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1.
Nat Commun ; 11(1): 4505, 2020 09 09.
Artigo em Inglês | MEDLINE | ID: mdl-32908148

RESUMO

Evidence for transgenerational inheritance of epigenetic information in vertebrates is scarce. Aberrant patterns of DNA methylation in gametes may set the stage for transmission into future generations. Here, we describe a viable hypomorphic allele of dnmt1 in zebrafish that causes widespread demethylation of CpG dinucleotides in sperm and somatic tissues. We find that homozygous mutants are essentially normal, with the exception of drastically impaired lymphopoiesis, affecting both larval and adult phases of T cell development. The phenotype of impaired larval (but not adult) T cell development is transmitted to subsequent generations by genotypically wildtype fish. We further find that about 200 differentially methylated regions in sperm DNA of transmitting and non-transmitting males, including hypermethylated sites associated with runx3 and rptor genes, whose reduced activities are associated with impaired larval T cell development. Our results indicate a particular sensitivity of larval T cell development to transgenerationally inherited epimutations.


Assuntos
Diferenciação Celular/genética , Genes Recessivos , Larva/crescimento & desenvolvimento , Linfopoese/genética , Linfócitos T/fisiologia , Alelos , Animais , Animais Geneticamente Modificados , Subunidade alfa 3 de Fator de Ligação ao Core/genética , DNA (Citosina-5-)-Metiltransferase 1/genética , DNA (Citosina-5-)-Metiltransferase 1/metabolismo , Metilação de DNA , Epigênese Genética , Feminino , Genética , Larva/citologia , Masculino , Mutação , Proteína Regulatória Associada a mTOR/genética , Espermatozoides/metabolismo , Peixe-Zebra/genética , Proteínas de Peixe-Zebra/genética , Proteínas de Peixe-Zebra/metabolismo
2.
Rinsho Shinkeigaku ; 60(8): 543-548, 2020 Aug 07.
Artigo em Japonês | MEDLINE | ID: mdl-32641631

RESUMO

We describe an additional patient with spastic paraplegia 48 (SPG48). A 52-year-old woman with gradually increasing gait disturbance was admitted to our hospital. When she was 47 years old, acquaintances noted a shuffling gait. Gait worsening was evident at 48 years. Spastic gait was apparent at 50, and she required a walking stick at 54. Her elder brother had similar gait disturbance. No consanguinity was known. Neurologic examination at 52 disclosed spasticity and moderate weakness in the lower limbs. Spasticity and brisk reflexes in all limbs. Laboratory studies including HTLV-1 titer detected no abnormalities. MRI demonstrated mild corpus callosum narrowing and prominent anterior periventricular hyperintensities in fluid attenuation inversion recovery images. In limb muscles, electromyography (EMG) showed a chronic neurogenic pattern including reduced interference. Gene analysis identified compound homozygosity in exon 7 of adaptor-related protein complex 5 subunit zeta 1 (AP5Z1), including a novel frameshift mutation, c.1662_1672del;p.Glu554Hfs*15 in the patient, and a heterozygous missense mutation in asymptomatic family members, including her mother, two siblings, and a daughter. The frameshift mutation is considered a pathogenic variant according to American College of Medical Genetics and Genomics standards and guidelines. Based on clinical features, imaging findings and genetic abnormalities, we diagnosed this patient with SPG48. Mutations in AP5Z1, which encodes the ζ subunit of AP-5, underlie SPG48. The AP-5 adaptor protein complex, which is mutated in SPG48, binds to both spastizin and spatacsin. While hereditary spastic paraplegias generally are clinically and genetically heterogenous, SPG48, SPG11, and SPG15 are clinically similar.


Assuntos
Proteínas Adaptadoras de Transporte Vesicular/genética , Mutação da Fase de Leitura , Paraparesia Espástica/genética , Ventrículos Cerebrais/diagnóstico por imagem , Ventrículos Cerebrais/patologia , Corpo Caloso/diagnóstico por imagem , Corpo Caloso/patologia , Feminino , Transtornos Neurológicos da Marcha/etiologia , Genes Recessivos , Homozigoto , Humanos , Angiografia por Ressonância Magnética , Masculino , Pessoa de Meia-Idade , Paraparesia Espástica/complicações
3.
Hum Genet ; 139(11): 1429-1441, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32488467

RESUMO

Autozygosity-driven exome analysis has been shown effective for identification of genes underlying recessive diseases especially in countries of the so-called Greater Middle East (GME), where high consanguinity unravels the phenotypic effects of recessive alleles and large family sizes facilitate homozygosity mapping. In Italy, as in most European countries, consanguinity is estimated low. Nonetheless, consanguineous Italian families are not uncommon in publications of genetic findings and are often key to new associations of genes with rare diseases. We collected 52 patients from 47 consanguineous families with suspected recessive diseases, 29 originated in GME countries and 18 of Italian descent. We performed autozygosity-driven exome analysis by detecting long runs of homozygosity (ROHs > 1.5 Mb) and by prioritizing candidate clinical variants within. We identified a pathogenic synonymous variant that had been previously missed in NARS2 and we increased an initial high diagnostic rate (47%) to 55% by matchmaking our candidate genes and including in the analysis shorter ROHs that may also happen to be autozygous. GME and Italian families contributed to diagnostic yield comparably. We found no significant difference either in the extension of the autozygous genome, or in the distribution of candidate clinical variants between GME and Italian families, while we showed that the average autozygous genome was larger and the mean number of candidate clinical variants was significantly higher (p = 0.003) in mutation-positive than in mutation-negative individuals, suggesting that these features influence the likelihood that the disease is autozygosity-related. We highlight the utility of autozygosity-driven genomic analysis also in countries and/or communities, where consanguinity is not widespread cultural tradition.


Assuntos
Testes Genéticos/métodos , Genoma Humano/genética , Mapeamento Cromossômico/métodos , Consanguinidade , Exoma/genética , Família , Feminino , Genes Recessivos/genética , Humanos , Itália , Masculino , Oriente Médio , Mutação/genética , Linhagem
4.
PLoS Genet ; 16(5): e1008639, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32453731

RESUMO

Hypertrophic cardiomyopathy (HCM) is characterized by thickening of the ventricular muscle without dilation and is often associated with dominant pathogenic variants in cardiac sarcomeric protein genes. Here, we report a family with two infants diagnosed with infantile-onset HCM and mitral valve dysplasia that led to death before one year of age. Using exome sequencing, we discovered that one of the affected children had a homozygous frameshift variant in Myosin light chain 2 (MYL2:NM_000432.3:c.431_432delCT: p.Pro144Argfs*57;MYL2-fs), which alters the last 20 amino acids of the protein and is predicted to impact the most C-terminal of the three EF-hand domains in MYL2. The parents are unaffected heterozygous carriers of the variant and the variant is absent in control cohorts from gnomAD. The absence of the phenotype in carriers and the infantile presentation of severe HCM is in contrast to HCM associated with dominant MYL2 variants. Immunohistochemical analysis of the ventricular muscle of the deceased patient with the MYL2-fs variant showed a marked reduction of MYL2 expression compared to an unaffected control. In vitro overexpression studies further indicate that the MYL2-fs variant is actively degraded. In contrast, an HCM-associated missense variant (MYL2:p.Gly162Arg) and three other MYL2 stop-gain variants (p.E22*, p.K62*, p.E97*) that result in loss of the EF domains are stably expressed but show impaired localization. The degradation of the MYL2-fs can be rescued by inhibiting the cell's proteasome function supporting a post-translational effect of the variant. In vivo rescue experiments with a Drosophila MYL2-homolog (Mlc2) knockdown model indicate that neither the MYL2-fs nor the MYL2:p.Gly162Arg variant supports normal cardiac function. The tools that we have generated provide a rapid screening platform for functional assessment of variants of unknown significance in MYL2. Our study supports an autosomal recessive model of inheritance for MYL2 loss-of-function variants in infantile HCM and highlights the variant-specific molecular differences found in MYL2-associated cardiomyopathy.


Assuntos
Miosinas Cardíacas/genética , Cardiomiopatia Hipertrófica/genética , Família , Mutação da Fase de Leitura , Cadeias Leves de Miosina/genética , Adulto , Animais , Animais Geneticamente Modificados , Cardiomiopatia Hipertrófica/classificação , Cardiomiopatia Hipertrófica/congênito , Cardiomiopatia Hipertrófica/patologia , Células Cultivadas , Consanguinidade , Drosophila , Evolução Fatal , Feminino , Genes Dominantes , Genes Recessivos , Heterozigoto , Humanos , Lactente , Morte do Lactente , Recém-Nascido , Masculino , Linhagem , Fenótipo , Irmãos
5.
Invest Ophthalmol Vis Sci ; 61(5): 28, 2020 05 11.
Artigo em Inglês | MEDLINE | ID: mdl-32421148

RESUMO

Purpose: Bestrophinopathies are a group of untreatable inherited retinal dystrophies caused by mutations in the retinal pigment epithelium (RPE) Cl- channel bestrophin 1. We tested whether sodium phenylbutyrate (4PBA) could rescue the function of mutant bestrophin 1 associated with autosomal dominant and recessive disease. We then sought analogues of 4PBA with increased potency and determined the mode of action for 4PBA and a lead compound 2-naphthoxyacetic acid (2-NOAA). Lastly, we tested if 4PBA and 2-NOAA could functionally rescue bestrophin 1 function in RPE generated from induced pluripotent stem cells (iPSC-RPEs) derived from patients with a dominant or recessive bestrophinopathy. Methods: Global and plasma membrane expression was determined by Western blot and immunofluorescent microscopy, respectively. The effect of 4PBA and 2-NOAA on transcription was measured by quantitative RT-PCR and the rate of protein turnover by cycloheximide chase and Western blot. Channel function was measured by whole-cell patch clamp. Results: 4PBA and 2-NOAA can rescue the global and membrane expression of mutant bestrophin 1 associated with autosomal dominant disease (Best vitelliform macular dystrophy [BVMD]) and autosome recessive bestrophinopathy (ARB), and these small molecules have different modes of action. Both 4PBA and 2-NOAA significantly increased the channel function of mutant BVMD and ARB bestrophin 1 in HEK293T and iPSC-RPE cells derived from patients with BVMD and ARB. For 4PBA, the increased mutant channel function in BVMD and ARB iPSC-RPE was equal to that of wild-type iPSC-RPE bestrophin 1. Conclusions: The restoration of bestrophin 1 function in patient-derived RPE confirms the US Food and Drug Administration-approved drug 4PBA as a promising therapeutic treatment for bestrophinopathies.


Assuntos
Antineoplásicos/farmacologia , Bestrofinas/genética , Oftalmopatias Hereditárias/tratamento farmacológico , Regulação da Expressão Gênica/fisiologia , Glicolatos/farmacologia , Fenilbutiratos/farmacologia , Doenças Retinianas/tratamento farmacológico , Epitélio Pigmentado da Retina/efeitos dos fármacos , Western Blotting , Membrana Celular/metabolismo , Canais de Cloreto/metabolismo , Cicloeximida/farmacologia , Eletroforese em Gel de Poliacrilamida , Oftalmopatias Hereditárias/genética , Oftalmopatias Hereditárias/metabolismo , Genes Recessivos , Células HEK293/efeitos dos fármacos , Humanos , Células-Tronco Pluripotentes Induzidas/metabolismo , Microscopia de Fluorescência , Técnicas de Patch-Clamp , Reação em Cadeia da Polimerase em Tempo Real , Doenças Retinianas/genética , Doenças Retinianas/metabolismo , Epitélio Pigmentado da Retina/metabolismo , Transfecção
6.
Am J Hum Genet ; 106(5): 623-631, 2020 05 07.
Artigo em Inglês | MEDLINE | ID: mdl-32275884

RESUMO

Nucleoporins (NUPs) are an essential component of the nuclear-pore complex, which regulates nucleocytoplasmic transport of macromolecules. Pathogenic variants in NUP genes have been linked to several inherited human diseases, including a number with progressive neurological degeneration. We present six affected individuals with bi-allelic truncating variants in NUP188 and strikingly similar phenotypes and clinical courses, representing a recognizable genetic syndrome; the individuals are from four unrelated families. Key clinical features include congenital cataracts, hypotonia, prenatal-onset ventriculomegaly, white-matter abnormalities, hypoplastic corpus callosum, congenital heart defects, and central hypoventilation. Characteristic dysmorphic features include small palpebral fissures, a wide nasal bridge and nose, micrognathia, and digital anomalies. All affected individuals died as a result of respiratory failure, and five of them died within the first year of life. Nuclear import of proteins was decreased in affected individuals' fibroblasts, supporting a possible disease mechanism. CRISPR-mediated knockout of NUP188 in Drosophila revealed motor deficits and seizure susceptibility, partially recapitulating the neurological phenotype seen in affected individuals. Removal of NUP188 also resulted in aberrant dendrite tiling, suggesting a potential role of NUP188 in dendritic development. Two of the NUP188 pathogenic variants are enriched in the Ashkenazi Jewish population in gnomAD, a finding we confirmed with a separate targeted population screen of an international sampling of 3,225 healthy Ashkenazi Jewish individuals. Taken together, our results implicate bi-allelic loss-of-function NUP188 variants in a recessive syndrome characterized by a distinct neurologic, ophthalmologic, and facial phenotype.


Assuntos
Alelos , Encéfalo/anormalidades , Proteínas de Drosophila/genética , Anormalidades do Olho/genética , Cardiopatias Congênitas/genética , Mutação com Perda de Função/genética , Complexo de Proteínas Formadoras de Poros Nucleares/genética , Transporte Ativo do Núcleo Celular , Animais , Núcleo Celular/metabolismo , Pré-Escolar , Dendritos/metabolismo , Dendritos/patologia , Drosophila melanogaster , Anormalidades do Olho/mortalidade , Feminino , Fibroblastos , Genes Recessivos , Cardiopatias Congênitas/mortalidade , Humanos , Lactente , Recém-Nascido , Judeus/genética , Masculino , Complexo de Proteínas Formadoras de Poros Nucleares/deficiência , Convulsões/metabolismo , Síndrome , beta Carioferinas/metabolismo
7.
BMC Med Genet ; 21(1): 79, 2020 04 15.
Artigo em Inglês | MEDLINE | ID: mdl-32295532

RESUMO

BACKGROUND: Congenital chloride diarrhea (CLD; OMIM 214700) is a rare autosomal recessive disorder caused by pathogenic variations in the solute carrier family 26 member A3 (SLC26A3) gene. Without salt substitution, this chronic diarrheal disorder causes severe dehydration and electrolyte disturbances. Homozygous variants in the nearby gene SLC26A4 disrupt anion exchange in the inner ear and the thyroid, causing Pendred syndrome (PDS; OMIM 274600), which is the most frequent form of syndromic deafness. CASE PRESENTATION: We report an unusual co-occurrence of two rare homozygous mutations in both the SLC26A3 and SLC26A4 genes, causing a rare combination of both CLD and PDS in two siblings. Although the clinical pictures were typical, the combined loss of these anion transporters might modulate the risk of renal injury associated with CLD. CONCLUSIONS: Familial presentation of two rare autosomal recessive disorders with loss of function of different SLC26 anion transporters is described. Independent homozygous variants in the SLC26A3 and SLC26A4 genes cause CLD and PDS in siblings, shedding light on co-occurrence of rare recessive traits in the progeny of consanguineous couples.


Assuntos
Antiportadores de Cloreto-Bicarbonato/genética , Diarreia/congênito , Bócio Nodular/genética , Perda Auditiva Neurossensorial/genética , Erros Inatos do Metabolismo/genética , Transportadores de Sulfato/genética , Diarreia/diagnóstico , Diarreia/genética , Diarreia/patologia , Feminino , Genes Recessivos/genética , Testes Genéticos , Bócio Nodular/diagnóstico , Bócio Nodular/patologia , Perda Auditiva Neurossensorial/diagnóstico , Perda Auditiva Neurossensorial/patologia , Humanos , Lactente , Erros Inatos do Metabolismo/diagnóstico , Erros Inatos do Metabolismo/patologia , Mutação , Linhagem , Gravidez , Doenças Raras/diagnóstico , Doenças Raras/genética , Doenças Raras/patologia , Irmãos
9.
Hum Genet ; 139(10): 1209-1231, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32274568

RESUMO

Abnormal development of the ocular anterior segment may lead to a spectrum of clinical phenotypes ranging from primary congenital glaucoma (PCG) to variable anterior segment dysgenesis (ASD). The main objective of this study was to identify the genetic alterations underlying recessive congenital glaucoma with ASD (CG-ASD). Next-generation DNA sequencing identified rare biallelic CPAMD8 variants in four patients with CG-ASD and in one case with PCG. CPAMD8 is a gene of unknown function and recently associated with ASD. Bioinformatic and in vitro functional evaluation of the variants using quantitative reverse transcription PCR and minigene analysis supported a loss-of-function pathogenic mechanism. Optical and electron microscopy of the trabeculectomy specimen from one of the CG-ASD cases revealed an abnormal anterior chamber angle, with altered extracellular matrix, and apoptotic trabecular meshwork cells. The CPAMD8 protein was immunodetected in adult human ocular fluids and anterior segment tissues involved in glaucoma and ASD (i.e., aqueous humor, non-pigmented ciliary epithelium, and iris muscles), as well as in periocular mesenchyme-like cells of zebrafish embryos. CRISPR/Cas9 disruption of this gene in F0 zebrafish embryos (96 hpf) resulted in varying degrees of gross developmental abnormalities, including microphthalmia, pharyngeal maldevelopment, and pericardial and periocular edemas. Optical and electron microscopy examination of these embryos showed iridocorneal angle hypoplasia (characterized by altered iris stroma cells, reduced anterior chamber, and collagen disorganized corneal stroma extracellular matrix), recapitulating some patients' features. Our data support the notion that CPAMD8 loss-of-function underlies a spectrum of recessive CG-ASD phenotypes associated with extracellular matrix disorganization and provide new insights into the normal and disease roles of this gene.


Assuntos
Complemento C3/genética , Matriz Extracelular/metabolismo , Anormalidades do Olho/genética , Glaucoma/genética , Mutação com Perda de Função , Inibidor da Tripsina Pancreática de Kazal/genética , alfa-Macroglobulinas/genética , Adulto , Animais , Câmara Anterior/metabolismo , Câmara Anterior/patologia , Câmara Anterior/cirurgia , Sistemas CRISPR-Cas , Estudos de Casos e Controles , Complemento C3/deficiência , Embrião não Mamífero , Matriz Extracelular/patologia , Anormalidades do Olho/metabolismo , Anormalidades do Olho/patologia , Anormalidades do Olho/cirurgia , Feminino , Edição de Genes , Expressão Gênica , Genes Recessivos , Glaucoma/metabolismo , Glaucoma/patologia , Glaucoma/cirurgia , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Masculino , Pessoa de Meia-Idade , Linhagem , Malha Trabecular/metabolismo , Malha Trabecular/patologia , Malha Trabecular/cirurgia , Trabeculectomia , Inibidor da Tripsina Pancreática de Kazal/deficiência , Peixe-Zebra , alfa-Macroglobulinas/deficiência
11.
Am J Hum Genet ; 106(3): 412-421, 2020 03 05.
Artigo em Inglês | MEDLINE | ID: mdl-32142645

RESUMO

Primary familial brain calcification (PFBC) is a rare neurodegenerative disorder characterized by a combination of neurological, psychiatric, and cognitive decline associated with calcium deposition on brain imaging. To date, mutations in five genes have been linked to PFBC. However, more than 50% of individuals affected by PFBC have no molecular diagnosis. We report four unrelated families presenting with initial learning difficulties and seizures and later psychiatric symptoms, cerebellar ataxia, extrapyramidal signs, and extensive calcifications on brain imaging. Through a combination of homozygosity mapping and exome sequencing, we mapped this phenotype to chromosome 21q21.3 and identified bi-allelic variants in JAM2. JAM2 encodes for the junctional-adhesion-molecule-2, a key tight-junction protein in blood-brain-barrier permeability. We show that JAM2 variants lead to reduction of JAM2 mRNA expression and absence of JAM2 protein in patient's fibroblasts, consistent with a loss-of-function mechanism. We show that the human phenotype is replicated in the jam2 complete knockout mouse (jam2 KO). Furthermore, neuropathology of jam2 KO mouse showed prominent vacuolation in the cerebral cortex, thalamus, and cerebellum and particularly widespread vacuolation in the midbrain with reactive astrogliosis and neuronal density reduction. The regions of the human brain affected on neuroimaging are similar to the affected brain areas in the myorg PFBC null mouse. Along with JAM3 and OCLN, JAM2 is the third tight-junction gene in which bi-allelic variants are associated with brain calcification, suggesting that defective cell-to-cell adhesion and dysfunction of the movement of solutes through the paracellular spaces in the neurovascular unit is a key mechanism in CNS calcification.


Assuntos
Idade de Início , Alelos , Encefalopatias/genética , Calcinose/genética , Moléculas de Adesão Celular/genética , Genes Recessivos , Adolescente , Adulto , Animais , Encefalopatias/diagnóstico por imagem , Calcinose/diagnóstico por imagem , Criança , Feminino , Humanos , Masculino , Camundongos , Pessoa de Meia-Idade , Linhagem
12.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 37(4): 445-448, 2020 Apr 10.
Artigo em Chinês | MEDLINE | ID: mdl-32219833

RESUMO

OBJECTIVE: To carry out genetic testing and prenatal diagnosis for a family affected with recessive dystrophic epidermolysis bullosa (RDEB). METHODS: All exons of the COL7A1 gene and their flanking regions were subjected to PCR and Sanger sequencing. Suspected variant was validated in family members, based on which prenatal diagnosis was provided. RESULTS: Sanger sequencing found that the proband has carried two variants of the COL7A1 gene, namely c.7289delC (p.Pro2430Glnfs*36) and c.7474C>T (p.Arg2492*), which were respectively derived from his mother and father. The same variants were not found among 100 healthy controls. By prenatal diagnosis, the fetus was found to have inherited the c.7474C>T (p.Arg2492*) variant from its father. CONCLUSION: The pathogenic variants of the COL7A1 gene of the RDEB family were clarified, based on which prenatal diagnosis was provided.


Assuntos
Colágeno Tipo VII/genética , Epidermólise Bolhosa Distrófica/genética , Testes Genéticos , Criança , Éxons , Feminino , Genes Recessivos , Humanos , Masculino , Mutação , Gravidez , Diagnóstico Pré-Natal , Análise de Sequência de DNA
13.
BMC Med Genet ; 21(1): 59, 2020 03 24.
Artigo em Inglês | MEDLINE | ID: mdl-32209057

RESUMO

BACKGROUND: Intellectual disability (ID) is both a clinically diverse and genetically heterogeneous group of disorder, with an onset of cognitive impairment before the age of 18 years. ID is characterized by significant limitations in intellectual functioning and adaptive behaviour. The identification of genetic variants causing ID and neurodevelopmental disorders using whole-exome sequencing (WES) has proven to be successful. So far more than 1222 primary and 1127 candidate genes are associated with ID. METHODS: To determine pathogenic variants causative of ID in three unrelated consanguineous Pakistani families, we used a combination of WES, homozygosity-by-descent mapping, de-deoxy sequencing and bioinformatics analysis. RESULTS: Rare pathogenic single nucleotide variants identified by WES which passed our filtering strategy were confirmed by traditional Sanger sequencing and segregation analysis. Novel and deleterious variants in VPS53, GLB1, and MLC1, genes previously associated with variable neurodevelopmental anomalies, were found to segregate with the disease in the three families. CONCLUSIONS: This study expands our knowledge on the molecular basis of ID as well as the clinical heterogeneity associated to different rare genetic causes of neurodevelopmental disorders. This genetic study could also provide additional knowledge to help genetic assessment as well as clinical and social management of ID in Pakistani families.


Assuntos
Consanguinidade , Deficiência Intelectual/genética , Proteínas de Membrana/genética , Polimorfismo Genético , Proteínas de Transporte Vesicular/genética , beta-Galactosidase/genética , Criança , Pré-Escolar , Família , Feminino , Genes Recessivos/genética , Heterogeneidade Genética , Testes Genéticos , Homozigoto , Humanos , Deficiência Intelectual/complicações , Deficiência Intelectual/patologia , Masculino , Transtornos do Neurodesenvolvimento/complicações , Transtornos do Neurodesenvolvimento/genética , Transtornos do Neurodesenvolvimento/patologia , Paquistão/epidemiologia , Linhagem , Sequenciamento Completo do Exoma
14.
PLoS One ; 15(3): e0229564, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32119688

RESUMO

The introduction of high-yielding semi-dwarf varieties of wheat into cultivation has led to a "green revolution." This has required intensive research into various sources of dwarfism in wheat. However, there has been very little advancement in research on dwarfing genes in rye in comparison to wheat or barley. So far, three dominant dwarfing genes (Ddw1, Ddw3, and Ddw4) and three recessive genes (ct1, ct2, and np) have been characterized and precisely mapped in rye. There is no complete catalog of dwarfing genes available in rye. This paper presents an identification of the source of dwarfism and preliminary characterization of the new recessive gene dw9 from the BK-1 line. The gene was mapped on the long arm of the 6R chromosome and belongs to the GA-insensitive group. The initial characterization of the influence of this gene on morphological traits shows that it significantly affects the decrease of yielding trait parameters. A full evaluation can be performed after detailed breeding studies.


Assuntos
Nanismo/genética , Secale/genética , Biometria/métodos , Mapeamento Cromossômico/métodos , Cromossomos de Plantas/genética , Resistência à Doença/genética , Genes de Plantas/genética , Genes Recessivos/genética , Fenótipo , Melhoramento Vegetal/métodos , Doenças das Plantas/genética
15.
BMC Plant Biol ; 20(1): 68, 2020 Feb 10.
Artigo em Inglês | MEDLINE | ID: mdl-32041529

RESUMO

BACKGROUND: Leaf color is a major agronomic trait, which has a strong influence on crop yields. Isolating leaf color mutants can represent valuable materials for research in chlorophyll (Chl) biosynthesis and metabolism regulation. RESULTS: In this study, we identified a stably inherited yellow leaf mutant derived from 'Huaguan' pakchoi variety via isolated microspore culture and designated as pylm. This mutant displayed yellow leaves after germination. Its etiolated phenotype was nonlethal and stable during the whole growth period. Its growth was weak and its hypocotyls were markedly elongated. Genetic analysis revealed that two recessive nuclear genes, named py1 and py2, are responsible for the etiolation phenotype. Bulked segregant RNA sequencing (BSR-Seq) showed that py1 and py2 were mapped on chromosomes A09 and A07, respectively. The genes were single Mendelian factors in F3:4 populations based on a 3:1 phenotypic segregation ratio. The py1 was localized to a 258.3-kb interval on a 34-gene genome. The differentially expressed gene BraA09004189 was detected in the py1 mapping region and regulated heme catabolism. One single-nucleotide polymorphism (SNP) of BraA09004189 occurred in pylm. A candidate gene-specific SNP marker in 1520 F3:4 yellow-colored individuals co-segregated with py1. For py2, 1860 recessive homozygous F3:4 individuals were investigated and localized py2 to a 4.4-kb interval. Of the five genes in this region, BraA07001774 was predicted as a candidate for py2. It encoded an embryo defective 1187 and a phosphotransferase related to chlorophyll deficiency and hypocotyl elongation. One SNP of BraA07001774 occurred in pylm. It caused a single amino acid mutation from Asp to Asn. According to quantitative real-time polymerase chain reaction (qRT-PCR), BraA07001774 was downregulated in pylm. CONCLUSIONS: Our study identified a Chl deficiency mutant pylm in pakchoi. Two recessive nuclear genes named py1 and py2 had a significant effect on etiolation. Candidate genes regulating etiolation were identified as BraA09004189 and BraA07001774, respectively. These findings will elucidate chlorophyll metabolism and the molecular mechanisms of the gene interactions controlling pakchoi etiolation.


Assuntos
Brassica rapa/genética , Estiolamento/genética , Genes de Plantas , Genes Recessivos , Proteínas de Plantas/genética , Sequência de Aminoácidos , Sequência de Bases , Brassica rapa/crescimento & desenvolvimento , Clorofila/metabolismo , Folhas de Planta , Proteínas de Plantas/química , Proteínas de Plantas/metabolismo , Alinhamento de Sequência
17.
Hum Genet ; 139(5): 569-574, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32056000

RESUMO

Extremely rare diseases are increasingly recognized due to wide-spread, inexpensive genomic sequencing. Understanding the incidence of rare disease is important for appreciating its health impact and allocating recourses for research. However, estimating incidence of rare disease is challenging because the individual contributory alleles are, themselves, extremely rare. We propose a new method to determine incidence of rare, severe, recessive disease in non-consanguineous populations that use known allele frequencies, estimate the combined allele frequency of observed alleles and estimate the number of causative alleles that are thus far unobserved in a disease cohort. Experiments on simulated and real data show that this approach is a feasible method to estimate the incidence of rare disease in European populations but due to several limitations in our ability to assess the full spectrum of pathogenic mutations serves as a useful tool to provide a lower threshold on disease incidence.


Assuntos
Genes Recessivos , Predisposição Genética para Doença , Mutação , Polimorfismo de Nucleotídeo Único , Doenças Raras/epidemiologia , Doenças Raras/genética , Estudos de Coortes , Frequência do Gene , Humanos , Incidência , Modelos Genéticos , Estados Unidos/epidemiologia
18.
PLoS One ; 15(2): e0229025, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32069299

RESUMO

Mutations in CYP4F22 cause autosomal recessive congenital ichthyosis (ARCI). However, less than 10% of all ARCI patients carry a mutation in CYP4F22. In order to identify the molecular basis of ARCI among our patients (a cohort of ninety-two Spanish individuals) we performed a mutational analysis using direct Sanger sequencing in combination with a multigene targeted NGS panel. From these, eight ARCI families (three of them with Moroccan origin) were found to carry five different CYP4F22 mutations, of which two were novel. Computational analysis showed that the mutations found were present in highly conserved residues of the protein and may affect its structure and function. Seven of the eight families were carriers of a highly recurrent CYP4F22 variant, c.1303C>T; p.(His435Tyr). A 12Mb haplotype was reconstructed in all c.1303C>T carriers by genotyping ten microsatellite markers flanking the CYP4F22 gene. A prevalent 2.52Mb haplotype was observed among Spanish carrier patients suggesting a recent common ancestor. A smaller core haplotype of 1.2Mb was shared by Spanish and Moroccan families. Different approaches were applied to estimate the time to the most recent common ancestor (TMRCA) of carrier patients with Spanish origin. The age of the mutation was calculated by using DMLE and BDMC2. The algorithms estimated that the c.1303C>T variant arose approximately 2925 to 4925 years ago, while Spanish carrier families derived from a common ancestor who lived in the XIII century. The present study reports five CYP4F22 mutations, two of them novel, increasing the number of CYP4F22 mutations currently listed. Additionally, our results suggest that the recurrent c.1303C>T change has a founder effect in Spanish population and c.1303C>T carrier families originated from a single ancestor with probable African ancestry.


Assuntos
Sistema Enzimático do Citocromo P-450/genética , Efeito Fundador , Genes Recessivos , Ictiose Lamelar/genética , Mutação , Alelos , Substituição de Aminoácidos , Criança , Pré-Escolar , Sistema Enzimático do Citocromo P-450/química , Feminino , Haplótipos , Humanos , Masculino , Pessoa de Meia-Idade , Modelos Moleculares , Linhagem , Fenótipo , Conformação Proteica , Espanha , Relação Estrutura-Atividade
19.
Nat Commun ; 11(1): 595, 2020 01 30.
Artigo em Inglês | MEDLINE | ID: mdl-32001716

RESUMO

Developmental epileptic encephalopathies are devastating disorders characterized by intractable epileptic seizures and developmental delay. Here, we report an allelic series of germline recessive mutations in UGDH in 36 cases from 25 families presenting with epileptic encephalopathy with developmental delay and hypotonia. UGDH encodes an oxidoreductase that converts UDP-glucose to UDP-glucuronic acid, a key component of specific proteoglycans and glycolipids. Consistent with being loss-of-function alleles, we show using patients' primary fibroblasts and biochemical assays, that these mutations either impair UGDH stability, oligomerization, or enzymatic activity. In vitro, patient-derived cerebral organoids are smaller with a reduced number of proliferating neuronal progenitors while mutant ugdh zebrafish do not phenocopy the human disease. Our study defines UGDH as a key player for the production of extracellular matrix components that are essential for human brain development. Based on the incidence of variants observed, UGDH mutations are likely to be a frequent cause of recessive epileptic encephalopathy.


Assuntos
Epilepsia/genética , Genes Recessivos , Mutação com Perda de Função/genética , Oxirredutases/genética , Uridina Difosfato Glucose Desidrogenase/genética , Adolescente , Alelos , Animais , Criança , Pré-Escolar , Feminino , Humanos , Lactente , Cinética , Masculino , Organoides/patologia , Oxirredutases/química , Linhagem , Domínios Proteicos , Síndrome , Peixe-Zebra
20.
Nat Commun ; 11(1): 995, 2020 02 21.
Artigo em Inglês | MEDLINE | ID: mdl-32081864

RESUMO

Very-early-onset inflammatory bowel disease (VEO-IBD) is a heterogeneous phenotype associated with a spectrum of rare Mendelian disorders. Here, we perform whole-exome-sequencing and genome-wide genotyping in 145 patients (median age-at-diagnosis of 3.5 years), in whom no Mendelian disorders were clinically suspected. In five patients we detect a primary immunodeficiency or enteropathy, with clinical consequences (XIAP, CYBA, SH2D1A, PCSK1). We also present a case study of a VEO-IBD patient with a mosaic de novo, pathogenic allele in CYBB. The mutation is present in ~70% of phagocytes and sufficient to result in defective bacterial handling but not life-threatening infections. Finally, we show that VEO-IBD patients have, on average, higher IBD polygenic risk scores than population controls (99 patients and 18,780 controls; P < 4 × 10-10), and replicate this finding in an independent cohort of VEO-IBD cases and controls (117 patients and 2,603 controls; P < 5 × 10-10). This discovery indicates that a polygenic component operates in VEO-IBD pathogenesis.


Assuntos
Doenças Inflamatórias Intestinais/genética , Mosaicismo , Adulto , Idade de Início , Estudos de Casos e Controles , Criança , Pré-Escolar , Estudos de Coortes , Feminino , Genes Recessivos , Predisposição Genética para Doença , Variação Genética , Humanos , Lactente , Recém-Nascido , Doenças Inflamatórias Intestinais/etiologia , Mutação com Perda de Função , Masculino , Herança Multifatorial , Mutação , NADPH Oxidase 2/genética , Linhagem , Doenças da Imunodeficiência Primária/complicações , Doenças da Imunodeficiência Primária/genética , Fatores de Risco , Sequenciamento Completo do Exoma
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