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1.
J Parkinsons Dis ; 14(2): 335-346, 2024.
Article En | MEDLINE | ID: mdl-38306061

Background: Increased prevalence of cardiovascular autonomic failure might play a key role on Parkinson's disease (PD) progression of glucocerebrosidase gene (GBA)-mutated patients, determining a malignant phenotype of disease in these patients. Objective: To objectively characterize, for the first time, the cardiovascular autonomic profile of GBA-mutated patients compared to idiopathic PD patients by means of cardiovascular reflex tests (CRTs). Methods: This is a case-control (1 : 2) study on PD patients belonging to well-characterized prospective cohorts. For each PD patient carrying GBA variants, two idiopathic PD patients, matched for sex and disease duration at CRTs, were selected. Patients recruited in these cohorts underwent a complete clinical and instrumental evaluation including specific autonomic questionnaires, CRTs and extensive genetic analysis. Results: A total of 23 GBA-PD patients (19 males, disease duration 7.7 years) were included and matched with 46 non-mutated PD controls. GBA-mutated patients were younger than controls (59.9±8.1 vs. 64.3±7.2 years, p = 0.0257) and showed a more severe phenotype. Despite GBA-mutated patients reported more frequently symptoms suggestive of orthostatic hypotension (OH) than non-mutated patients (39.1% vs 6.5%, p = 0.001), the degree of cardiovascular autonomic dysfunction, when instrumentally assessed, did not differ between the two groups, showing the same prevalence of neurogenic OH, delayed OH and cardiovascular reflex impairment (pathological Valsalva maneuver). Conclusion: GBA-PD patients did not show different instrumental cardiovascular autonomic pattern than non-mutated PD. Our findings suggested that symptoms suggestive of OH should be promptly investigated by clinicians to confirm their nature and improve patient care and management.


Autonomic Nervous System Diseases , Hypotension, Orthostatic , Parkinson Disease , Humans , Male , Autonomic Nervous System Diseases/diagnosis , Autonomic Nervous System Diseases/etiology , Case-Control Studies , Glucosylceramidase/genetics , Mutation , Parkinson Disease/complications , Parkinson Disease/genetics , Prospective Studies
2.
Front Genet ; 14: 1322067, 2023.
Article En | MEDLINE | ID: mdl-38152653

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease with a complex genetic architecture, showing monogenic, oligogenic, and polygenic inheritance. In this study, we describe the case of a 71 years-old man diagnosed with ALS with atypical clinical features consisting in progressive ocular ptosis and sensorineural deafness. Genetic analyses revealed two heterozygous variants, in the SOD1 (OMIM*147450) and the TBK1 (OMIM*604834) genes respectively, and furthermore mitochondrial DNA (mtDNA) sequencing identified the homoplasmic m.14484T>C variant usually associated with Leber's Hereditary Optic Neuropathy (LHON). We discuss how all these variants may synergically impinge on mitochondrial function, possibly contributing to the pathogenic mechanisms which might ultimately lead to the neurodegenerative process, shaping the clinical ALS phenotype enriched by adjunctive clinical features.

3.
Nature ; 604(7906): 509-516, 2022 04.
Article En | MEDLINE | ID: mdl-35396579

Rare coding variation has historically provided the most direct connections between gene function and disease pathogenesis. By meta-analysing the whole exomes of 24,248 schizophrenia cases and 97,322 controls, we implicate ultra-rare coding variants (URVs) in 10 genes as conferring substantial risk for schizophrenia (odds ratios of 3-50, P < 2.14 × 10-6) and 32 genes at a false discovery rate of <5%. These genes have the greatest expression in central nervous system neurons and have diverse molecular functions that include the formation, structure and function of the synapse. The associations of the NMDA (N-methyl-D-aspartate) receptor subunit GRIN2A and AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid) receptor subunit GRIA3 provide support for dysfunction of the glutamatergic system as a mechanistic hypothesis in the pathogenesis of schizophrenia. We observe an overlap of rare variant risk among schizophrenia, autism spectrum disorders1, epilepsy and severe neurodevelopmental disorders2, although different mutation types are implicated in some shared genes. Most genes described here, however, are not implicated in neurodevelopment. We demonstrate that genes prioritized from common variant analyses of schizophrenia are enriched in rare variant risk3, suggesting that common and rare genetic risk factors converge at least partially on the same underlying pathogenic biological processes. Even after excluding significantly associated genes, schizophrenia cases still carry a substantial excess of URVs, which indicates that more risk genes await discovery using this approach.


Mutation , Neurodevelopmental Disorders , Schizophrenia , Case-Control Studies , Exome , Genetic Predisposition to Disease/genetics , Humans , Neurodevelopmental Disorders/genetics , Receptors, N-Methyl-D-Aspartate/genetics , Schizophrenia/genetics
4.
Am J Hum Genet ; 107(5): 802-814, 2020 11 05.
Article En | MEDLINE | ID: mdl-33022222

The cause of autosomal-dominant retinitis pigmentosa (adRP), which leads to loss of vision and blindness, was investigated in families lacking a molecular diagnosis. A refined locus for adRP on Chr17q22 (RP17) was delineated through genotyping and genome sequencing, leading to the identification of structural variants (SVs) that segregate with disease. Eight different complex SVs were characterized in 22 adRP-affected families with >300 affected individuals. All RP17 SVs had breakpoints within a genomic region spanning YPEL2 to LINC01476. To investigate the mechanism of disease, we reprogrammed fibroblasts from affected individuals and controls into induced pluripotent stem cells (iPSCs) and differentiated them into photoreceptor precursor cells (PPCs) or retinal organoids (ROs). Hi-C was performed on ROs, and differential expression of regional genes and a retinal enhancer RNA at this locus was assessed by qPCR. The epigenetic landscape of the region, and Hi-C RO data, showed that YPEL2 sits within its own topologically associating domain (TAD), rich in enhancers with binding sites for retinal transcription factors. The Hi-C map of RP17 ROs revealed creation of a neo-TAD with ectopic contacts between GDPD1 and retinal enhancers, and modeling of all RP17 SVs was consistent with neo-TADs leading to ectopic retinal-specific enhancer-GDPD1 accessibility. qPCR confirmed increased expression of GDPD1 and increased expression of the retinal enhancer that enters the neo-TAD. Altered TAD structure resulting in increased retinal expression of GDPD1 is the likely convergent mechanism of disease, consistent with a dominant gain of function. Our study highlights the importance of SVs as a genomic mechanism in unsolved Mendelian diseases.


Chromosomes, Human, Pair 17/chemistry , Nuclear Proteins/genetics , Phosphoric Diester Hydrolases/genetics , Retinal Cone Photoreceptor Cells/metabolism , Retinitis Pigmentosa/genetics , Transcription Factors/genetics , Adult , Amino Acid Sequence , Cell Differentiation , Cellular Reprogramming , Child , Chromosome Mapping , Cohort Studies , Enhancer Elements, Genetic , Female , Fibroblasts/metabolism , Fibroblasts/pathology , Gene Expression , Genes, Dominant , Genome, Human , Humans , Induced Pluripotent Stem Cells/metabolism , Induced Pluripotent Stem Cells/pathology , Male , Nuclear Proteins/metabolism , Organoids/metabolism , Organoids/pathology , Phosphoric Diester Hydrolases/metabolism , Polymorphism, Genetic , Primary Cell Culture , Retinal Cone Photoreceptor Cells/pathology , Retinitis Pigmentosa/diagnosis , Retinitis Pigmentosa/metabolism , Retinitis Pigmentosa/pathology , Transcription Factors/metabolism , Whole Genome Sequencing
5.
Am J Ophthalmol ; 210: 59-70, 2020 02.
Article En | MEDLINE | ID: mdl-31704230

PURPOSE: To describe the natural history of Leber congenital amaurosis (LCA) associated with GUCY2D variants (GUCY2D-LCA) in a cohort of children and adults, in preparation for trials of novel therapies. DESIGN: Retrospective case series. METHODS: Participants: Patients with GUCY2D-LCA at a single referral center. PROCEDURES: Review of clinical notes, retinal imaging including fundus autofluorescence (FAF) and optical coherence tomography (OCT), electroretinography (ERG), and molecular genetic testing. MAIN OUTCOME MEASURES: Demographic data, symptoms at presentation, visual acuity, evidence of progression, OCT and FAF findings, ERG assessment, and molecular genetics. RESULTS: Twenty-one subjects with GUCY2D-LCA were included, with a mean follow-up ± standard deviation (SD) of 10 ± 11.85 years. Marked reduction in visual acuity (VA) and nystagmus was documented in all patients within the first 3 years of life. Fifty-seven percent (n = 12) exhibited photophobia and 38% (n = 8) had nyctalopia. VA was worse than hand motion in 71% of the patients (n = 15). Longitudinal assessment of VA showed stability in all patients, except 1 patient who experienced deterioration over a follow-up of 44 years. Hyperopia was reported in 13 of the 17 subjects (71%) with available refraction data. Eighteen subjects had either normal fundus appearance (n = 14) or a blond fundus (n = 3), while only 4 of the eldest subjects had mild retinal pigment epithelium (RPE) atrophy (mean, 49 years; range 40-54 years). OCT data were available for 11 subjects and 4 different grades of ellipsoid zone (EZ) integrity were identified: (1) continuous/intact EZ (n = 6), (2) focally disrupted EZ (n = 2), (3) focally disrupted with RPE changes (n = 2), and (4) diffuse EZ disruption with RPE changes (n = 1). All examined subjects had stable OCT findings over the long follow-up period. Full-field ERGs showed evidence of a severe cone-rod dystrophy in 5 of 6 patients and undetectable ERGs in 1 subject. Novel genotype-phenotype correlations are also reported. CONCLUSION: GUCY2D-LCA is a severe early-onset retinal dystrophy associated with very poor VA from birth. Despite the severely affected photoreceptor function, the relatively preserved photoreceptor structure based on EZ integrity until late in the disease in the majority of subjects suggests a wide therapeutic window for gene therapy trials.


Guanylate Cyclase/genetics , Leber Congenital Amaurosis/pathology , Receptors, Cell Surface/genetics , Adolescent , Adult , Child , Child, Preschool , Disease Progression , Female , Humans , Leber Congenital Amaurosis/genetics , Male , Middle Aged , Photoreceptor Cells, Vertebrate/pathology , Retinal Pigment Epithelium/pathology , Retrospective Studies , Tomography, Optical Coherence , Vision Disorders/etiology , Visual Acuity
6.
Am J Med Genet B Neuropsychiatr Genet ; 180(4): 258-265, 2019 06.
Article En | MEDLINE | ID: mdl-30859703

A rare microcephalin 1 gene (MCPH1) variant rs61749465A>G (p.Asp61Gly) with prior evidence for association with schizophrenia (p = 3.78 × 10-7 ) was tested for association in 2,300 bipolar disorder (BPD) participants, 1,930 SCZ participants and 1,820 normal comparison subjects. We report evidence for association of rs61749465A>G with BPD (p = 0.0009). rs61749465 is located in the N-terminal of the BRCT1 domain of MCPH1. Bioinformatic analysis predicted the Asp61Gly substitution to be damaging to MCPH1 function. A second MCPH1 BRCT1 domain variant (rs199422124C>G; p.Thr27Arg), reported to cause autosomal recessive microcephaly, was not detected in the participants tested here. We sought to characterize the functional effects of these variants on MCPH1 function. Cell count assays indicated that rs199422124 allele G had a greater impact on cell survival compared to the G allele of rs61749465. Gene expression analysis combined with gene network and pathway analysis indicated that rs61749465 allele G may impact protein translation and cell cycle control. The evidence for association between rs61749465A>G and psychosis in both BPD and SCZ warrants further replication. Likewise, the data from the functional analyses point to molecular mechanisms that may underlie the proposed MCPH1 mediated risk of psychosis and pathogenesis in autosomal recessive microcephaly require additional experimental validation.


Bipolar Disorder/genetics , Cell Cycle Proteins/genetics , Cytoskeletal Proteins/genetics , Genetic Association Studies , Genetic Predisposition to Disease , Genetic Variation , Schizophrenia/genetics , Alleles , DNA Damage/genetics , Gene Expression Regulation , HEK293 Cells , Humans , RNA Stability/genetics , RNA, Messenger/genetics , RNA, Messenger/metabolism
7.
Mol Vis ; 24: 603-612, 2018.
Article En | MEDLINE | ID: mdl-30210231

Purpose: Mutations in ARL2BP, encoding ADP-ribosylation factor-like 2 binding protein, have recently been implicated as a cause of autosomal recessive retinitis pigmentosa (arRP), with three homozygous variants identified to date. In this study, we performed next-generation sequencing to reveal additional arRP cases associated with ARL2BP variants. Methods: Whole-genome sequencing (WGS) or whole-exome sequencing (WES) was performed in 1,051 unrelated individuals recruited for the UK Inherited Retinal Disease Consortium and NIHR-BioResource Rare Diseases research studies. Sanger sequencing was used to validate the next-generation sequencing data, and reverse transcriptase (RT)-PCR analysis was performed on RNA extracted from blood from affected individuals to test for altered splicing of ARL2BP. Detailed phenotyping was performed, including clinical evaluation, electroretinography, fundus photography, fundus autofluorescence imaging, and spectral-domain optical coherence tomography. Results: Homozygous variants in ARL2BP (NM_012106.3) were identified in two unrelated individuals with RP. The variants, c.207+1G>A and c.390+5G>A, at conserved splice donor sites for intron 3 and intron 5, respectively, were predicted to alter the pre-mRNA splicing of ARL2BP. RT-PCR spanning the affected introns revealed that both variants caused abnormal splicing of ARL2BP in samples from affected individuals. Conclusions: This study identified two homozygous variants in ARL2BP as a rare cause of arRP. Further studies are required to define the underlying disease mechanism causing retinal degeneration as a result of mutations in ARL2BP and any phenotype-genotype correlation associated with residual levels of the wild-type transcript.


Carrier Proteins/genetics , Mutation , Retinitis Pigmentosa/genetics , Adult , DNA Mutational Analysis , Electroretinography , Exome , Female , Genes, Recessive , Genetic Association Studies , High-Throughput Nucleotide Sequencing , History, 16th Century , Homozygote , Humans , Male , Pedigree , Phenotype , RNA Splicing , Reverse Transcriptase Polymerase Chain Reaction , Tomography, Optical Coherence , Transcription Factors , Whole Genome Sequencing
8.
Hum Mutat ; 39(1): 80-91, 2018 01.
Article En | MEDLINE | ID: mdl-28967191

Retinal dystrophies are a heterogeneous group of disorders of visual function leading to partial or complete blindness. We report the genetic basis of an unusual retinal dystrophy in five families with affected females and no affected males. Heterozygous missense variants were identified in the X-linked phosphoribosyl pyrophosphate synthetase 1 (PRPS1) gene: c.47C > T, p.(Ser16Phe); c.586C > T, p.(Arg196Trp); c.641G > C, p.(Arg214Pro); and c.640C > T, p.(Arg214Trp). Missense variants in PRPS1 are usually associated with disease in male patients, including Arts syndrome, Charcot-Marie-Tooth, and nonsyndromic sensorineural deafness. In our study families, affected females manifested a retinal dystrophy with interocular asymmetry. Three unrelated females from these families had hearing loss leading to a diagnosis of Usher syndrome. Other neurological manifestations were also observed in three individuals. Our data highlight the unexpected X-linked inheritance of retinal degeneration in females caused by variants in PRPS1 and suggest that tissue-specific skewed X-inactivation or variable levels of pyrophosphate synthetase-1 deficiency are the underlying mechanism(s). We speculate that the absence of affected males in the study families suggests that some variants may be male embryonic lethal when inherited in the hemizygous state. The unbiased nature of next-generation sequencing enables all possible modes of inheritance to be considered for association of gene variants with novel phenotypic presentation.


Genes, X-Linked , Mutation, Missense , Retinal Degeneration/diagnosis , Retinal Degeneration/genetics , Ribose-Phosphate Pyrophosphokinase/genetics , Adolescent , Adult , Aged , Aged, 80 and over , Alleles , Amino Acid Sequence , Amino Acid Substitution , Female , Genetic Association Studies , Genotype , Humans , Models, Molecular , Pedigree , Phenotype , Protein Conformation , Ribose-Phosphate Pyrophosphokinase/chemistry , Young Adult
9.
Ann Hum Genet ; 82(2): 88-92, 2018 03.
Article En | MEDLINE | ID: mdl-29148569

Schizophrenia (SCZ) is a severe, highly heritable psychiatric disorder. Elucidation of the genetic architecture of the disorder will facilitate greater understanding of the altered underlying neurobiological mechanisms. The aim of this study was to identify likely aetiological variants in subjects affected with SCZ. Exome sequence data from a SCZ cas-control sample from Sweden was analysed for likely aetiological variants using a weighted burden test. Suggestive evidence implicated the UNC-51-like kinase (ULK1) gene, and it was observed that four rare variants that were more common in the Swedish SCZ cases were also more common in UK10K SCZ cases, as compared to obesity cases. These three missense variants and one intronic variant were genotyped in the University College London cohort of 1304 SCZ cases and 1348 ethnically matched controls. All four variants were more common in the SCZ cases than controls and combining them produced a result significant at P = 0.02. The results presented here demonstrate the importance of following up exome sequencing studies using additional datasets. The roles of ULK1 in autophagy and mTOR signalling strengthen the case that these pathways may be important in the pathophysiology of SCZ. The findings reported here await independent replication.


Autophagy-Related Protein-1 Homolog/genetics , Exome , Intracellular Signaling Peptides and Proteins/genetics , Schizophrenia/genetics , Case-Control Studies , Genotype , Humans , Introns , Mutation, Missense , Sweden , Exome Sequencing
10.
Am J Hum Genet ; 100(4): 592-604, 2017 Apr 06.
Article En | MEDLINE | ID: mdl-28285769

Pre-mRNA splicing factors play a fundamental role in regulating transcript diversity both temporally and spatially. Genetic defects in several spliceosome components have been linked to a set of non-overlapping spliceosomopathy phenotypes in humans, among which skeletal developmental defects and non-syndromic retinitis pigmentosa (RP) are frequent findings. Here we report that defects in spliceosome-associated protein CWC27 are associated with a spectrum of disease phenotypes ranging from isolated RP to severe syndromic forms. By whole-exome sequencing, recessive protein-truncating mutations in CWC27 were found in seven unrelated families that show a range of clinical phenotypes, including retinal degeneration, brachydactyly, craniofacial abnormalities, short stature, and neurological defects. Remarkably, variable expressivity of the human phenotype can be recapitulated in Cwc27 mutant mouse models, with significant embryonic lethality and severe phenotypes in the complete knockout mice while mice with a partial loss-of-function allele mimic the isolated retinal degeneration phenotype. Our study describes a retinal dystrophy-related phenotype spectrum as well as its genetic etiology and highlights the complexity of the spliceosomal gene network.


Abnormalities, Multiple/genetics , Cyclophilins/genetics , Mutation , Peptidylprolyl Isomerase/genetics , Retinal Degeneration/genetics , Adolescent , Animals , Child , Child, Preschool , Cyclophilins/metabolism , Female , Humans , Male , Mice , Pedigree , Peptidylprolyl Isomerase/metabolism , Young Adult
11.
Bioinformatics ; 33(15): 2421-2423, 2017 Aug 01.
Article En | MEDLINE | ID: mdl-28334266

SUMMARY: Phenopolis is an open-source web server providing an intuitive interface to genetic and phenotypic databases. It integrates analysis tools such as variant filtering and gene prioritization based on phenotype. The Phenopolis platform will accelerate clinical diagnosis, gene discovery and encourage wider adoption of the Human Phenotype Ontology in the study of rare genetic diseases. AVAILABILITY AND IMPLEMENTATION: A demo of the website is available at https://phenopolis.github.io . If you wish to install a local copy, source code and installation instruction are available at https://github.com/phenopolis . The software is implemented using Python, MongoDB, HTML/Javascript and various bash shell scripts. CONTACT: n.pontikos@ucl.ac.uk. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Computational Biology/methods , Genetic Diseases, Inborn/genetics , Phenotype , Software , Databases, Factual , Genetic Diseases, Inborn/diagnosis , Genetic Diseases, Inborn/pathology , Humans , Rare Diseases/diagnosis , Rare Diseases/genetics , Rare Diseases/pathology
12.
Am J Hum Genet ; 100(2): 334-342, 2017 Feb 02.
Article En | MEDLINE | ID: mdl-28132693

Mutations in more than 250 genes are implicated in inherited retinal dystrophy; the encoded proteins are involved in a broad spectrum of pathways. The presence of unsolved families after highly parallel sequencing strategies suggests that further genes remain to be identified. Whole-exome and -genome sequencing studies employed here in large cohorts of affected individuals revealed biallelic mutations in ARHGEF18 in three such individuals. ARHGEF18 encodes ARHGEF18, a guanine nucleotide exchange factor that activates RHOA, a small GTPase protein that is a key component of tight junctions and adherens junctions. This biological pathway is known to be important for retinal development and function, as mutation of CRB1, encoding another component, causes retinal dystrophy. The retinal structure in individuals with ARHGEF18 mutations resembled that seen in subjects with CRB1 mutations. Five mutations were found on six alleles in the three individuals: c.808A>G (p.Thr270Ala), c.1617+5G>A (p.Asp540Glyfs∗63), c.1996C>T (p.Arg666∗), c.2632G>T (p.Glu878∗), and c.2738_2761del (p.Arg913_Glu920del). Functional tests suggest that each disease genotype might retain some ARHGEF18 activity, such that the phenotype described here is not the consequence of nullizygosity. In particular, the p.Thr270Ala missense variant affects a highly conserved residue in the DBL homology domain, which is required for the interaction and activation of RHOA. Previously, knock-out of Arhgef18 in the medaka fish has been shown to cause larval lethality which is preceded by retinal defects that resemble those seen in zebrafish Crumbs complex knock-outs. The findings described here emphasize the peculiar sensitivity of the retina to perturbations of this pathway, which is highlighted as a target for potential therapeutic strategies.


Cell Polarity , Epithelial Cells/metabolism , Retinal Degeneration/genetics , Rho Guanine Nucleotide Exchange Factors/genetics , Adult , Alleles , Amino Acid Sequence , Exome , Eye Proteins/genetics , Eye Proteins/metabolism , Female , Genetic Variation , Genome-Wide Association Study , Genotype , Humans , Male , Membrane Proteins/genetics , Membrane Proteins/metabolism , Middle Aged , Mutation, Missense , Nerve Tissue Proteins/genetics , Nerve Tissue Proteins/metabolism , Pedigree , Phenotype , Retina/metabolism , Retinal Degeneration/diagnosis , Retinal Dystrophies/genetics , rhoA GTP-Binding Protein/genetics , rhoA GTP-Binding Protein/metabolism
13.
Am J Hum Genet ; 99(6): 1305-1315, 2016 Dec 01.
Article En | MEDLINE | ID: mdl-27889058

Retinitis pigmentosa (RP) is the most frequent form of inherited retinal dystrophy. RP is genetically heterogeneous and the genes identified to date encode proteins involved in a wide range of functional pathways, including photoreceptor development, phototransduction, the retinoid cycle, cilia, and outer segment development. Here we report the identification of biallelic mutations in Receptor Expression Enhancer Protein 6 (REEP6) in seven individuals with autosomal-recessive RP from five unrelated families. REEP6 is a member of the REEP/Yop1 family of proteins that influence the structure of the endoplasmic reticulum but is relatively unstudied. The six variants identified include three frameshift variants, two missense variants, and a genomic rearrangement that disrupts exon 1. Human 3D organoid optic cups were used to investigate REEP6 expression and confirmed the expression of a retina-specific isoform REEP6.1, which is specifically affected by one of the frameshift mutations. Expression of the two missense variants (c.383C>T [p.Pro128Leu] and c.404T>C [p.Leu135Pro]) and the REEP6.1 frameshift mutant in cultured cells suggest that these changes destabilize the protein. Furthermore, CRISPR-Cas9-mediated gene editing was used to produce Reep6 knock-in mice with the p.Leu135Pro RP-associated variant identified in one RP-affected individual. The homozygous knock-in mice mimic the clinical phenotypes of RP, including progressive photoreceptor degeneration and dysfunction of the rod photoreceptors. Therefore, our study implicates REEP6 in retinal homeostasis and highlights a pathway previously uncharacterized in retinal dystrophy.


Eye Proteins/genetics , Genes, Recessive/genetics , Membrane Transport Proteins/genetics , Mutation/genetics , Retinitis Pigmentosa/genetics , Adolescent , Alleles , Animals , Child , Child, Preschool , Eye Proteins/chemistry , Eye Proteins/metabolism , Female , Humans , Induced Pluripotent Stem Cells/cytology , Male , Membrane Proteins , Mice , Mutation, Missense/genetics , Phenotype , Photoreceptor Cells, Vertebrate/cytology , Photoreceptor Cells, Vertebrate/metabolism , Young Adult
14.
Bipolar Disord ; 18(8): 650-656, 2016 12.
Article En | MEDLINE | ID: mdl-27864917

OBJECTIVE: rs12576775 was found to be associated with bipolar disorder (BD) in a genome-wide association study (GWAS). The GWAS signal implicates genes for the microRNAs miR-708 and miR-5579 and the first exon of the Odd Oz/ten-m homolog 4 gene (ODZ4). In the present study, miR-708, its surrounding region, and its targets were analyzed for potential BD-associated functional variants. METHODS: The miR-708 gene and surrounding regions were screened for variation using high-resolution melting (HRM) analysis in 1099 cases of BD, followed by genotyping of rare variants in an enlarged sample of 2078 subjects with BD, 1303 subjects with schizophrenia, and 1355 healthy controls. Whole-genome sequencing data from 99 subjects with BD were analyzed for variation in potential miR-708 binding sites. The minor allele frequencies (MAFs) of these variants were compared with those reported in reference individuals. RESULTS: Three variants detected by HRM were selected to be genotyped. rs754333774 was detected in three cases of BD, two cases of schizophrenia, and no controls. This variant is located 260 base pairs upstream from miR-708 and may play a role in controlling the expression of the miR. Four variants were identified in miR-708 targets binding sites. The MAFs of each of these variants were similar in BD and reference samples. CONCLUSIONS: We report a single recurrent variant located near the miR-708 gene that may have a role in BD and schizophrenia susceptibility. These findings await replication in independent cohorts, as do functional analyses of the potential consequences of this variant.


Bipolar Disorder/genetics , MicroRNAs/genetics , Schizophrenia/genetics , Adult , Female , Gene Frequency , Genetic Predisposition to Disease , Genetic Variation , Humans , Male , Polymorphism, Single Nucleotide
15.
JAMA Ophthalmol ; 134(8): 924-7, 2016 Aug 01.
Article En | MEDLINE | ID: mdl-27281386

IMPORTANCE: Mutations in phototransduction and retinal signaling genes are implicated in many retinopathies. To our knowledge, GNB3 encoding the G-protein ß subunit 3 (Gß3) has not previously been implicated in human disease. OBSERVATIONS: In this brief report, whole-exome sequencing was conducted on a patient with distinct inherited retinal disease presenting in childhood, with a phenotype characterized by nystagmus, normal retinal examination, and mild disturbance of the central macula on detailed retinal imaging. This sequencing revealed a homozygous GNB3 nonsense mutation (c.124C>T; p.Arg42Ter). Whole-exome sequencing was conducted from April 2015 to July 2015. CONCLUSIONS AND RELEVANCE: Expressed in cone photoreceptors and ON-bipolar cells, Gß3 is essential in phototransduction and ON-bipolar cell signaling. Knockout of Gnb3 in mice results in dysfunction of cone photoreceptors and ON-bipolar cells and a naturally occurring chicken mutation leads to retinal degeneration. Identification of further affected patients may allow description of the phenotypic and genotypic spectrum of disease associated with GNB3 retinopathy.


Codon, Nonsense , DNA/genetics , Heterotrimeric GTP-Binding Proteins/genetics , Retina/diagnostic imaging , Retinal Diseases/genetics , Child , DNA Mutational Analysis , Electroretinography , Genes, Recessive , Genotype , Heterotrimeric GTP-Binding Proteins/metabolism , Humans , Male , Pedigree , Retinal Diseases/diagnosis , Retinal Diseases/metabolism , Tomography, Optical Coherence
18.
Eur J Hum Genet ; 23(9): 1200-6, 2015 Sep.
Article En | MEDLINE | ID: mdl-25406999

The SLC1A2 gene encodes the excitatory amino acid transporter 2 (EAAT2). Glutamate is the major mediator of excitatory neurotransmission and EAAT2 is responsible for clearing the neurotransmitter from the synaptic cleft. Genetic variation in SLC1A2 has been implicated in a range of neurological and neuropsychiatric conditions including schizophrenia (SZ), autism and in core phenotypes of bipolar disorder (BD). The coding and putative regulatory regions of SLC1A2 gene were screened for variants using high resolution melting or sequenced in 1099 or in 32 BD subjects. Thirty-two variants were detected in the SLC1A2 gene. Fifteen potentially etiological variants were selected for genotyping in 1099 BD and 1095 control samples. Five amino acid changing variants were also genotyped in 630 participants suffering from SZ. None of the variants were found to be associated with BD or SZ or with the two diseases combined. However, two recurrent missense variants (rs145827578:G>A, p.(G6S); rs199599866:G>A, p.(R31Q)) and one recurrent 5'-untranslated region (UTR) variant (ss825678885:G>T) were detected in cases only. Combined analysis of the recurrent-case-only missense variants and of the case-only missense and 5'-UTR variants showed nominal evidence for association with the combined diseases (Fisher's P=0.019 and 0.0076). These findings are exploratory in nature and await replication in larger cohorts, however, they provide intriguing evidence that potentially functional rare variants in the SLC1A2 gene may confer susceptibility to psychotic disorders.


Bipolar Disorder/genetics , Genetic Predisposition to Disease , Glutamate Plasma Membrane Transport Proteins/genetics , Mutation , Polymorphism, Single Nucleotide , Schizophrenia/genetics , 5' Untranslated Regions , Bipolar Disorder/diagnosis , Bipolar Disorder/pathology , Case-Control Studies , DNA Mutational Analysis , Excitatory Amino Acid Transporter 2 , Gene Expression , Genotype , Humans , Nucleic Acid Denaturation , Open Reading Frames , Phenotype , Schizophrenia/diagnosis , Schizophrenia/pathology
19.
Am J Hum Genet ; 95(6): 744-53, 2014 Dec 04.
Article En | MEDLINE | ID: mdl-25434007

Schizophrenia (SZ) genome-wide association studies (GWASs) have identified common risk variants in >100 susceptibility loci; however, the contribution of rare variants at these loci remains largely unexplored. One of the strongly associated loci spans MIR137 (miR137) and MIR2682 (miR2682), two microRNA genes important for neuronal function. We sequenced ∼6.9 kb MIR137/MIR2682 and upstream regulatory sequences in 2,610 SZ cases and 2,611 controls of European ancestry. We identified 133 rare variants with minor allele frequency (MAF) <0.5%. The rare variant burden in promoters and enhancers, but not insulators, was associated with SZ (p = 0.021 for MAF < 0.5%, p = 0.003 for MAF < 0.1%). A rare enhancer SNP, 1:g.98515539A>T, presented exclusively in 11 SZ cases (nominal p = 4.8 × 10(-4)). We further identified its risk allele T in 2 of 2,434 additional SZ cases, 11 of 4,339 bipolar (BP) cases, and 3 of 3,572 SZ/BP study controls and 1,688 population controls; yielding combined p values of 0.0007, 0.0013, and 0.0001 for SZ, BP, and SZ/BP, respectively. The risk allele T of 1:g.98515539A>T reduced enhancer activity of its flanking sequence by >50% in human neuroblastoma cells, predicting lower expression of MIR137/MIR2682. Both empirical and computational analyses showed weaker transcription factor (YY1) binding by the risk allele. Chromatin conformation capture (3C) assay further indicated that 1:g.98515539A>T influenced MIR137/MIR2682, but not the nearby DPYD or LOC729987. Our results suggest that rare noncoding risk variants are associated with SZ and BP at MIR137/MIR2682 locus, with risk alleles decreasing MIR137/MIR2682 expression.


Bipolar Disorder/genetics , Gene Expression Regulation/genetics , Genetic Variation , MicroRNAs/genetics , Schizophrenia/genetics , Alleles , Base Sequence , Cell Line, Tumor , Gene Frequency , Genes, Reporter , Genetic Loci , Genetic Predisposition to Disease , Genome-Wide Association Study , Humans , Molecular Sequence Data , Polymorphism, Single Nucleotide , Promoter Regions, Genetic/genetics , Risk , Sequence Analysis, DNA
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