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1.
BMC Ophthalmol ; 20(1): 487, 2020 Dec 11.
Artigo em Inglês | MEDLINE | ID: mdl-33308182

RESUMO

BACKGROUND: Choroidal ganglioneuroma is an extremely rare tumor, and there is little knowledge regarding its pathogenesis. We aimed to investigate the phenotypic and genetic alterations in one sporadic patient with a rare case of bilateral choroidal ganglioneuroma. METHODS: A 6-year-old boy with histological diagnosis of bilateral ganglioneuroma was recruited for the study. Comprehensive ophthalmic examinations were performed. Genomic DNA was extracted from the peripheral blood samples collected from the patient, his unaffected family members, and 200 unrelated control subjects from the same population. Whole exome sequencing was performed and raw reads were aligned to the human genome reference (hg19) using Burrows-Wheeler Aligner. DNA from all available family members was Sanger sequenced for segregation analysis. RESULTS: Extensive bilateral retinal detachments were observed via optical coherence tomography. Diffuse thickening of choroid was identified with ultrasound B scan and magnetic resonance imaging. Genetic analysis revealed the presence of a novel heterozygous PTEN frameshift mutation, c.498delA (p.Thr167LeufsTer16), in exon 6. It was present in the affected individual, but not in any of the family members. Genetic analysis revealed that there was no mutation in neurofibromatosis-related genes in the family. Upon performing comprehensive systemic examinations, no obvious abnormalities in other organs were observed. CONCLUSIONS: A novel de novo PTEN mutation was identified in a patient with bilateral choroidal ganglioneuroma. Although PTEN mutations are known to induce multiple abnormalities, choroidal ganglioneuroma can be the first manifestation without abnormalities in other organs. Further studies are needed to confirm the association between choroidal ganglioneuroma and PTEN mutation.


Assuntos
Neoplasias da Coroide/genética , Mutação da Fase de Leitura/genética , Ganglioneuroma/genética , PTEN Fosfo-Hidrolase/genética , Adulto , Criança , Neoplasias da Coroide/diagnóstico por imagem , Neoplasias da Coroide/patologia , Análise Mutacional de DNA , DNA de Neoplasias/genética , Feminino , Ganglioneuroma/diagnóstico por imagem , Ganglioneuroma/patologia , Humanos , Imagem por Ressonância Magnética , Masculino , Pessoa de Meia-Idade , Linhagem , Descolamento Retiniano/diagnóstico por imagem , Tomografia de Coerência Óptica , Sequenciamento Completo do Genoma
2.
Sci Rep ; 10(1): 19986, 2020 11 17.
Artigo em Inglês | MEDLINE | ID: mdl-33203948

RESUMO

Nanophthalmos is a rare condition defined by a small, structurally normal eye with resultant high hyperopia. While six genes have been implicated in this hereditary condition (MFRP, PRSS56, MYRF, TMEM98, CRB1,VMD2/BEST1), the relative contribution of these to nanophthalmos or to less severe high hyperopia (≥ + 5.50 spherical equivalent) has not been fully elucidated. We collected probands and families (n = 56) with high hyperopia or nanophthalmos (≤ 21.0 mm axial length). Of 53 families that passed quality control, plausible genetic diagnoses were identified in 10/53 (18.8%) by high-throughput panel or pooled exome sequencing. These include 1 TMEM98 family (1.9%), 5 MFRP families (9.4%), and 4 PRSS56 families (7.5%), with 4 additional families having single allelic hits in MFRP or PRSS56 (7.5%). A novel deleterious TMEM98 variant (NM_015544.3, c.602G>C, p.(Arg201Pro)) segregated with disease in 4 affected members of a family. Multiple novel missense and frameshift variants in MFRP and PRSS56 were identified. PRSS56 families were more likely to have choroidal folds than other solved families, while MFRP families were more likely to have retinal degeneration. Together, this study defines the prevalence of nanophthalmos gene variants in high hyperopia and nanophthalmos and indicates that a large fraction of cases remain outside of single gene coding sequences.


Assuntos
Oftalmopatias Hereditárias/genética , Mutação da Fase de Leitura/genética , Hiperopia/genética , Proteínas de Membrana/genética , Microftalmia/genética , Mutação de Sentido Incorreto/genética , Serina Proteases/genética , Alelos , Estudos de Coortes , Olho/metabolismo , Feminino , Humanos , Masculino , Linhagem , Estados Unidos
3.
Nat Commun ; 11(1): 3800, 2020 07 30.
Artigo em Inglês | MEDLINE | ID: mdl-32733040

RESUMO

Frameshift insertion/deletions (fs-indels) are an infrequent but highly immunogenic mutation subtype. Although fs-indels are degraded through the nonsense-mediated decay (NMD) pathway, we hypothesise that some fs-indels escape degradation and elicit anti-tumor immune responses. Using allele-specific expression analysis, expressed fs-indels are enriched in genomic positions predicted to escape NMD, and associated with higher protein expression, consistent with degradation escape (NMD-escape). Across four independent melanoma cohorts, NMD-escape mutations are significantly associated with clinical-benefit to checkpoint inhibitor (CPI) therapy (Pmeta = 0.0039). NMD-escape mutations are additionally found to associate with clinical-benefit in the low-TMB setting. Furthermore, in an adoptive cell therapy treated melanoma cohort, NMD-escape mutation count is the most significant biomarker associated with clinical-benefit. Analysis of functional T cell reactivity screens from personalized vaccine studies shows direct evidence of fs-indel derived neoantigens eliciting immune response, particularly those with highly elongated neo open reading frames. NMD-escape fs-indels represent an attractive target for biomarker optimisation and immunotherapy design.


Assuntos
Melanoma/genética , Melanoma/imunologia , Degradação do RNAm Mediada por Códon sem Sentido/genética , Linfócitos T/imunologia , Evasão Tumoral/genética , Transferência Adotiva , Antígenos de Neoplasias/imunologia , Biomarcadores Tumorais/genética , Mutação da Fase de Leitura/genética , Humanos , Mutação INDEL/genética , Imunoterapia Adotiva , Linfócitos T/transplante , Sequenciamento Completo do Exoma
4.
Neuron ; 108(1): 111-127.e6, 2020 10 14.
Artigo em Inglês | MEDLINE | ID: mdl-32795398

RESUMO

Cajal recognized that the elaborate shape of neurons is fundamental to their function in the brain. However, there are no simple and generalizable genetic methods to study neuronal or glial cell morphology in the mammalian brain. Here, we describe four mouse lines conferring Cre-dependent sparse cell labeling based on mononucleotide repeat frameshift (MORF) as a stochastic translational switch. Notably, the optimized MORF3 mice, with a membrane-bound multivalent immunoreporter, confer Cre-dependent sparse and bright labeling of thousands of neurons, astrocytes, or microglia in each brain, revealing their intricate morphologies. MORF3 mice are compatible with imaging in tissue-cleared thick brain sections and with immuno-EM. An analysis of 151 MORF3-labeled developing retinal horizontal cells reveals novel morphological cell clusters and axonal maturation patterns. Our study demonstrates a conceptually novel, simple, generalizable, and scalable mouse genetic solution to sparsely label and illuminate the morphology of genetically defined neurons and glia in the mammalian brain.


Assuntos
Astrócitos/ultraestrutura , Encéfalo/ultraestrutura , Microglia/ultraestrutura , Neurônios/ultraestrutura , Células Horizontais da Retina/ultraestrutura , Animais , Astrócitos/metabolismo , Astrócitos/patologia , Encéfalo/metabolismo , Encéfalo/patologia , Mutação da Fase de Leitura/genética , Proteínas de Fluorescência Verde/genética , Integrases , Camundongos , Camundongos Transgênicos , Microglia/metabolismo , Microglia/patologia , Repetições de Microssatélites/genética , Neurônios/metabolismo , Neurônios/patologia , Células Horizontais da Retina/metabolismo , Células Horizontais da Retina/patologia
5.
Sci Rep ; 10(1): 13757, 2020 08 13.
Artigo em Inglês | MEDLINE | ID: mdl-32792587

RESUMO

Nighttime surges in melatonin levels activate melatonin receptors, which synchronize cellular activities with the natural light/dark cycle. Melatonin receptors are expressed in several cell types in the retina, including the photon-sensitive rods and cones. Previous studies suggest that long-term photoreceptor survival and retinal health is in part reliant on melatonin orchestration of circadian homeostatic activities. This scenario would accordingly envisage that disruption of melatonin receptor signaling is detrimental to photoreceptor health. Using in vivo CRISPR/Cas9 genomic editing, we discovered that a small deletion mutation of the Mel1a melatonin receptor (mtnr1a) gene causes a loss of rod photoreceptors in retinas of developing Xenopus tropicalis heterozygous, but not homozygous mutant tadpoles. Cones were relatively spared from degeneration, and the rod loss phenotype was not obvious after metamorphosis. Localization of Mel1a receptor protein appeared to be about the same in wild type and mutant retinas, suggesting that the mutant protein is expressed at some level in mutant retinal cells. The severe impact on early rod photoreceptor viability may signify a previously underestimated critical role in circadian influences on long-term retinal health and preservation of sight. These data offer evidence that disturbance of homeostatic, circadian signaling, conveyed through a mutated melatonin receptor, is incompatible with rod photoreceptor survival.


Assuntos
Receptores de Melatonina/genética , Degeneração Retiniana/genética , Células Fotorreceptoras Retinianas Bastonetes/patologia , Proteínas de Xenopus/genética , Xenopus/genética , Sequência de Aminoácidos , Animais , Animais Geneticamente Modificados , Sistemas CRISPR-Cas , Ritmo Circadiano/genética , Mutação da Fase de Leitura/genética , Melatonina/metabolismo , Células Fotorreceptoras Retinianas Cones/patologia , Deleção de Sequência/genética , Transdução de Sinais/genética
6.
Proc Natl Acad Sci U S A ; 117(29): 17151-17155, 2020 07 21.
Artigo em Inglês | MEDLINE | ID: mdl-32636268

RESUMO

Inherited bone marrow failure (BMF) syndromes are a heterogeneous group of diseases characterized by defective hematopoiesis and often predisposing to myelodysplastic syndrome (MDS) and acute myelogenous leukemia. We have studied a large family consisting of several affected individuals with hematologic abnormalities, including one family member who died of acute leukemia. By whole-exome sequencing, we identified a novel frameshift variant in the ubiquitously expressed transcription factor specificity protein 1 (SP1). This heterozygous variant (c.1995delA) truncates the canonical Sp1 molecule in the highly conserved C-terminal DNA-binding zinc finger domains. Transcriptomic analysis and gene promoter characterization in patients' blood revealed a hypermorphic effect of this Sp1 variant, triggering superactivation of Sp1-mediated transcription and driving significant up-regulation of Sp1 target genes. This familial genetic study indicates a central role for Sp1 in causing autosomal dominant transmission of BMF, thereby confirming its critical role in hematopoiesis in humans.


Assuntos
Transtornos da Insuficiência da Medula Óssea/genética , Mutação da Fase de Leitura/genética , Fator de Transcrição Sp1/genética , Transcrição Genética/genética , Feminino , Humanos , Masculino , Linhagem , Transcriptoma/genética , Regulação para Cima/genética , Dedos de Zinco/genética
7.
Nat Med ; 26(9): 1444-1451, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32719489

RESUMO

CLN3 Batten disease is an autosomal recessive, neurodegenerative, lysosomal storage disease caused by mutations in CLN3, which encodes a lysosomal membrane protein1-3. There are no disease-modifying treatments for this disease that affects up to 1 in 25,000 births, has an onset of symptoms in early childhood and typically is fatal by 20-30 years of life4-7. Most patients with CLN3 Batten have a deletion encompassing exons 7 and 8 (CLN3∆ex7/8), creating a reading frameshift7,8. Here we demonstrate that mice with this deletion can be effectively treated using an antisense oligonucleotide (ASO) that induces exon skipping to restore the open reading frame. A single treatment of neonatal mice with an exon 5-targeted ASO-induced robust exon skipping for more than a year, improved motor coordination, reduced histopathology in Cln3∆ex7/8 mice and increased survival in a new mouse model of the disease. ASOs also induced exon skipping in cell lines derived from patients with CLN3 Batten disease. Our findings demonstrate the utility of ASO-based reading-frame correction as an approach to treat CLN3 Batten disease and broaden the therapeutic landscape for ASOs in the treatment of other diseases using a similar strategy.


Assuntos
Glicoproteínas de Membrana/genética , Chaperonas Moleculares/genética , Lipofuscinoses Ceroides Neuronais/tratamento farmacológico , Lipofuscinoses Ceroides Neuronais/genética , Oligonucleotídeos Antissenso/uso terapêutico , Animais , Linhagem Celular , Códon sem Sentido/genética , Modelos Animais de Doenças , Mutação da Fase de Leitura/genética , Humanos , Camundongos
8.
Hum Genet ; 139(12): 1565-1574, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-32562050

RESUMO

COCH is the most abundantly expressed gene in the cochlea. Unsurprisingly, mutations in COCH underly hearing loss in mice and humans. Two forms of hearing loss are linked to mutations in COCH, the well-established autosomal dominant nonsyndromic hearing loss, with or without vestibular dysfunction (DFNA9) via a gain-of-function/dominant-negative mechanism, and more recently autosomal recessive nonsyndromic hearing loss (DFNB110) via nonsense variants. Using a combination of targeted gene panels, exome sequencing, and functional studies, we identified four novel pathogenic variants (two nonsense variants, one missense, and one inframe deletion) in COCH as the cause of autosomal recessive hearing loss in a multi-ethnic cohort. To investigate whether the non-truncating variants exert their effect via a loss-of-function mechanism, we used minigene splicing assays. Our data showed both the missense and inframe deletion variants altered RNA splicing by creating an exon splicing silencer and abolishing an exon splicing enhancer, respectively. Both variants create frameshifts and are predicted to result in a null allele. This study confirms the involvement of loss-of-function mutations in COCH in autosomal recessive nonsyndromic hearing loss, expands the mutational landscape of DFNB110 to include coding variants that alter RNA splicing, and highlights the need to investigate the effect of coding variants on RNA splicing.


Assuntos
Surdez/genética , Proteínas da Matriz Extracelular/genética , Genes Recessivos/genética , Mutação com Perda de Função/genética , Adolescente , Adulto , Criança , Pré-Escolar , Cóclea/metabolismo , Cóclea/patologia , Códon sem Sentido/genética , Surdez/patologia , Éxons/genética , Feminino , Mutação da Fase de Leitura/genética , Humanos , Masculino , Linhagem
9.
Cell Prolif ; 53(5): e12820, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32350961

RESUMO

OBJECTIVES: Recently developed CRISPR-dependent cytosine base editor (CBE), converting four codons (CAA, CAG, CGA and TGG) into stop codons without DNA double-strand breaks (DSB), serves as an efficient gene disruption strategy besides uncontrollable CRISPR-mediated frameshift. However, the detailed difference of gene knockout between the two systems has not been clarified. MATERIALS AND METHODS: Here, we selected some sgRNAs with different position background, then HEK293T cells were transfected with CBE/Cas9 plasmids together with sgRNAs. GFP-positive cells were harvested by fluorescence-activated cell sorting (FACS) 48 hours after transfection. Genomic DNA was collected for deep sequencing to analyse editing efficiency and genotype. RNA and protein were extracted to analyse gene mRNA level using qPCR analysis and Western blot. RESULTS: Here, we compared the gene disruption by CBE-mediated iSTOP with CRISPR/Cas9-mediated frameshift. We found BE-mediated gene knockout yielded fewer genotypes. BE-mediated gene editing precisely achieved silencing of two neighbouring genes, while CRISPR/Cas9 may delete the large fragment between two target sites. All of three stop codons could efficiently disrupt the target genes. It is worth notifying, Cas9-mediated gene knockout showed a more impact on neighbouring genes mRNA level than the BE editor. CONCLUSIONS: Our results reveal the differences between the two gene knockout strategies and provide useful information for choosing the appropriate gene disruption strategy.


Assuntos
Sistemas CRISPR-Cas/genética , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas/genética , Citosina/metabolismo , Mutação da Fase de Leitura/genética , Sequência de Bases , Linhagem Celular , Edição de Genes/métodos , Genótipo , Células HEK293 , Humanos , Plasmídeos/genética , RNA Mensageiro/genética , Transfecção/métodos
10.
BMC Med Genet ; 21(1): 100, 2020 05 11.
Artigo em Inglês | MEDLINE | ID: mdl-32393339

RESUMO

BACKGROUND: Neuronal ceroid lipofuscinosis type 5 (CLN5) is a rare form of neuronal ceroid lipofuscinoses (NCLs) which are a group of inherited neurodegenerative diseases characterized by progressive intellectual and motor deterioration, visual failure, seizures, behavioral changes and premature death. CLN5 was initially named Finnish variant late infantile NCL, it is now known to be present in other ethnic populations and with variable age of onset. Few CLN5 patients had been reported in Chinese population. CASE PRESENTATION: In this paper, we report the symptoms of a Chinese patient who suffer from developmental regression and grand mal epilepsy for several years. The DNA was extracted from peripheral blood of proband and both parents, and then whole exome sequencing was performed using genomic DNA. Both sequence variants and copy number variants (CNVs) were analyzed and classified according to guidelines. As the result, a novel frameshift mutation c.718_719delAT/p.Met240fs in CLN5 and a de novo large deletion at 13q21.33-q31.1 which unmasked the frameshift mutation were identified in the proband. Despite the large de novo deletion, which can be classified as a pathogenic copy number variant (CNV), the patient's clinical presentation is mostly consistent with that of CLN5, except for early developmental delay which is believed due to the large deletion. Both variants were detected simultaneously by exome sequencing. CONCLUSIONS: This is the first report of whole gene deletion in combination with a novel pathogenic sequence variant in a CLN5 patient. The two mutations detected with whole exome sequencing simultaneously proved the advantage of the sequencing technology for genetic diagnostics.


Assuntos
Variações do Número de Cópias de DNA/genética , Glicoproteínas de Membrana Associadas ao Lisossomo/genética , Lipofuscinoses Ceroides Neuronais/genética , Sequenciamento Completo do Exoma , Criança , Pré-Escolar , Feminino , Mutação da Fase de Leitura/genética , Deleção de Genes , Homozigoto , Humanos , Lactente , Masculino , Proteínas de Membrana/genética , Lipofuscinoses Ceroides Neuronais/patologia
11.
BMC Neurol ; 20(1): 207, 2020 May 25.
Artigo em Inglês | MEDLINE | ID: mdl-32450808

RESUMO

BACKGROUND: Homozygous frameshift mutation in RUBCN (KIAA0226), known to result in endolysosomal machinery defects, has previously been reported in a single Saudi family with autosomal recessive spinocerebellar ataxia (Salih ataxia, SCAR15, OMIM # 615705). The present report describes the clinical, neurophysiologic, neuroimaging, and genetic findings in a second unrelated Saudi family with two affected children harboring identical homozygous frameshift mutation in the gene. It also explores and documents an ancient founder cerebellar ataxia mutation in the Arabian Peninsula. CASE PRESENTATION: The present family has two affected males (aged 6.5 and 17 years) with unsteady gait apparent since learning to walk at 2.5 and 3 years, respectively. The younger patient showed gait ataxia and normal reflexes. The older patient had saccadic eye movement, dysarthria, mild upper and lower limb and gait ataxia (on tandem walking), and enhanced reflexes in the lower limbs. Cognitive abilities were mildly impaired in the younger sibling (IQ 67) and borderline in the older patient (IQ 72). Nerve conduction studies were normal in both patients. MRI was normal at 2.5 years in the younger sibling. Brain MRI showed normal cerebellar volume and folia in the older sibling at the age of 6 years, and revealed minimal superior vermian atrophy at the age of 16 years. Autozygome and exome analysis showed both affected have previously reported homoallelic mutation in RUBCN (NM_014687:exon18:c.2624delC:p.A875fs), whereas the parents are carriers. Autozygosity mapping focused on smallest haplotype on chromosome 3 and mutation age analysis revealed the mutation occurred approximately 1550 years ago spanning about 62 generations. CONCLUSIONS: Our findings validate the slowly progressive phenotype of Salih ataxia (SCAR15, OMIM # 615705) by an additional family. Haplotype sharing attests to a common founder, an ancient RUBCN mutation in the Arab population.


Assuntos
Proteínas Relacionadas à Autofagia/genética , Mutação da Fase de Leitura/genética , Ataxias Espinocerebelares , Adolescente , Cerebelo/diagnóstico por imagem , Criança , Disfunção Cognitiva , Marcha Atáxica , Humanos , Imagem por Ressonância Magnética , Masculino , Ataxias Espinocerebelares/diagnóstico , Ataxias Espinocerebelares/genética
12.
Genome ; 63(6): 291-305, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32406757

RESUMO

Biological conclusions based on DNA barcoding and metabarcoding analyses can be strongly influenced by the methods utilized for data generation and curation, leading to varying levels of success in the separation of biological variation from experimental error. The 5' region of cytochrome c oxidase subunit I (COI-5P) is the most common barcode gene for animals, with conserved structure and function that allows for biologically informed error identification. Here, we present coil ( https://CRAN.R-project.org/package=coil ), an R package for the pre-processing and frameshift error assessment of COI-5P animal barcode and metabarcode sequence data. The package contains functions for placement of barcodes into a common reading frame, accurate translation of sequences to amino acids, and highlighting insertion and deletion errors. The analysis of 10 000 barcode sequences of varying quality demonstrated how coil can place barcode sequences in reading frame and distinguish sequences containing indel errors from error-free sequences with greater than 97.5% accuracy. Package limitations were tested through the analysis of COI-5P sequences from the plant and fungal kingdoms as well as the analysis of potential contaminants: nuclear mitochondrial pseudogenes and Wolbachia COI-5P sequences. Results demonstrated that coil is a strong technical error identification method but is not reliable for detecting all biological contaminants.


Assuntos
Código de Barras de DNA Taxonômico/métodos , Complexo IV da Cadeia de Transporte de Elétrons/genética , Filogenia , Pseudogenes/genética , Animais , DNA Mitocondrial/genética , Mutação da Fase de Leitura/genética , Humanos
13.
BMC Med Genet ; 21(1): 77, 2020 04 15.
Artigo em Inglês | MEDLINE | ID: mdl-32293312

RESUMO

BACKGROUND: Myopathy with extrapyramidal signs (MPXPS) is an autosomal recessive mitochondrial disorder which is caused by mutation in mitochondrial calcium uptake 1 (MICU1) gene located on chromosome 10q22.1. Next Generation Sequencing (NGS) technology is the most effective method for identification of pathogenic variants with the ability to overcome some limitations which Sanger sequencing may encountered. There are few reports on this rare disease around the world and here in this study we first revealed genetic identification of two affected individuals in an Iranian family with a novel mutation. CASE PRESENTATION: The proband was a 5-year-old girl from consanguenous parents. She was first clinically suspicious of affected with limb-girdle muscular dystrophy (LGMD). Muscle biopsy studies and autozygosity mapping, using four short tandem repeat (STR) markers linked to 6 genes of the most prevalent forms of LGMD, ruled out calpainopathy, dysferlinopathy, and sarcoglycanopathis. DNA sample of the proband was sent for NGS. Whole exome sequencing (WES) revealed a novel mutation c.1295delA in exon 13 of MICU1 gene. This homozygous deletion creates a frameshift and a premature stop codon downstream of canonical EF4 calcium binding motif of MICU1. According to the American College of Medical Genetics and Genomics (ACMG) guidline for sequence interpretation, this variant was a pathogenic one. Sanger sequencing in all family members confirmed the results of the WES. CONCLUSIONS: This study was the first report of MPXPS in Iranian population which also revealed a novel mutation in the MICU1 gene.


Assuntos
Proteínas de Ligação ao Cálcio/genética , Proteínas de Transporte de Cátions/genética , Repetições de Microssatélites/genética , Proteínas de Transporte da Membrana Mitocondrial/genética , Doenças Musculares/genética , Distrofia Muscular do Cíngulo dos Membros/genética , Pré-Escolar , Exoma/genética , Éxons/genética , Tratos Extrapiramidais/metabolismo , Tratos Extrapiramidais/patologia , Feminino , Mutação da Fase de Leitura/genética , Sequenciamento de Nucleotídeos em Larga Escala , Homozigoto , Humanos , Irã (Geográfico)/epidemiologia , Doenças Musculares/patologia , Distrofia Muscular do Cíngulo dos Membros/patologia , Linhagem , Deleção de Sequência/genética , Sequenciamento Completo do Exoma
14.
Mol Genet Genomics ; 295(4): 923-931, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32246227

RESUMO

Amelogenesis imperfecta type IG (AI1G) is caused by mutations in FAM20A. Genotypic and phenotypic features of AI1G are diverse and their full spectra remain to be characterized. The aim of this study was to identify and summarize variants in FAM20A in a broad population of patients with AI1G. We identified a Thai female (Pt-1) and a Saudi male (Pt-2) affected with AI1G. Both had hypoplastic enamel, gingival hyperplasia, and intrapulpal calcification. Pt-1 also had rapidly progressive embedding of unerupted teeth, early eruption of permanent teeth, and spontaneous dental infection. Uniquely, Pt-2 had all permanent teeth erupted which was uncommon in AI1G patients. Whole exome sequencing (WES) identified that Pt-1 was heterozygous for FAM20A, c.758A > G (p.Tyr253Cys), inherited from her father. The mutation on maternal allele was not detected by WES. Pt-2 possessed compound heterozygous mutations, c.1248dupG (p.Phe417Valfs*7); c.1081C > T (p.Arg361Cys) in FAM20A. Array comparative genomic hybridization (aCGH), cDNA sequencing, and whole genome sequencing successfully identified 7531 bp deletion on Pt-1's maternal allele. This was the largest FAM20A deletion ever found. A review of all 70 patients from 50 independent families with AI1G (including two families in this study) showed that the penetrance of hypoplastic enamel and gingival hyperplasia was complete. Unerupted permanent teeth were found in all 70 patients except Pt-2. Exons 1 and 11 were mutation-prone. Most mutations were frameshift. Certain variants showed founder effect. To conclude, this study reviews and expands phenotypic and genotypic spectra of AI1G. A large deletion missed by WES can be detected by WGS. Hypoplastic enamel, gingival hyperplasia, and unerupted permanent teeth prompt genetic testing of FAM20A. Screening of nephrocalcinosis, early removal of embedded teeth, and monitoring of dental infection are recommended.


Assuntos
Amelogênese Imperfeita/genética , Proteínas do Esmalte Dentário/genética , Nefrocalcinose/genética , Deleção de Sequência/genética , Adolescente , Adulto , Amelogênese Imperfeita/patologia , Criança , Hibridização Genômica Comparativa , Éxons/genética , Feminino , Mutação da Fase de Leitura/genética , Genótipo , Heterozigoto , Homozigoto , Humanos , Masculino , Mutação/genética , Nefrocalcinose/patologia , Linhagem , Fenótipo
15.
Am J Med Genet A ; 182(5): 1278-1283, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32150337

RESUMO

Waardenburg syndrome (WS) is a group of genetic disorders associated with varying components of sensorineural hearing loss and abnormal pigmentation of the hair, skin, and eyes. There exist four different WS subtypes, each defined by the absence or presence of additional features. One of the genes associated with WS is SOX10, a key transcription factor for the development of neural crest-derived lineages. Here we report a 12-year-old boy with a novel de novo SOX10 frameshift mutation and unique combination of clinical features including primary peripheral demyelinating neuropathy, hearing loss and visual impairment but absence of Hirschsprung disease and the typical pigmentary changes of hair or skin. This expands the spectrum of currently recognized phenotypes associated with WS and illustrates the phenotypic heterogeneity of SOX10-associated WS.


Assuntos
Predisposição Genética para Doença , Doença de Hirschsprung/genética , Fatores de Transcrição SOXE/genética , Síndrome de Waardenburg/genética , Doenças Autoimunes do Sistema Nervoso/genética , Doenças Autoimunes do Sistema Nervoso/fisiopatologia , Criança , Doenças Desmielinizantes/genética , Doenças Desmielinizantes/fisiopatologia , Mutação da Fase de Leitura/genética , Doença de Hirschsprung/fisiopatologia , Humanos , Masculino , Linhagem , Fenótipo , Síndrome de Waardenburg/fisiopatologia
16.
Am J Hum Genet ; 106(4): 438-452, 2020 04 02.
Artigo em Inglês | MEDLINE | ID: mdl-32197073

RESUMO

The neuro-oncological ventral antigen 2 (NOVA2) protein is a major factor regulating neuron-specific alternative splicing (AS), previously associated with an acquired neurologic condition, the paraneoplastic opsoclonus-myoclonus ataxia (POMA). We report here six individuals with de novo frameshift variants in NOVA2 affected with a severe neurodevelopmental disorder characterized by intellectual disability (ID), motor and speech delay, autistic features, hypotonia, feeding difficulties, spasticity or ataxic gait, and abnormal brain MRI. The six variants lead to the same reading frame, adding a common proline rich C-terminal part instead of the last KH RNA binding domain. We detected 41 genes differentially spliced after NOVA2 downregulation in human neural cells. The NOVA2 variant protein shows decreased ability to bind target RNA sequences and to regulate target AS events. It also fails to complement the effect on neurite outgrowth induced by NOVA2 downregulation in vitro and to rescue alterations of retinotectal axonal pathfinding induced by loss of NOVA2 ortholog in zebrafish. Our results suggest a partial loss-of-function mechanism rather than a full heterozygous loss-of-function, although a specific contribution of the novel C-terminal extension cannot be excluded.


Assuntos
Mutação da Fase de Leitura/genética , Proteínas do Tecido Nervoso/genética , Transtornos do Neurodesenvolvimento/genética , Neurônios/fisiologia , Processamento de RNA/genética , Proteínas de Ligação a RNA/genética , Processamento Alternativo/genética , Animais , Orientação de Axônios/genética , Sequência de Bases/genética , Células Cultivadas , Pré-Escolar , Regulação para Baixo/genética , Feminino , Heterozigoto , Humanos , Deficiência Intelectual/genética , Transtornos do Desenvolvimento da Linguagem/genética , Masculino , Camundongos , Hipotonia Muscular/genética , Peixe-Zebra/genética
17.
J Assist Reprod Genet ; 37(4): 811-820, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32170493

RESUMO

PURPOSE: To identify the genetic cause of patients with primary ciliary dyskinesia (PCD) and male infertility from two unrelated Han Chinese families. METHODS: We conducted whole-exome sequencing of three individuals with PCD and male infertility from two unrelated Chinese families, and performed a targeted look-up for DNAAF6 variants in our previously reported cohort of 442 individuals (219 with isolated oligoasthenospermia and 223 fertile controls). Ultrastructural and immunostaining analyses of patients' spermatozoa were performed. The pathogenicity of the variants was validated using patient's spermatozoa and HEK293T cells. Intracytoplasmic sperm injection (ICSI) treatment was conducted in two patients. RESULTS: We identified one novel hemizygous frameshift variant (NM_173494, c.319_329del: p.R107fs) of DNAAF6 gene (previously named PIH1D3) in family 1 and one novel hemizygous missense variant (c.290G>T: p.G97V) in family 2. No hemizygous deleterious variants in DNAAF6 were detected in the control cohort of 442 individuals. Ultrastructural and immunostaining analyses of patients' spermatozoa showed the absence of outer and inner dynein arms in sperm flagella. Both variants were proven to lead to DNAAF6 protein degradation in HEK293T cells. Both patients carrying DNAAF6 variants underwent one ICSI cycle and delivered one healthy child each. CONCLUSION: We identified novel DNAAF6 variants causing male infertility and PCD in Han Chinese patients. This finding extended the spectrum of variants in DNAAF6 and revealed new light on the impact of DNAAF6 variants in sperm flagella.


Assuntos
Transtornos da Motilidade Ciliar/genética , Infertilidade Masculina/genética , Peptídeos e Proteínas de Sinalização Intracelular/genética , Sequenciamento Completo do Exoma , Adulto , Axonema/genética , Axonema/patologia , Transtornos da Motilidade Ciliar/patologia , Exoma/genética , Feminino , Flagelos/genética , Mutação da Fase de Leitura/genética , Células HEK293 , Hemizigoto , Humanos , Infertilidade Masculina/patologia , Masculino , Injeções de Esperma Intracitoplásmicas/métodos , Cauda do Espermatozoide/metabolismo , Cauda do Espermatozoide/patologia , Espermatozoides/patologia
18.
PLoS Genet ; 16(3): e1008659, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32150541

RESUMO

Retinitis pigmentosa (RP) is the leading cause of blindness with nearly two million people affected worldwide. Many genes have been implicated in RP, yet in 30-80% of the RP patients the genetic cause remains unknown. A similar phenotype, progressive retinal atrophy (PRA), affects many dog breeds including the Miniature Schnauzer. We performed clinical, genetic and functional experiments to identify the genetic cause of PRA in the breed. The age of onset and pattern of disease progression suggested that at least two forms of PRA, types 1 and 2 respectively, affect the breed, which was confirmed by genome-wide association study that implicated two distinct genomic loci in chromosomes 15 and X, respectively. Whole-genome sequencing revealed a fully segregating recessive regulatory variant in type 1 PRA. The associated variant has a very recent origin based on haplotype analysis and lies within a regulatory site with the predicted binding site of HAND1::TCF3 transcription factor complex. Luciferase assays suggested that mutated regulatory sequence increases expression. Case-control retinal expression comparison of six best HAND1::TCF3 target genes were analyzed with quantitative reverse-transcriptase PCR assay and indicated overexpression of EDN2 and COL9A2 in the affected retina. Defects in both EDN2 and COL9A2 have been previously associated with retinal degeneration. In summary, our study describes two genetically different forms of PRA and identifies a fully penetrant variant in type 1 form with a possible regulatory effect. This would be among the first reports of a regulatory variant in retinal degeneration in any species, and establishes a new spontaneous dog model to improve our understanding of retinal biology and gene regulation while the affected breed will benefit from a reliable genetic testing.


Assuntos
Doenças do Cão/genética , Degeneração Retiniana/genética , Retinite Pigmentosa/genética , Animais , Estudos de Casos e Controles , Colágeno Tipo IX/genética , Colágeno Tipo IX/metabolismo , Cães , Endotelina-2/genética , Endotelina-2/metabolismo , Feminino , Mutação da Fase de Leitura/genética , Estudo de Associação Genômica Ampla/métodos , Haplótipos/genética , Masculino , Modelos Animais , Mutação/genética , Linhagem , Fenótipo , Retina/metabolismo , Retinite Pigmentosa/metabolismo
19.
Gene ; 738: 144371, 2020 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-32001375

RESUMO

MCTPs (multiple C2 domain proteins with two transmembrane regions) have been proposed as novel endoplasmic reticulum calcium sensors; however, their function remains largely unknown. Here we report the structure of the four mctp genes from zebrafish (mctp1a, mctp1b, mctp2a and mctp2b), their diversity, expression pattern during embryonic development and in adult tissue and the effect of knocking down the expression of Mctp2b by CRISPR/Cas9. The four mctp genes are expressed from early development and exhibit differential expression patterns but are found mainly in the nervous and muscular systems. Mctp2b tagged with fluorescent proteins and expressed in HEK-293 cells and neurons of the fish spinal cord localized mostly in the endoplasmic reticulum but also in lysosomes and late and recycling endosomes. Knocking down mctp2b expression impaired embryonic development, suggesting that the functional participation of this gene is relevant, at least during the early stages of development.


Assuntos
Proteínas de Membrana/metabolismo , Alelos , Animais , Sistemas CRISPR-Cas , Cálcio/metabolismo , Desenvolvimento Embrionário/genética , Retículo Endoplasmático/metabolismo , Mutação da Fase de Leitura/genética , Regulação da Expressão Gênica no Desenvolvimento/genética , Células HEK293 , Humanos , Proteínas de Membrana/genética , Receptores de Detecção de Cálcio/genética , Peixe-Zebra/genética , Proteínas de Peixe-Zebra/genética
20.
BMC Med Genet ; 21(1): 42, 2020 02 27.
Artigo em Inglês | MEDLINE | ID: mdl-32106822

RESUMO

BACKGROUND: von Hippel-Lindau (VHL) disease is a familial neoplasia syndrome that results from the germline mutation of VHL. Pathogenic VHL mutations include deletion, frameshift, nonsense and missense mutations. Synonymous mutations are expected to be phenotypically silent and their role in VHL disease remains poorly understood. CASE PRESENTATION: We report a Caucasian male with a family history of pheochromocytoma and the synonymous VHL mutation c.414A > G (p.Pro138Pro). At 47-years, MRI revealed pheochromocytoma in the left adrenal gland and hemangioblastomas in the spine and brain. Pheochromocytoma was treated by adrenalectomy. Radiotherapy, followed by craniotomy and resection were needed to reduce hemangioblastomas to residual lesions. Two of three of the proband's children inherited the mutation and both presented with retinal hemangioblastomas without pheochromocytoma at age 7: one twin needed four laser treatments. Primary skin fibroblasts carrying the heterozygous mutation or wild type VHL were established from the family. Mutant fibroblasts downregulated full-length VHL mRNA and protein, and upregulated the short VHL mRNA isoform (a result of exon 2 skipping in splicing) at the mRNA level but not at the protein level. CONCLUSIONS: Our study shows that the synonymous VHL mutation c.414A > G can within 7 years induce pediatric retinal hemangioblastoma in absence of pheochromocytoma. This highlights the need to include splicing-altering synonymous mutations into the screening for VHL disease. This is also the first report on detecting and validating a synonymous VHL mutation using patient-derived fibroblasts. The mutation c.414A > G translates to p.Pro138Pro, yet it is not functionally silent, because it causes aberrant splicing by skipping exon 2. The reduced but not completely abolished pVHL protein in a loss-of-heterozygosity genetic backdrop may underlie the etiology of VHL disease.


Assuntos
Neoplasias Cerebelares/genética , Hemangioblastoma/genética , Processamento de RNA/genética , Mutação Silenciosa , Proteína Supressora de Tumor Von Hippel-Lindau/genética , Neoplasias das Glândulas Suprarrenais/complicações , Neoplasias das Glândulas Suprarrenais/diagnóstico , Neoplasias das Glândulas Suprarrenais/genética , Neoplasias Cerebelares/complicações , Neoplasias Cerebelares/diagnóstico , Criança , Pré-Escolar , Família , Feminino , Mutação da Fase de Leitura/genética , Mutação em Linhagem Germinativa , Hemangioblastoma/complicações , Hemangioblastoma/diagnóstico , Humanos , Masculino , Pessoa de Meia-Idade , Neoplasias Primárias Múltiplas/diagnóstico , Neoplasias Primárias Múltiplas/genética , Linhagem , Feocromocitoma/complicações , Feocromocitoma/diagnóstico , Feocromocitoma/genética , Prolina/genética , Neoplasias da Retina/complicações , Neoplasias da Retina/diagnóstico , Neoplasias da Retina/genética , Neoplasias da Coluna Vertebral/complicações , Neoplasias da Coluna Vertebral/diagnóstico , Neoplasias da Coluna Vertebral/genética , Doença de von Hippel-Lindau/complicações , Doença de von Hippel-Lindau/genética
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