De novo Mutations From Whole Exome Sequencing in Neurodevelopmental and Psychiatric Disorders: From Discovery to Application

Neurodevelopmental and psychiatric disorders are a highly disabling and heterogeneous group of developmental and mental disorders, resulting from complex interactions of genetic and environmental risk factors. The nature of multifactorial traits and the presence of comorbidity and polygenicity in these disorders present challenges in both disease risk identification and clinical diagnoses. The genetic component has been firmly established, but the identification of all the causative variants remains elusive. The development of next-generation sequencing, especially whole exome sequencing (WES), has greatly enriched our knowledge of the precise genetic alterations of human diseases, including brain-related disorders. In particular, the extensive usage of WES in research studies has uncovered the important contribution of de novo mutations (DNMs) to these disorders. Trio and quad familial WES are a particularly useful approach to discover DNMs. Here, we review the major WES studies in neurodevelopmental and psychiatric disorders and summarize how genes hit by discovered DNMs are shared among different disorders. Next, we discuss different integrative approaches utilized to interrogate DNMs and to identify biological pathways that may disrupt brain development and shed light on our understanding of the genetic architecture underlying these disorders. Lastly, we discuss the current state of the transition from WES research to its routine clinical application. This review will assist researchers and clinicians in the interpretation of variants obtained from WES studies, and highlights the need to develop consensus analytical protocols and validated lists of genes appropriate for clinical laboratory analysis, in order to reach the growing demands

L'evolució del règim general de foment de l'estudi en el sistema educatiu espanyol i el traspàs de les beques i dels ajuts a la Generalitat de Catalunya

A Catalunya, tant el Parlament com el Govern han considerat prioritàries les polítiques de foment de l’estudi, i han mantingut una intensa activitat per assolir el ple reconeixement de les competències estatutàries i perquè s’efectuïn les adaptacions necessàries del règim general de beques i ajuts, per tal que esdevingui un instrument de garantia real que permeti compensar els dèficits històrics que pateixen els estudiants catalans. La Generalitat ha reclamat històricament el traspàs de serveis en aquesta matèria tan important, i quan s’ha requerit ha portat la iniciativa en la conflictivitat competencial. L’abast de les competències estatals i autonòmiques es va concretar doctrinalment en la STC 188/2001 que va suposar un impuls, encara que amb molts matisos, a les aspiracions de Catalunya. Han transcorregut nou anys des de la sentència i més de dotze de les primeres aproximacions al traspàs, sense que les reivindicacions de Catalunya hagin quedat resoltes; continua oberta la negociació a la Comissió Mixta de Transferències, i els avenços en l’autonomia de gestió són fruit de la col•laboració entre administracions i no de l’exercici efectiu de la titularitat de la competència. Al marge d’aquesta situació, el règim de foment general de l’estudi en el sistema educatiu espanyol ha anat evolucionant, tant en la seva configuració jurídica com en una més gran especialització i diversificació de l’oferta, a la qual s’han incorporat els préstecs, per aproximació als models seguits en els països més avançats. Catalunya precisa, però, un marc regulatori estatal més obert, que permeti l’adaptació real a les seves necessitats socioeconòmiques, territorials i culturals; i també una dotació econòmica suficient per dur a terme les seves pròpies polítiques públiques. Aquest article tracta resumidament el marc regulatori, competencial i doctrinal aplicable al foment general de l’estudi; exposa els aspectes més destacables de l’evolució del traspàs de serveis i efectua una aproximació a la problemàtica del present i a les expectatives de futur.In Catalonia both the Parliament and the Government consider policies to foster education as a priority, and have made every effort to ensure the full recognition of statutory powers and that the necessary adaptations be made to the general system of scholarships and grants, so that it may become a true instrument of guarantee to enable the historical deficits our students suffer to be made up for. Historically, the Government of Catalonia has demanded the transfer of services in this important area, and, when necessary, has led conflicts concerning areas of power. The scope of state and autonomous community power was specified doctrinally in Constitutional Court Sentence 188/2001, which provided a boost, albeit with many nuances, for the aspirations of Catalonia. It has been over nine years since that sentence and more than twelve since the transfer was first approached, and Catalonia’s demands are still to be fulfilled. Negotiations continue in the Mixed Transfer Commission, and advances in self-administration are the result of collaboration between government agencies and not of the effective exercise of power. This situation aside, the general funding of education within the Spanish education system has evolved, both in its legal makeup and in greater specialisation and diversification of the courses on offer, and loans have been included, by approximation to the models used in more advanced countries. However, Catalonia requires a more open state regulatory framework that enables real adaptation to its socioeconomic, territorial and cultural needs; and also sufficient funding to be able to implement its own public policies. This article summarises the regulatory, authoritative and doctrinal framework applied to the general funding of education; sets out the most outstanding aspects of the evolution of the transfer of services and provides an approach to current problems and to future prospects.En Cataluña, tanto el Parlamento como el Gobierno han considerado prioritarias las políticas de fomento del estudio, y han mantenido una intensa actividad para alcanzar el pleno reconocimiento de las competencias estatutarias y para que se efectúen las adaptaciones necesarias del régimen general de becas y ayudas, a fin de que llegue a ser un instrumento de garantía real que permita compensar los déficits históricos que soportan los estudiantes catalanes. La Generalitat ha reclamado históricamente el traspaso de servicios en esta importante materia, y cuando se ha requerido ha conducido la iniciativa a la conflictividad competencial. El alcance de las competencias estatales y autonómicas fue concretado doctrinalmente en la STC 188/2001 que supuso un impulso, aunque con muchos matices, a las aspiraciones de Cataluña. Han transcurrido nueve años desde la sentencia y más de doce de las primeras aproximaciones al traspaso, sin que las reivindicaciones de Cataluña hayan quedado resueltas; continúa abierta la negociación en la Comisión Mixta de Transferencias, y los avances en la autonomía de gestión son fruto de la colaboración entre administraciones y no del efectivo ejercicio de la titularidad de la competencia. Al margen de esta situación, el régimen del fomento general del estudio en el sistema educativo español ha ido evolucionando, tanto en su configuración jurídica como en una mayor especialización y diversificación de la oferta, a la que se han incorporado los préstamos, por aproximación a los modelos seguidos en los países más avanzados. Cataluña precisa, sin embargo, un marco regulador estatal más abierto, que permita la adaptación real a sus necesidades socioeconómicas, territoriales y culturales; y también una dotación económica suficiente para llevar a cabo sus propias políticas públicas. Este artículo trata resumidamente el marco regulador, competencial y doctrinal aplicable al fomento general del estudio; expone los aspectos más destacables de la evolución del traspaso de servicios y efectúa una aproximación a la problemática del presente y a las expectativas de futuro

De novo Mutations From Whole Exome Sequencing in Neurodevelopmental and Psychiatric Disorders: From Discovery to Application.

Neurodevelopmental and psychiatric disorders are a highly disabling and heterogeneous group of developmental and mental disorders, resulting from complex interactions of genetic and environmental risk factors. The nature of multifactorial traits and the presence of comorbidity and polygenicity in these disorders present challenges in both disease risk identification and clinical diagnoses. The genetic component has been firmly established, but the identification of all the causative variants remains elusive. The development of next-generation sequencing, especially whole exome sequencing (WES), has greatly enriched our knowledge of the precise genetic alterations of human diseases, including brain-related disorders. In particular, the extensive usage of WES in research studies has uncovered the important contribution of de novo mutations (DNMs) to these disorders. Trio and quad familial WES are a particularly useful approach to discover DNMs. Here, we review the major WES studies in neurodevelopmental and psychiatric disorders and summarize how genes hit by discovered DNMs are shared among different disorders. Next, we discuss different integrative approaches utilized to interrogate DNMs and to identify biological pathways that may disrupt brain development and shed light on our understanding of the genetic architecture underlying these disorders. Lastly, we discuss the current state of the transition from WES research to its routine clinical application. This review will assist researchers and clinicians in the interpretation of variants obtained from WES studies, and highlights the need to develop consensus analytical protocols and validated lists of genes appropriate for clinical laboratory analysis, in order to reach the growing demands

Derivation of induced pluripotent stem cells (iPSCs) by retroviral transduction of skin fibroblasts from four patients suffering 7q11.23 microduplication syndrome

Skin fibroblasts were obtained from four patients with 7q11.23 microduplication syndrome carrying the reciprocal rearrangement of Williams-Beuren syndrome at the 7q11.23 genomic region. Induced pluripotent stem cells (iPSCs) were generated by retroviral infection of fibroblasts with polycystronic vectors. The generated iPSC clones ESi058B, ESi057B, ESi070A and ESi071A had the 7q11.23 duplication with no additional genomic alterations, a stable karyotype, expressed pluripotency markers and could differentiate towards the three germ layers in vitro via embryoid body formation and in vivo by teratoma formation. Patient's derived iPSCs are a valuable resource for in vitro modeling of 7q11.23 microduplication syndrome

The pleiotropic contribution of genes in dopaminergic and serotonergic pathways to addiction and related behavioral traits

Introduction: Co-occurrence of substance use disorders (SUD) and other behavioral conditions, such as stress-related, aggressive or risk-taking behaviors, in the same individual has been frequently described. As dopamine (DA) and serotonin (5-HT) have been previously identified as key neurotransmitters for some of these phenotypes, we explored the genetic contribution of these pathways to SUD and these comorbid phenotypes in order to better understand the genetic relationship between them. Methods: We tested the association of 275 dopaminergic genes and 176 serotonergic genes with these phenotypes by performing gene-based, gene-set and transcriptome-wide association studies in 11 genome-wide association studies (GWAS) datasets on SUD and related behaviors. Results: At the gene-wide level, 68 DA and 27 5-HT genes were found to be associated with at least one GWAS on SUD or related behavior. Among them, six genes had a pleiotropic effect, being associated with at least three phenotypes: ADH1C, ARNTL, CHRNA3, HPRT1, HTR1B and DRD2. Additionally, we found nominal associations between the DA gene sets and SUD, opioid use disorder, antisocial behavior, irritability and neuroticism, and between the 5-HT-core gene set and neuroticism. Predicted gene expression correlates in brain were also found for 19 DA or 5-HT genes. Discussion: Our study shows a pleiotropic contribution of dopaminergic and serotonergic genes to addiction and related behaviors such as anxiety, irritability, neuroticism and risk-taking behavior, highlighting a role for DA genes, which could explain, in part, the co-occurrence of these phenotype

Cortisol Response to Stress in Adults with Attention Deficit Hyperactivity Disorder

Differences in the cortisol response have been reported between children exhibiting the inattentive and hyperactive/impulsive subtypes of attention deficit hyperactivity disorder. However, there is no such information about adults. The aim of the present study was to determine the possible differences between the combined and inattentive subtypes in the cortisol response to stress. Ninety-six adults with attention deficit hyperactivity disorder, 38 inattentive and 58 combined, without any medical or psychiatric comorbidities and 25 healthy controls were included. The Trier Social Stress Test was used to assess physiological stress responses. Clinical data and subjective stress levels, including the Perceived Stress Scale, were also recorded. No significant differences in the cortisol response to the Trier Social Stress Test were found between patients and controls. However, albeit there were no basal differences, lower cortisol levels at 15 (P =.015), 30 (P=. 015), and 45 minutes (P=. 045) were observed in the combined compared with the inattentive subtype after the stress induction; these differences disappeared 60 minutes after the stress. In contrast, the subjective stress responses showed significant differences between attention deficit hyperactivity disorder patients and controls (P <.001), but no differences were seen between attention deficit hyperactivity disorder subtypes. In turn, subjective stress measures, such as the Perceived Stress Scale, positively correlated with the whole cortisol stress response (P <.027). Both the combined and inattentive attention deficit hyperactivity disorder adults exhibited a normal cortisol response to stress when challenged. Nevertheless, the inattentive patients displayed a higher level of cortisol after stress compared with the combined patients. Despite the differences in the cortisol response, adults with attention deficit hyperactivity disorder reported high levels of subjective stress in their every-day lif

Two-stage case-control association study of dopamine-related genes and migraine

Background We previously reported risk haplotypes for two genes related with serotonin and dopamine metabolism: MAOA in migraine without aura and DDC in migraine with aura. Herein we investigate the contribution to migraine susceptibility of eight additional genes involved in dopamine neurotransmission. Methods We performed a two-stage case-control association study of 50 tag single nucleotide polymorphisms (SNPs), selected according to genetic coverage parameters. The first analysis consisted of 263 patients and 274 controls and the replication study was composed by 259 cases and 287 controls. All cases were diagnosed according to ICHD-II criteria, were Spanish Caucasian, and were sex-matched with control subjects. Results Single-marker analysis of the first population identified nominal associations of five genes with migraine. After applying a false discovery rate correction of 10%, the differences remained significant only for DRD2 (rs2283265) and TH (rs2070762). Multiple-marker analysis identified a five-marker T-C-G-C-G (rs12363125-rs2283265-rs2242592-rs1554929-rs2234689) risk haplotype in DRD2 and a two-marker A-C (rs6356-rs2070762) risk haplotype in TH that remained significant after correction by permutations. These results, however, were not replicated in the second independent cohort. Conclusion The present study does not support the involvement of the DRD1, DRD2, DRD3, DRD5, DBH, COMT, SLC6A3 and TH genes in the genetic predisposition to migraine in the Spanish population

Full-length isoform transcriptome of the developing human brain provides further insights into autism.

Alternative splicing plays an important role in brain development, but its global contribution to human neurodevelopmental diseases (NDDs) requires further investigation. Here we examine the relationships between splicing isoform expression in the brain and de novo loss-of-function mutations from individuals with NDDs. We analyze the full-length isoform transcriptome of the developing human brain and observe differentially expressed isoforms and isoform co-expression modules undetectable by gene-level analyses. These isoforms are enriched in loss-of-function mutations and microexons, are co-expressed with a unique set of partners, and have higher prenatal expression. We experimentally test the effect of splice-site mutations and demonstrate exon skipping in five NDD risk genes, including SCN2A, DYRK1A, and BTRC. Our results suggest that the splice site mutation in BTRC reduces translational efficiency, likely affecting Wnt signaling through impaired degradation of β-catenin. We propose that functional effects of mutations should be investigated at the isoform- rather than gene-level resolution

Screening of CACNA1A and ATP1A2 genes in hemiplegic migraine: clinical, genetic and functional studies

Hemiplegic migraine (HM) is a rare and severe subtype of autosomal dominant migraine, characterized by a complex aura including some degree of motor weakness. Mutations in four genes (CACNA1A, ATP1A2, SCN1A and PRRT2) have been detected in familial and in sporadic cases. This genetically and clinically heterogeneous disorder is often accompanied by permanent ataxia, epileptic seizures, mental retardation, and chronic progressive cerebellar atrophy. Here we report a mutation screening in the CACNA1A and ATP1A2 genes in 18 patients with HM. Furthermore, intragenic copy number variant (CNV) analysis was performed in CACNA1A using quantitative approaches. We identified four previously described missense CACNA1A mutations (p.Ser218Leu, p.Thr501Met, p.Arg583Gln, and p.Thr666Met) and two missense changes in the ATP1A2 gene, the previously described p.Ala606Thr and the novel variant p.Glu825Lys. No structural variants were found. This genetic screening allowed the identification of more than 30% of the disease alleles, all present in a heterozygous state. Functional consequences of the CACNA1A-p.Thr501Met mutation, previously described only in association with episodic ataxia, and ATP1A2-p.Glu825Lys, were investigated by means of electrophysiological studies, cell viability assays or Western blot analysis. Our data suggest that both these variants are disease-causing

A mutation in the first intracellular loop of CACNA1A prevents P/Q channel modulation by SNARE proteins and lowers exocytosis

Familial hemiplegic migraine (FHM)-causing mutations in the gene encoding the P/Q Ca2+ channel α1A subunit (CACNA1A) locate to the pore and voltage sensor regions and normally involve gain-of-channel function. We now report on a mutation identified in the first intracellular loop of CACNA1A (α1A(A454T)) that does not cause FHM but is associated with the absence of sensorimotor symptoms in a migraine with aura pedigree. α1A(A454T) channels showed weakened regulation of voltage-dependent steady-state inactivation by CaVβ subunits. More interestingy, A454T mutation suppressed P/Q channel modulation by syntaxin 1A or SNAP-25 and decreased exocytosis. Our findings reveal the importance of I-II loop structural integrity in the functional interaction between P/Q channel and proteins of the vesicle-docking/fusion machinery, and that genetic variation in CACNA1A may be not only a cause but also a modifier of migraine phenotype