in males with normal IQ and autism; mutations in SHANK2 were present in 0.17% of patients with ASD and mild intellectual disability; mutations in SHANK3 were present in 0.69% of patients with ASD and up to 2.12% of the cases with moderate to profound intellectual disability. In summary, mutations of the SHANK genes were detected in the whole spectrum of autism with a gradient of severity in cognitive impairment. Given the rare frequency of SHANK1 and SHANK2 deleterious mutations, the clinical relevance of these genes remains to be ascertained. In contrast, the frequency and the penetrance of SHANK3 mutations in individuals with ASD and intellectual disability-more than 1 in 50-warrant its consideration for mutation screening in clinical practice

Distal Xq duplication and functional Xq disomy

Distal Xq duplications refer to chromosomal disorders resulting from involvement of the long arm of the X chromosome (Xq). Clinical manifestations widely vary depending on the gender of the patient and on the gene content of the duplicated segment. Prevalence of Xq duplications remains unknown. About 40 cases of Xq28 functional disomy due to cytogenetically visible rearrangements, and about 50 cases of cryptic duplications encompassing the MECP2 gene have been reported. The most frequently reported distal duplications involve the Xq28 segment and yield a recognisable phenotype including distinctive facial features (premature closure of the fontanels or ridged metopic suture, broad face with full cheeks, epicanthal folds, large ears, small and open mouth, ear anomalies, pointed nose, abnormal palate and facial hypotonia), major axial hypotonia, severe developmental delay, severe feeding difficulties, abnormal genitalia and proneness to infections. Xq duplications may be caused either by an intrachromosomal duplication or an unbalanced X/Y or X/autosome translocation. In XY males, structural X disomy always results in functional disomy. In females, failure of X chromosome dosage compensation could result from a variety of mechanisms, including an unfavourable pattern of inactivation, a breakpoint separating an X segment from the X-inactivation centre in cis, or a small ring chromosome. The MECP2 gene in Xq28 is the most important dosage-sensitive gene responsible for the abnormal phenotype in duplications of distal Xq. Diagnosis is based on clinical features and is confirmed by CGH array techniques. Differential diagnoses include Prader-Willi syndrome and Alpha thalassaemia-mental retardation, X linked (ATR-X). The recurrence risk is significant if a structural rearrangement is present in one of the parent, the most frequent situation being that of an intrachromosomal duplication inherited from the mother. Prenatal diagnosis is performed by cytogenetic testing including FISH and/or DNA quantification methods. Management is multi-specialist and only symptomatic, with special attention to prevention of malnutrition and recurrent infections. Educational and rehabilitation support should be offered to all patients

The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies

Despite the clinical significance of balanced chromosomal abnormalities (BCAs), their characterization has largely been restricted to cytogenetic resolution. We explored the landscape of BCAs at nucleotide resolution in 273 subjects with a spectrum of congenital anomalies. Whole-genome sequencing revised 93% of karyotypes and demonstrated complexity that was cryptic to karyotyping in 21% of BCAs, highlighting the limitations of conventional cytogenetic approaches. At least 33.9% of BCAs resulted in gene disruption that likely contributed to the developmental phenotype, 5.2% were associated with pathogenic genomic imbalances, and 7.3% disrupted topologically associated domains (TADs) encompassing known syndromic loci. Remarkably, BCA breakpoints in eight subjects altered a single TAD encompassing MEF2C, a known driver of 5q14.3 microdeletion syndrome, resulting in decreased MEF2C expression. We propose that sequence-level resolution dramatically improves prediction of clinical outcomes for balanced rearrangements and provides insight into new pathogenic mechanisms, such as altered regulation due to changes in chromosome topology

Effects of eight neuropsychiatric copy number variants on human brain structure

Many copy number variants (CNVs) confer risk for the same range of neurodevelopmental symptoms and psychiatric conditions including autism and schizophrenia. Yet, to date neuroimaging studies have typically been carried out one mutation at a time, showing that CNVs have large effects on brain anatomy. Here, we aimed to characterize and quantify the distinct brain morphometry effects and latent dimensions across 8 neuropsychiatric CNVs. We analyzed T1-weighted MRI data from clinically and non-clinically ascertained CNV carriers (deletion/duplication) at the 1q21.1 (n = 39/28), 16p11.2 (n = 87/78), 22q11.2 (n = 75/30), and 15q11.2 (n = 72/76) loci as well as 1296 non-carriers (controls). Case-control contrasts of all examined genomic loci demonstrated effects on brain anatomy, with deletions and duplications showing mirror effects at the global and regional levels. Although CNVs mainly showed distinct brain patterns, principal component analysis (PCA) loaded subsets of CNVs on two latent brain dimensions, which explained 32 and 29% of the variance of the 8 Cohen’s d maps. The cingulate gyrus, insula, supplementary motor cortex, and cerebellum were identified by PCA and multi-view pattern learning as top regions contributing to latent dimension shared across subsets of CNVs. The large proportion of distinct CNV effects on brain morphology may explain the small neuroimaging effect sizes reported in polygenic psychiatric conditions. Nevertheless, latent gene brain morphology dimensions will help subgroup the rapidly expanding landscape of neuropsychiatric variants and dissect the heterogeneity of idiopathic conditions

Influence des séquences subtélomériques sur la régulation des télomères : exemple du locus de la Dystrophie Facio-Scapulo-Humérale en 4q35 et implication en pathologie

Subtelomeres form the transition between chromosome specific sequences and terminal telomeric repeats. They might influence telomeric functions but underlying mechanisms are still unclear. Nevertheless, subtelomeres are associated with a number of human pathologies such as facioscapulohumeral muscular dystrophy (FSHD), an autosomal dominant disease secondary to the contraction of an array of D4Z4 macrosatellite repeats in the subtelomeric region 4q35. In order to study the biological function of the D4Z4 sequence, we created contructs that mimic the genomic organization of the 4q35 locus. We showed that D4Z4 is able to localize a telomere at the nuclear periphery. This perinuclear activity was dependant on interactions with CTCF and A type lamins and lied within a 80 bp proximal sequence that harbors an insulator activity. Moreover, the peripheral positionning of a telomere by D4Z4 is accompanied by a late replication timing of the telomere. We also searched for sequences able to counteract telomeric position effect (TPE) and identified a 30 bp element containing a CTCF binding site in the proximal region of D4Z4. In another construct, the introduction of a poly-adenylation signal between a reporter gene and telomeric repeats counteracted TPE. This effect is accompanied by the production of a hybrid transcript encompassing the reporter gene and telomeric repeats, suggesting a role for the TERRAs telomeric transcripts in TPE regulation. This work contibuted to characterize the role of subtelomeric sequences, especially the D4Z4 macrosatellite, in telomere regulation, their nuclear compartimentalization, their replication or the telomeric position effect. We will discuss the implications in the understanding of the pathophysiology of FSHD and other subtelomeric diseases.Les subtélomères forment la transition entre les séquences spécifiques des chromosomes et les répétitions télomériques terminales. Ils semblent capables d’influencer les fonctions télomériques mais les connaissances sur les mécanismes mis en jeu sont encore limitées. Les subtélomères sont pourtant associés à de nombreuses pathologies comme la myopathie facio-scapulo-humérale (FSHD), une dystrophie musculaire secondaire à la contraction de répétitions macrosatellites D4Z4 dans la région subtélomérique 4q35. Afin d’étudier les propriétés de la séquence subtélomérique D4Z4, nous avons créé des constructions reproduisant l’organisation génomique au locus 4q35. Nous avons montré que D4Z4 est capable d’adresser un télomère à la périphérie du noyau. Cette activité est couplée à une activité insulatrice au niveau d’une séquence proximale de 80 pb et est dépendante de CTCF et des Lamines A. De plus, la relocalisation périphérique d’un télomère par D4Z4 s’accompagne d’une réplication plus tardive de celui-ci. Par ailleurs, la recherche de séquences capables de s’opposer à l’effet de position télomérique (TPE) a identifié un élément de 30 pb contenant un site CTCF dans la séquence insulatrice proximale de D4Z4. De même,   l’introduction d’un signal de poly-adénylation entre un gène rapporteur et les répétitions télomériques interfère avec le TPE et est accompagnée d’une diminution d’un transcrit hybride contenant le gène rapporteur et des répétitions télomériques, suggérant un rôle des transcrits télomériques TERRAs dans la régulation du TPE. En conclusion, ce travail a permis de caractériser l’implication de séquences subtélomériques, et notamment D4Z4, dans la régulation des télomères, leur compartimentalisation nucléaire, la réplication ou l’effet de position télomérique. De plus, il apporte un éclairage nouveau sur la physiopathologie de la FSHD et ouvre des perspectives dans la compréhension d’autres pathologies liées aux subtélomères

Influence of subtelomeric sequences on telomere regulation : example of the facioscapulohumeral muscular dystrophy locus in 4q35 and implication in human pathology

Les subtélomères forment la transition entre les séquences spécifiques des chromosomes et les répétitions télomériques terminales. Ils semblent capables d’influencer les fonctions télomériques mais les connaissances sur les mécanismes mis en jeu sont encore limitées. Les subtélomères sont pourtant associés à de nombreuses pathologies comme la myopathie facio-scapulo-humérale (FSHD), une dystrophie musculaire secondaire à la contraction de répétitions macrosatellites D4Z4 dans la région subtélomérique 4q35. Afin d’étudier les propriétés de la séquence subtélomérique D4Z4, nous avons créé des constructions reproduisant l’organisation génomique au locus 4q35. Nous avons montré que D4Z4 est capable d’adresser un télomère à la périphérie du noyau. Cette activité est couplée à une activité insulatrice au niveau d’une séquence proximale de 80 pb et est dépendante de CTCF et des Lamines A. De plus, la relocalisation périphérique d’un télomère par D4Z4 s’accompagne d’une réplication plus tardive de celui-ci. Par ailleurs, la recherche de séquences capables de s’opposer à l’effet de position télomérique (TPE) a identifié un élément de 30 pb contenant un site CTCF dans la séquence insulatrice proximale de D4Z4. De même,   l’introduction d’un signal de poly-adénylation entre un gène rapporteur et les répétitions télomériques interfère avec le TPE et est accompagnée d’une diminution d’un transcrit hybride contenant le gène rapporteur et des répétitions télomériques, suggérant un rôle des transcrits télomériques TERRAs dans la régulation du TPE. En conclusion, ce travail a permis de caractériser l’implication de séquences subtélomériques, et notamment D4Z4, dans la régulation des télomères, leur compartimentalisation nucléaire, la réplication ou l’effet de position télomérique. De plus, il apporte un éclairage nouveau sur la physiopathologie de la FSHD et ouvre des perspectives dans la compréhension d’autres pathologies liées aux subtélomères.Subtelomeres form the transition between chromosome specific sequences and terminal telomeric repeats. They might influence telomeric functions but underlying mechanisms are still unclear. Nevertheless, subtelomeres are associated with a number of human pathologies such as facioscapulohumeral muscular dystrophy (FSHD), an autosomal dominant disease secondary to the contraction of an array of D4Z4 macrosatellite repeats in the subtelomeric region 4q35. In order to study the biological function of the D4Z4 sequence, we created contructs that mimic the genomic organization of the 4q35 locus. We showed that D4Z4 is able to localize a telomere at the nuclear periphery. This perinuclear activity was dependant on interactions with CTCF and A type lamins and lied within a 80 bp proximal sequence that harbors an insulator activity. Moreover, the peripheral positionning of a telomere by D4Z4 is accompanied by a late replication timing of the telomere. We also searched for sequences able to counteract telomeric position effect (TPE) and identified a 30 bp element containing a CTCF binding site in the proximal region of D4Z4. In another construct, the introduction of a poly-adenylation signal between a reporter gene and telomeric repeats counteracted TPE. This effect is accompanied by the production of a hybrid transcript encompassing the reporter gene and telomeric repeats, suggesting a role for the TERRAs telomeric transcripts in TPE regulation. This work contibuted to characterize the role of subtelomeric sequences, especially the D4Z4 macrosatellite, in telomere regulation, their nuclear compartimentalization, their replication or the telomeric position effect. We will discuss the implications in the understanding of the pathophysiology of FSHD and other subtelomeric diseases