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1.
Am J Hum Genet ; 110(10): 1750-1768, 2023 10 05.
Artículo en Inglés | MEDLINE | ID: mdl-37802044

RESUMEN

Whole-exome sequencing of autism spectrum disorder (ASD) probands and unaffected family members has identified many genes harboring de novo variants suspected to play a causal role in the disorder. Of these, chromodomain helicase DNA-binding protein 8 (CHD8) is the most recurrently mutated. Despite the prevalence of CHD8 mutations, we have little insight into how CHD8 loss affects genome organization or the functional consequences of these molecular alterations in neurons. Here, we engineered two isogenic human embryonic stem cell lines with CHD8 loss-of-function mutations and characterized differences in differentiated human cortical neurons. We identified hundreds of genes with altered expression, including many involved in neural development and excitatory synaptic transmission. Field recordings and single-cell electrophysiology revealed a 3-fold decrease in firing rates and synaptic activity in CHD8+/- neurons, as well as a similar firing-rate deficit in primary cortical neurons from Chd8+/- mice. These alterations in neuron and synapse function can be reversed by CHD8 overexpression. Moreover, CHD8+/- neurons displayed a large increase in open chromatin across the genome, where the greatest change in compaction was near autism susceptibility candidate 2 (AUTS2), which encodes a transcriptional regulator implicated in ASD. Genes with changes in chromatin accessibility and expression in CHD8+/- neurons have significant overlap with genes mutated in probands for ASD, intellectual disability, and schizophrenia but not with genes mutated in healthy controls or other disease cohorts. Overall, this study characterizes key molecular alterations in genome structure and expression in CHD8+/- neurons and links these changes to impaired neuronal and synaptic function.


Asunto(s)
Trastorno del Espectro Autista , Trastorno Autístico , Humanos , Animales , Ratones , Trastorno Autístico/genética , Trastorno del Espectro Autista/genética , Cromatina/genética , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/metabolismo , Expresión Génica , Factores de Transcripción/genética
2.
Biochem Soc Trans ; 52(1): 15-27, 2024 02 28.
Artículo en Inglés | MEDLINE | ID: mdl-38288845

RESUMEN

Heterozygous, de novo, loss-of-function variants of the CHD8 gene are associated with a high penetrance of autism and other neurodevelopmental phenotypes. Identifying the neurodevelopmental functions of high-confidence autism risk genes like CHD8 may improve our understanding of the neurodevelopmental mechanisms that underlie autism spectrum disorders. Over the last decade, a complex picture of pleiotropic CHD8 functions and mechanisms of action has emerged. Multiple brain and non-brain cell types and progenitors appear to be affected by CHD8 haploinsufficiency. Behavioural, cellular and synaptic phenotypes are dependent on the nature of the gene mutation and are modified by sex and genetic background. Here, I review some of the CHD8-interacting proteins and molecular mechanisms identified to date, as well as the impacts of CHD8 deficiency on cellular processes relevant to neurodevelopment. I endeavour to highlight some of the critical questions that still require careful and concerted attention over the next decade to bring us closer to the goal of understanding the salient mechanisms whereby CHD8 deficiency causes neurodevelopmental disorders.


Asunto(s)
Trastorno del Espectro Autista , Trastornos del Neurodesarrollo , Humanos , Factores de Transcripción/genética , Proteínas de Unión al ADN/genética , Trastorno del Espectro Autista/genética , Trastorno del Espectro Autista/complicaciones , Mutación , Trastornos del Neurodesarrollo/genética
3.
Int J Mol Sci ; 25(15)2024 Aug 01.
Artículo en Inglés | MEDLINE | ID: mdl-39125997

RESUMEN

The transmembrane protein ß-amyloid precursor protein (APP) is central to the pathophysiology of Alzheimer's disease (AD). The ß-amyloid hypothesis posits that aberrant processing of APP forms neurotoxic ß-amyloid aggregates, which lead to the cognitive impairments observed in AD. Although numerous additional factors contribute to AD, there is a need to better understand the synaptic function of APP. We have found that Drosophila APP-like (APPL) has both shared and non-shared roles at the synapse with Kismet (Kis), a chromatin helicase binding domain (CHD) protein. Kis is the homolog of CHD7 and CHD8, both of which are implicated in neurodevelopmental disorders including CHARGE Syndrome and autism spectrum disorders, respectively. Loss of function mutations in kis and animals expressing human APP and BACE in their central nervous system show reductions in the glutamate receptor subunit, GluRIIC, the GTPase Rab11, and the bone morphogenetic protein (BMP), pMad, at the Drosophila larval neuromuscular junction (NMJ). Similarly, processes like endocytosis, larval locomotion, and neurotransmission are deficient in these animals. Our pharmacological and epistasis experiments indicate that there is a functional relationship between Kis and APPL, but Kis does not regulate appl expression at the larval NMJ. Instead, Kis likely influences the synaptic localization of APPL, possibly by promoting rab11 transcription. These data identify a potential mechanistic connection between chromatin remodeling proteins and aberrant synaptic function in AD.


Asunto(s)
Precursor de Proteína beta-Amiloide , Proteínas de Drosophila , Unión Neuromuscular , Proteínas de Unión al GTP rab , Animales , Unión Neuromuscular/metabolismo , Proteínas de Drosophila/metabolismo , Proteínas de Drosophila/genética , Proteínas de Unión al GTP rab/metabolismo , Proteínas de Unión al GTP rab/genética , Precursor de Proteína beta-Amiloide/metabolismo , Precursor de Proteína beta-Amiloide/genética , Drosophila melanogaster/metabolismo , Drosophila melanogaster/genética , Transmisión Sináptica , Sinapsis/metabolismo , Receptores de Glutamato/metabolismo , Receptores de Glutamato/genética , Proteínas de Unión al ADN/metabolismo , Proteínas de Unión al ADN/genética , Humanos , ADN Helicasas/metabolismo , ADN Helicasas/genética , Proteínas de la Membrana , Proteínas del Tejido Nervioso , Proteínas de Homeodominio , Receptores Ionotrópicos de Glutamato
4.
J Neurosci ; 42(44): 8373-8392, 2022 11 02.
Artículo en Inglés | MEDLINE | ID: mdl-36127134

RESUMEN

The chromatin remodeler CHD8 represents a high-confidence risk factor in autism, a multistage progressive neurologic disorder, however the underlying stage-specific functions remain elusive. In this study, by analyzing Chd8 conditional knock-out mice (male and female), we find that CHD8 controls cortical neural stem/progenitor cell (NSC) proliferation and survival in a stage-dependent manner. Strikingly, inducible genetic deletion reveals that CHD8 is required for the production and fitness of transit-amplifying intermediate progenitors (IPCs) essential for upper-layer neuron expansion in the embryonic cortex. p53 loss of function partially rescues apoptosis and neurogenesis defects in the Chd8-deficient brain. Further, transcriptomic and epigenomic profiling indicates that CHD8 regulates the chromatin accessibility landscape to activate neurogenesis-promoting factors including TBR2, a key regulator of IPC neurogenesis, while repressing DNA damage- and p53-induced apoptotic programs. In the adult brain, CHD8 depletion impairs forebrain neurogenesis by impeding IPC differentiation from NSCs in both subventricular and subgranular zones; however, unlike in embryos, it does not affect NSC proliferation and survival. Treatment with an antidepressant approved by the Federal Drug Administration (FDA), fluoxetine, partially restores adult hippocampal neurogenesis in Chd8-ablated mice. Together, our multistage functional studies identify temporally specific roles for CHD8 in developmental and adult neurogenesis, pointing to a potential strategy to enhance neurogenesis in the CHD8-deficient brain.SIGNIFICANCE STATEMENT The role of the high-confidence autism gene CHD8 in neurogenesis remains incompletely understood. Here, we identify a stage-specific function of CHD8 in development of NSCs in developing and adult brains by conserved, yet spatiotemporally distinct, mechanisms. In embryonic cortex, CHD8 is critical for the proliferation, survival, and differentiation of both NSC and IPCs during cortical neurogenesis. In adult brain, CHD8 is required for IPC generation but not the proliferation and survival of adult NSCs. Treatment with FDA-approved antidepressant fluoxetine partially rescues the adult neurogenesis defects in CHD8 mutants. Thus, our findings help resolve CHD8 functions throughout life during embryonic and adult neurogenesis and point to a potential avenue to promote neurogenesis in CHD8 deficiency.


Asunto(s)
Trastorno Autístico , Cromatina , Proteínas de Unión al ADN , Neurogénesis , Animales , Femenino , Masculino , Ratones , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/metabolismo , Fluoxetina , Hipocampo/metabolismo , Ratones Noqueados , Neurogénesis/fisiología , Proteína p53 Supresora de Tumor , Prosencéfalo
5.
Proc Natl Acad Sci U S A ; 117(36): 22331-22340, 2020 09 08.
Artículo en Inglés | MEDLINE | ID: mdl-32839322

RESUMEN

The chromatin remodeler CHD8 is among the most frequently mutated genes in autism spectrum disorder (ASD). CHD8 has a dosage-sensitive role in ASD, but when and how it becomes critical to human social function is unclear. Here, we conducted genomic analyses of heterozygous and homozygous Chd8 mouse embryonic stem cells and differentiated neural progenitors. We identify dosage-sensitive CHD8 transcriptional targets, sites of regulated accessibility, and an unexpected cooperation with SOX transcription factors. Collectively, our findings reveal that CHD8 negatively regulates expression of neuronal genes to maintain pluripotency and also during differentiation. Thus, CHD8 is essential for both the maintenance of pluripotency and neural differentiation, providing mechanistic insight into its function with potential implications for ASD.


Asunto(s)
Proteínas de Unión al ADN , Dosificación de Gen/genética , Neurogénesis/genética , Animales , Trastorno del Espectro Autista , Células Cultivadas , Ensamble y Desensamble de Cromatina/genética , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/metabolismo , Células Madre Embrionarias/metabolismo , Ratones , Ratones Noqueados
6.
Cancer Sci ; 112(1): 254-264, 2021 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-33141432

RESUMEN

Diabetes is a major risk factor in the development and progression of several cancers including cholangiocarcinoma (CCA). However, the molecular mechanism by which hyperglycemia potentiates progression of CCA is not clearly understood. Here, we showed that a high glucose condition significantly increased reactive oxygen species (ROS) production and promoted aggressive phenotypes of CCA cells, including proliferation and migration activities. Mannosidase alpha class 2a member 2 (MAN2A2), was upregulated at both mRNA and protein levels in a high glucose- and ROS-dependent manner. In addition, cell proliferation and migration were significantly reduced by MAN2A2 knockdown. Based on our proteome and in silico analyses, we further found that chromodomain helicase DNA-binding protein 8 (CHD8) was induced by ROS signaling and regulated MAN2A2 expression. Overexpression of CHD8 increased MAN2A2 expression, while CHD8 knockdown dramatically reduced proliferation and migration as well as MAN2A2 expression in CCA cells. Moreover, both MAN2A2 and CHD8 were highly expressed with positive correlation in CCA tumor tissues. Collectively, these data suggested that high glucose conditions promote CCA progression through ROS-mediated upregulation of MAN2A2 and CHD8. Thus, glucose metabolism is a promising therapeutic target to control tumor progression in patients with CCA and diabetes.


Asunto(s)
Neoplasias de los Conductos Biliares/metabolismo , Colangiocarcinoma/metabolismo , Proteínas de Unión al ADN/metabolismo , Glucosa/metabolismo , Manosidasas/metabolismo , Factores de Transcripción/metabolismo , Neoplasias de los Conductos Biliares/patología , Línea Celular Tumoral , Movimiento Celular/fisiología , Proliferación Celular/fisiología , Colangiocarcinoma/patología , Progresión de la Enfermedad , Regulación Neoplásica de la Expresión Génica/fisiología , Humanos , Hiperglucemia/metabolismo , Especies Reactivas de Oxígeno/metabolismo , Regulación hacia Arriba
7.
BMC Neurosci ; 22(1): 32, 2021 05 01.
Artículo en Inglés | MEDLINE | ID: mdl-33933000

RESUMEN

BACKGROUND: Autism spectrum disorder (ASD) is characterized by the core symptoms of impaired social interactions. Increasing evidence suggests that ASD has a strong genetic link with mutations in chromodomain helicase DNA binding protein 8 (CHD8), a gene encoding a chromatin remodeler. It has previously been shown that Chd8 haplodeficient male mice manifest ASD-like behavioral characteristics such as anxiety and altered social behavior. Along with that, oxytocin (OT) is one of the main neuropeptides involved in social behavior. Administration of OT has shown improvement of social behavior in genetic animal models of ASD. The present study was undertaken to further explore behavioral abnormalities of Chd8 haplodeficient mice of both sexes, their link with OT, and possible effects of OT administration. First, we performed a battery of behavioral tests on wild-type and Chd8+/∆SL female and male mice. Next, we measured plasma OT levels and finally studied the effects of intraperitoneal OT injection on observed behavioral deficits. RESULTS: We showed general anxiety phenotype in Chd8+/∆SL mice regardless of sex, the depressive phenotype in Chd8+/∆SL female mice only and bidirectional social deficit in female and male mice. We observed decreased level of OT in Chd+/∆SL mice, possibly driven by males. Mice injected by OT demonstrated recovery of social behavior, while reduced anxiety was observed only in male mice. CONCLUSIONS: Here, we demonstrated that abnormal social behaviors were observed in both male and female Chd8+/∆SL mice. The ability of peripheral OT administration to affect such behaviors along with altered plasma OT levels indicated a possible link between Chd8 + /∆SL and OT in the pathogenesis of ASD as well as the possible usefulness of OT as a therapeutic tool for ASD patients with CHD8 mutations.


Asunto(s)
Trastorno Autístico/tratamiento farmacológico , Trastorno Autístico/genética , Proteínas de Unión al ADN/genética , Haploinsuficiencia/efectos de los fármacos , Oxitocina/uso terapéutico , Conducta Social , Animales , Trastorno Autístico/metabolismo , Proteínas de Unión al ADN/deficiencia , Femenino , Haploinsuficiencia/fisiología , Masculino , Aprendizaje por Laberinto/efectos de los fármacos , Aprendizaje por Laberinto/fisiología , Ratones , Ratones Transgénicos , Oxitocina/farmacología
8.
Int J Mol Sci ; 22(6)2021 Mar 23.
Artículo en Inglés | MEDLINE | ID: mdl-33806835

RESUMEN

Chromodomain helicase domain 8 (CHD8) is one of the most frequently mutated and most penetrant genes in the autism spectrum disorder (ASD). Individuals with CHD8 mutations show leading symptoms of autism, macrocephaly, and facial dysmorphisms. The molecular and cellular mechanisms underpinning the early onset and development of these symptoms are still poorly understood and prevent timely and more efficient therapies of patients. Progress in this area will require an understanding of "when, why and how cells deviate from their normal trajectories". High-throughput single-cell RNA sequencing (sc-RNAseq) directly quantifies information-bearing RNA molecules that enact each cell's biological identity. Here, we discuss recent insights from sc-RNAseq of CRISPR/Cas9-editing of Chd8/CHD8 during mouse neocorticogenesis and human cerebral organoids. Given that the deregulation of the balance between excitation and inhibition (E/I balance) in cortical and subcortical circuits is thought to represent a major etiopathogenetic mechanism in ASD, we focus on the question of whether, and to what degree, results from current sc-RNAseq studies support this hypothesis. Beyond that, we discuss the pros and cons of these approaches and further steps to be taken to harvest the full potential of these transformative techniques.


Asunto(s)
Trastorno Autístico/etiología , Trastorno Autístico/metabolismo , Proteínas de Unión al ADN/genética , Susceptibilidad a Enfermedades , Factores de Transcripción/genética , Transcriptoma , Animales , Trastorno Autístico/psicología , Encéfalo/metabolismo , Encéfalo/fisiopatología , Proteínas de Unión al ADN/metabolismo , Perfilación de la Expresión Génica , Regulación de la Expresión Génica , Redes Reguladoras de Genes , Humanos , Mutación , Neurogénesis , Análisis de la Célula Individual/métodos , Factores de Transcripción/metabolismo
9.
Neurogenetics ; 21(1): 67-72, 2020 01.
Artículo en Inglés | MEDLINE | ID: mdl-31823155

RESUMEN

Microdeletions encompassing 14q11.2 locus, involving SUPT16H and CHD8, were shown to cause developmental delay, intellectual disability, autism spectrum disorders and macrocephaly. Variations leading to CHD8 haploinsufficiency or loss of function were also shown to lead to a similar phenotype. Recently, a 14q11.2 microduplication syndrome, encompassing CHD8 and SUPT16H, has been described, highlighting the importance of a tight control of at least CHD8 gene-dosage for a normal development. There have been only a few reports of 14q11.2 microduplications. Patients showed variable neurodevelopmental issues of variable severity. Breakpoints of the microduplications were non-recurrent, making interpretation of the CNV and determination of their clinical relevance difficult. Here, we report on two patients with 14q11.2 microduplication encompassing CHD8 and SUPT16H, one of whom had normal intelligence. Review of previous reports describing patients with comparable microduplications allowed for a more precise delineation of the condition and widening of the phenotypic spectrum.


Asunto(s)
Encéfalo/patología , Proteínas de Ciclo Celular/genética , Proteínas de Unión al ADN/genética , Duplicación de Gen , Trastornos del Neurodesarrollo/genética , Trastornos del Neurodesarrollo/patología , Factores de Transcripción/genética , Encéfalo/diagnóstico por imagen , Niño , Femenino , Humanos , Masculino , Trastornos del Neurodesarrollo/diagnóstico por imagen , Fenotipo
10.
Biochem Biophys Res Commun ; 532(2): 190-194, 2020 11 05.
Artículo en Inglés | MEDLINE | ID: mdl-32854944

RESUMEN

Chromodomain-Helicase-DNA-binding protein 8 (CHD8) is a chromatin remodeler that is central to regulation of gene expression pathways during brain development. Many loss-of-function mutations in transcribed regions of the chd8 gene have been identified in autism spectrum disorder patients. Nothing is known about transcription of the human chd8 gene. Defects in expression of this gene could represent another mechanism leading to reduced amount of CHD8. We identify two major promoters for the human chd8 gene, both of which are located many thousand base pairs upstream of the coding region. Each proximal promoter directs a similar transcriptional efficiency in transfected cells. At least two elements within 200bp of the 5'flanking regions of these promoters are important to drive highest transcriptional levels in transient transfection experiments. RNA polymerase II occupancy levels at each promoter are roughly equivalent. Lastly, each promoter directs a dispersed set of start sites in a cultured cell line. This work could provide the framework for future studies to investigate the importance of chd8 gene expression for diseases associated with brain and neuronal development.


Asunto(s)
Proteínas de Unión al ADN/genética , Regiones Promotoras Genéticas , Factores de Transcripción/genética , Trastorno del Espectro Autista/genética , Sitios de Unión , Células HEK293 , Humanos , Eliminación de Secuencia , Transactivadores/metabolismo , Transcripción Genética
11.
Am J Med Genet C Semin Med Genet ; 181(4): 557-564, 2019 12.
Artículo en Inglés | MEDLINE | ID: mdl-31721432

RESUMEN

CHD8 has been reported as an autism susceptibility/intellectual disability gene but emerging evidence suggests that it additionally causes an overgrowth phenotype. This study reports 27 unrelated patients with pathogenic or likely pathogenic CHD8 variants (25 null variants, two missense variants) and a male:female ratio of 21:6 (3.5:1, p < .01). All patients presented with intellectual disability, with 85% in the mild or moderate range, and 85% had a height and/or head circumference ≥2 standard deviations above the mean, meeting our clinical criteria for overgrowth. Behavioral problems were reported in the majority of patients (78%), with over half (56%) either formally diagnosed with an autistic spectrum disorder or described as having autistic traits. Additional clinical features included neonatal hypotonia (33%), and less frequently seizures, pes planus, scoliosis, fifth finger clinodactyly, umbilical hernia, and glabellar hemangioma (≤15% each). These results suggest that, in addition to its established link with autism and intellectual disability, CHD8 causes an overgrowth phenotype, and should be considered in the differential diagnosis of patients presenting with increased height and/or head circumference in association with intellectual disability.


Asunto(s)
Cadherinas/genética , Trastornos del Crecimiento/genética , Fenotipo , Adolescente , Adulto , Niño , Preescolar , Femenino , Humanos , Lactante , Discapacidad Intelectual/genética , Masculino , Síndrome , Adulto Joven
12.
Clin Genet ; 96(1): 72-84, 2019 07.
Artículo en Inglés | MEDLINE | ID: mdl-31001818

RESUMEN

Variants in the chromodomain helicase DNA-binding protein 8 (CHD8) have been associated with intellectual disability (ID), autism spectrum disorders (ASDs) and overgrowth and CHD8 is one of the causative genes for OGID (overgrowth and ID). We investigated 25 individuals with CHD8 protein truncating variants (PTVs), including 10 previously unreported patients and found a male to female ratio of 2.7:1 (19:7) and a pattern of common features: macrocephaly (62.5%), tall stature (47%), developmental delay and/or intellectual disability (81%), ASDs (84%), sleep difficulties (50%), gastrointestinal problems (40%), and distinct facial features. Most of the individuals in this cohort had moderate-to-severe ID, some had regression of speech (37%), seizures (27%) and hypotonia (27%) and two individuals were non-ambulant. Our study shows that haploinsufficiency of CHD8 is associated with a distinctive OGID syndrome with pronounced autistic traits and supports a sex-dependent penetrance of CHD8 PTVs in humans.


Asunto(s)
Proteínas de Unión al ADN/genética , Estudios de Asociación Genética , Predisposición Genética a la Enfermedad , Variación Genética , Fenotipo , Factores de Transcripción/genética , Adolescente , Alelos , Sustitución de Aminoácidos , Niño , Preescolar , Facies , Femenino , Estudios de Asociación Genética/métodos , Genotipo , Humanos , Masculino , Trastornos del Neurodesarrollo/diagnóstico , Trastornos del Neurodesarrollo/genética
13.
J Med Genet ; 55(3): 181-188, 2018 03.
Artículo en Inglés | MEDLINE | ID: mdl-29079706

RESUMEN

BACKGROUND: Multiple single nucleotide polymorphisms (SNPs) have been associated with colorectal cancer (CRC) risk. The role of structural or copy number variants (CNV) in CRC, however, remained unclear. We investigated the role of CNVs in patients with sporadic CRC. METHODS: A genome-wide association study (GWAS) was performed on 1000 Singapore Chinese patients aged 50 years or more with no family history of CRC and 1000 ethnicity-matched, age-matched and gender-matched healthy controls using the Affymetrix SNP 6 platform. After 16 principal component corrections, univariate and multivariate segmentations followed by association testing were performed on 1830 samples that passed quality assurance tests. RESULTS: A rare CNV region (CNVR) at chromosome 14q11 (OR=1.92 (95% CI 1.59 to 2.32), p=2.7e-12) encompassing CHD8, and common CNVR at chromosomes 3q13.12 (OR=1.54 (95% CI 1.33 to 1.77), p=2.9e-9) and 12p12.3 (OR=1.69 (95% CI 1.41 to 2.01), p=2.8e-9) encompassing CD47 and RERG/ARHGDIB, respectively, were significantly associated with CRC risk. CNV loci were validated in an independent replication panel using an optimised copy number assay. Whole-genome expression data in matched tumours of a subset of cases demonstrated that copy number loss at CHD8 was significantly associated with dysregulation of several genes that perturb the Wnt, TP53 and inflammatory pathways. CONCLUSIONS: A rare CNVR at 14q11 encompassing the chromatin modifier CHD8 was significantly associated with sporadic CRC risk. Copy number loss at CHD8 altered expressions of genes implicated in colorectal tumourigenesis.


Asunto(s)
Neoplasias Colorrectales/genética , Proteínas de Unión al ADN/genética , Predisposición Genética a la Enfermedad , Estudio de Asociación del Genoma Completo , Factores de Transcripción/genética , Adulto , Anciano , Carcinogénesis/genética , Neoplasias Colorrectales/patología , Variaciones en el Número de Copia de ADN/genética , Femenino , Regulación Neoplásica de la Expresión Génica , Humanos , Masculino , Persona de Mediana Edad , Polimorfismo de Nucleótido Simple/genética , Factores de Riesgo , Proteína p53 Supresora de Tumor/genética
14.
Proteins ; 86(2): 135-151, 2018 02.
Artículo en Inglés | MEDLINE | ID: mdl-29098713

RESUMEN

Recent advances in computing power and machine learning empower functional annotation of protein sequences and their transcript variations. Here, we present an automated prediction system UniGOPred, for GO annotations and a database of GO term predictions for proteomes of several organisms in UniProt Knowledgebase (UniProtKB). UniGOPred provides function predictions for 514 molecular function (MF), 2909 biological process (BP), and 438 cellular component (CC) GO terms for each protein sequence. UniGOPred covers nearly the whole functionality spectrum in Gene Ontology system and it can predict both generic and specific GO terms. UniGOPred was run on CAFA2 challenge target protein sequences and it is categorized within the top 10 best performing methods for the molecular function category. In addition, the performance of UniGOPred is higher compared to the baseline BLAST classifier in all categories of GO. UniGOPred predictions are compared with UniProtKB/TrEMBL database annotations as well. Furthermore, the proposed tool's ability to predict negatively associated GO terms that defines the functions that a protein does not possess, is discussed. UniGOPred annotations were also validated by case studies on PTEN protein variants experimentally and on CHD8 protein variants with literature. UniGOPred protein functional annotation system is available as an open access tool at http://cansyl.metu.edu.tr/UniGOPred.html.


Asunto(s)
Aprendizaje Automático , Fosfohidrolasa PTEN/metabolismo , Proteómica/métodos , Animales , Bases de Datos de Proteínas , Ontología de Genes , Humanos , Modelos Biológicos , Fosfohidrolasa PTEN/química , Fosfohidrolasa PTEN/genética , Análisis de Secuencia de Proteína , Transcriptoma
15.
J Anat ; 233(6): 755-769, 2018 12.
Artículo en Inglés | MEDLINE | ID: mdl-30277262

RESUMEN

Recent large-scale exome sequencing studies have identified mutations in several members of the CHD (Chromodomain Helicase DNA-binding protein) gene family in neurodevelopmental disorders. Mutations in the CHD2 gene have been linked to developmental delay, intellectual disability, autism and seizures, CHD8 mutations to autism and intellectual disability, whereas haploinsufficiency of CHD7 is associated with executive dysfunction and intellectual disability. In addition to these neurodevelopmental features, a wide range of other developmental defects are associated with mutants of these genes, especially with regards to CHD7 haploinsufficiency, which is the primary cause of CHARGE syndrome. Whilst the developmental expression of CHD7 has been reported previously, limited information on the expression of CHD2 and CHD8 during development is available. Here, we compare the expression patterns of all three genes during mouse development directly. We find high, widespread expression of these genes at early stages of development that gradually becomes restricted during later developmental stages. Chd2 and Chd8 are widely expressed in the developing central nervous system (CNS) at all stages of development, with moderate expression remaining in the neocortex, hippocampus, olfactory bulb and cerebellum of the postnatal brain. Similarly, Chd7 expression is seen throughout the CNS during late embryogenesis and early postnatal development, with strong enrichment in the cerebellum, but displays low expression in the cortex and neurogenic niches in early life. In addition to expression in the brain, novel sites of Chd2 and Chd8 expression are reported. These findings suggest additional roles for these genes in organogenesis and predict that mutation of these genes may predispose individuals to a range of other, non-neurological developmental defects.


Asunto(s)
Trastorno Autístico/genética , Proteínas de Unión al ADN/biosíntesis , Transcriptoma , Animales , Embrión de Mamíferos , Ratones , Neurogénesis/genética , Fenotipo
16.
Proc Natl Acad Sci U S A ; 111(42): E4468-77, 2014 Oct 21.
Artículo en Inglés | MEDLINE | ID: mdl-25294932

RESUMEN

Truncating mutations of chromodomain helicase DNA-binding protein 8 (CHD8), and of many other genes with diverse functions, are strong-effect risk factors for autism spectrum disorder (ASD), suggesting multiple mechanisms of pathogenesis. We explored the transcriptional networks that CHD8 regulates in neural progenitor cells (NPCs) by reducing its expression and then integrating transcriptome sequencing (RNA sequencing) with genome-wide CHD8 binding (ChIP sequencing). Suppressing CHD8 to levels comparable with the loss of a single allele caused altered expression of 1,756 genes, 64.9% of which were up-regulated. CHD8 showed widespread binding to chromatin, with 7,324 replicated sites that marked 5,658 genes. Integration of these data suggests that a limited array of direct regulatory effects of CHD8 produced a much larger network of secondary expression changes. Genes indirectly down-regulated (i.e., without CHD8-binding sites) reflect pathways involved in brain development, including synapse formation, neuron differentiation, cell adhesion, and axon guidance, whereas CHD8-bound genes are strongly associated with chromatin modification and transcriptional regulation. Genes associated with ASD were strongly enriched among indirectly down-regulated loci (P < 10(-8)) and CHD8-bound genes (P = 0.0043), which align with previously identified coexpression modules during fetal development. We also find an intriguing enrichment of cancer-related gene sets among CHD8-bound genes (P < 10(-10)). In vivo suppression of chd8 in zebrafish produced macrocephaly comparable to that of humans with inactivating mutations. These data indicate that heterozygous disruption of CHD8 precipitates a network of gene-expression changes involved in neurodevelopmental pathways in which many ASD-associated genes may converge on shared mechanisms of pathogenesis.


Asunto(s)
Trastornos Generalizados del Desarrollo Infantil/genética , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/fisiología , Regulación del Desarrollo de la Expresión Génica , Células-Madre Neurales/fisiología , Factores de Transcripción/genética , Factores de Transcripción/fisiología , Proteínas de Pez Cebra/fisiología , Animales , Axones/metabolismo , Sitios de Unión , Trastornos Generalizados del Desarrollo Infantil/metabolismo , Cromatina/metabolismo , ADN Helicasas/metabolismo , Perfilación de la Expresión Génica , Regulación Neoplásica de la Expresión Génica , Redes Reguladoras de Genes , Genoma , Heterocigoto , Humanos , Megalencefalia/metabolismo , Mutación , Neoplasias/metabolismo , Neuronas/metabolismo , Unión Proteica , Factores de Riesgo , Análisis de Secuencia de ARN , Programas Informáticos , Pez Cebra , Proteínas de Pez Cebra/genética
17.
Am J Med Genet A ; 170A(5): 1225-35, 2016 May.
Artículo en Inglés | MEDLINE | ID: mdl-26789910

RESUMEN

Mutations in chromodomain helicase DNA-binding domain 8 (CHD8) have been identified in independent genotyping studies of autism spectrum disorder. To better understand the phenotype associated with CHD8 mutations, we genotyped all CHD8 exons in carefully assessed cohorts of autism (n = 142), schizophrenia (SCZ; n = 143), and intellectual disability (ID; n = 94). We identified one frameshift mutation, seven non-synonymous variants, and six synonymous variants. The frameshift mutation, p.Asn2092Lysfs*2, which creates a premature stop codon leading to the loss of 212 amino acids of the protein, was from an autism case on whom we present multiple clinical assessments and pharmacological treatments spanning more than 10 years. RNA and protein analysis support a model where the transcript generated from the mutant allele results in haploinsufficiency of CHD8. This case report supports the association of CHD8 mutations with classical autism, macrocephaly, infantile hypotonia, speech delay, lack of major ID, and psychopathology in late adolescence caused by insufficient dosage of CHD8. Review of 16 other CHD8 mutation cases suggests that clinical features and their severity vary considerably across individuals; however, these data support a CHD8 mutation syndrome, further highlighting the importance of genomic medicine to guide clinical assessment and treatment.


Asunto(s)
Trastorno del Espectro Autista/genética , Proteínas de Unión al ADN/genética , Esquizofrenia/genética , Factores de Transcripción/genética , Adolescente , Trastorno del Espectro Autista/fisiopatología , Niño , Preescolar , Hibridación Genómica Comparativa , Exones/genética , Femenino , Mutación del Sistema de Lectura , Regulación del Desarrollo de la Expresión Génica , Genotipo , Humanos , Masculino , Esquizofrenia/fisiopatología
18.
Am J Med Genet A ; 170A(5): 1325-9, 2016 May.
Artículo en Inglés | MEDLINE | ID: mdl-26834018

RESUMEN

Neurodevelopmental disorders have long been associated with chromosomal abnormalities, including microdeletions and microduplications. Submicroscopic 14q11.2 deletions involving the CHD8 and SUPT16H genes have been reported in patients with developmental delay (DD)/intellectual disability (ID) or autism spectrum disorders (ASDs) and/or macrocephaly. Recently, disruptive CHD8 mutations were described in patients with similar phenotypes further showing pivotal role of CHD8 gene in the pathogenesis of DD/ID or ASDs. We report here the first case of ~445 kb de novo microduplication, encompassing the minimal critical 14q11.2 deletion region, in 8-year-old boy showing DD, cognitive impairment and facial dysmorphism. Our results suggest that gain of the chromosomal region 14q11.2 is causative for clinical findings present in the patient.


Asunto(s)
Trastorno del Espectro Autista/genética , Proteínas de Ciclo Celular/genética , Proteínas de Unión al ADN/genética , Discapacidades del Desarrollo/genética , Factores de Transcripción/genética , Trastorno del Espectro Autista/fisiopatología , Niño , Aberraciones Cromosómicas , Deleción Cromosómica , Cromosomas Humanos Par 14/genética , Hibridación Genómica Comparativa , Discapacidades del Desarrollo/fisiopatología , Eliminación de Gen , Humanos , Discapacidad Intelectual/genética , Discapacidad Intelectual/fisiopatología , Masculino
19.
Am J Med Genet A ; 167A(4): 837-41, 2015 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-25735987

RESUMEN

We identified a de novo deletion of 14q11.2 in a Czech patient with developmental delay, mild autistic features, macrosomy, macrocephaly, orthognathic deformities, and dysmorphic facial features. The clinical follow-up of the patient lasting 14 years documented changes in the facial dysmorphism from infancy to adolescence. The deletion affects approximately 200 kb of DNA with five protein-coding genes and two snoRNA genes. Two of the protein-coding genes, SUPT16H and CHD8, have been proposed as candidate genes for a new microdeletion syndrome. Our patient further supports the existence of this syndrome and extends its phenotypic spectrum, especially points to the possibility that orthognathic deformities may be associated with microdeletions of 14q11.2. CHD8 mutations have been found in patients with neurodevelopmental disorders and macrocephaly. The HNRNPC gene, repeatedly deleted in patients with developmental delay, is another candidate as its 5́ end is adjacent to the deletion, and the expression of this gene may be affected by position effect.


Asunto(s)
Anomalías Múltiples/diagnóstico , Deleción Cromosómica , Cromosomas Humanos Par 14/genética , Proteínas de Unión al ADN/genética , Factores de Transcripción/genética , Anomalías Múltiples/genética , Adolescente , Discapacidades del Desarrollo/diagnóstico , Discapacidades del Desarrollo/genética , Estudios de Seguimiento , Humanos , Discapacidad Intelectual/diagnóstico , Discapacidad Intelectual/genética , Masculino , Megalencefalia/diagnóstico , Megalencefalia/genética
20.
Am J Med Genet A ; 164A(1): 190-3, 2014 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-24243641

RESUMEN

We report on a 21-year old woman with intellectual disability, autistic features, severe obesity, and facial dysmorphisms suggestive of Wolf-Hirschhorn syndrome (WHS). Array-CGH analysis showed a 2.89 Mb deletion on chromosome 14q11.2 containing 47 known genes. The most interesting genes included in this deletion are CHD8, a chromodomain helicase DNA binding protein that is associated with autism spectrum disorders, and MMP14, a matrix metalloproteinase that has been linked to obesity and type 2 diabetes. This report shows that 14q11.2 microdeletions can mimic WHS and suggests that gene(s) in the deleted interval that may be responsible for a phenocopy of WHS.


Asunto(s)
Deleción Cromosómica , Cromosomas Humanos Par 4 , Fenotipo , Síndrome de Wolf-Hirschhorn/diagnóstico , Síndrome de Wolf-Hirschhorn/genética , Trastorno Autístico/diagnóstico , Trastorno Autístico/genética , Preescolar , Anomalías Craneofaciales/diagnóstico , Anomalías Craneofaciales/genética , Diagnóstico Diferencial , Facies , Femenino , Humanos , Recién Nacido , Obesidad/diagnóstico , Obesidad/genética , Adulto Joven
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