RESUMO
We present a case of a male term neonate with lethargy, hypotonia, hypoventilation and severe encephalopathy. The infant had a history of two siblings who died in the neonatal period from unclear causes. The infant exhibited skin and hair abnormalities, including desquamation of the extremities, angular stomatitis, cheilitis, neonatal acne and thin, sparse hair. Additionally, the infant had a tall stature; long, slender fingers and toes; and facial dysmorphism characterised by a long, narrow face with increased interpalpebral distance. The condition deteriorated rapidly, and unfortunately, death occurred before a definitive diagnosis could be established. Tandem mass spectrometry suggested low methionine and clinical exome sequencing identified a nonsense mutation in the MTHFR gene.
Assuntos
Metilenotetra-Hidrofolato Redutase (NADPH2) , Humanos , Masculino , Recém-Nascido , Metilenotetra-Hidrofolato Redutase (NADPH2)/genética , Evolução Fatal , Alopecia/genética , Alopecia/diagnóstico , Encefalopatias/genética , Encefalopatias/diagnóstico , Códon sem Sentido , MutaçãoRESUMO
OBJECTIVE: To analyze clinical and genetic characteristics of patients with the verified rare forms of autosomal recessive spinocerebellar ataxias, ATX-ANO10 and ATX-SYNE1. MATERIAL AND METHODS: Six unrelated patients with established diagnoses were examined: 4 patients with ATX-ANO10 and 2 patients with ATX-SYNE1. Brain MRI and nerve conduction study were performed. To screen for cognitive impairment, the scale for the Assessment and Rating of Ataxia (SARA), and the Montreal Cognitive Assessment Scale (MoCA) were used. Mutation screening included panel sequencing on the Illumina MiSeq platform. RESULTS: Six variants were found in the ANO10 gene: the previously described pathogenic nonsense mutations c.G1025A (p.W342X) and c.C1244G (p.S415X), as well as novel probably pathogenic variants c.1477-2A>G and c.G101T (p.W34L) and missense mutations c.A110C (p.N37T) and c.T104C (p.L35P) of undetermined significance. A novel nonsense mutation c.C8911T (p.Q2971X) and a previously described pathogenic variant c.C4939T (p.Q1647X) were found in the SYNE1 gene. The clinical presentation of the ATX-ANO10 and ATX-SYNE1 was typical presenting with slowly progressive cerebellar ataxia with pyramidal signs, with young onset and cerebellar atrophy according to brain MRI study. CONCLUSION: We provided first-ever data on clinical features and mutation spectrum In Russian patients with ATX-ANO10 and ATX-SYNE1. The phenotype of these ataxias is nonspecific, so the method of choice for molecular diagnostics is massive parallel sequencing.
Assuntos
Anoctaminas , Proteínas do Citoesqueleto , Proteínas do Tecido Nervoso , Ataxias Espinocerebelares , Humanos , Ataxias Espinocerebelares/genética , Ataxias Espinocerebelares/diagnóstico por imagem , Masculino , Feminino , Proteínas do Tecido Nervoso/genética , Adulto , Proteínas do Citoesqueleto/genética , Anoctaminas/genética , Mutação , Proteínas Nucleares/genética , Pessoa de Meia-Idade , Imageamento por Ressonância Magnética , Códon sem Sentido , Mutação de Sentido Incorreto , Adolescente , Adulto JovemRESUMO
Highlights Maturity-onset diabetes of the young type 6 (MODY6) is a rare form of monogenic diabetes mellitus due to NEUROD1 gene mutation on chromosome 2q32. A 21-year-old woman exhibiting weight loss, polyuria, and hyperglycemia was initially misdiagnosed with type 1 diabetes mellitus. Considering the early-onset age, a three-generation family history of diabetes, and negative autoimmune antibodies, a MODY diagnosis was suspected. Genetic analysis revealed that she inherited a novel heterozygous nonsense NEUROD1 mutation c.747C>G (p.Tyr249*) from her father. Correct MODY6 diagnosis facilitates appropriate interventions.
Assuntos
Fatores de Transcrição Hélice-Alça-Hélice Básicos , Códon sem Sentido , Diabetes Mellitus Tipo 2 , Linhagem , Humanos , Feminino , Diabetes Mellitus Tipo 2/genética , Diabetes Mellitus Tipo 2/diagnóstico , Fatores de Transcrição Hélice-Alça-Hélice Básicos/genética , Adulto Jovem , Povo Asiático/genética , China , Masculino , Adulto , População do Leste AsiáticoRESUMO
Advances in next-generation sequencing technologies have led to elucidation of sensorineural hearing loss genetics and associated clinical impacts. However, studies on the functional pathogenicity of variants of uncertain significance (VUS), despite their close association with clinical phenotypes, are lacking. Here we identified compound heterozygous variants in ESRRB transcription factor gene linked to DFNB35, specifically a novel splicing variant (NM_004452.4(ESRRB): c.397 + 2T>G) in trans with a missense variant (NM_004452.4(ESRRB): c.1144C>T p.(Arg382Cys)) whose pathogenicity remains unclear. The splicing variant (c.397 + 2T>G) caused exon 4 skipping, leading to premature stop codon formation and nonsense-mediated decay. The p.(Arg382Cys) variant was classified as a VUS due to its particularly higher allele frequency among East Asian population despite disease-causing in-silico predictions. However, functional assays showed that p.(Arg382Cys) variant disrupted key intramolecular interactions, leading to protein instability. This variant also reduced transcriptional activity and altered expression of downstream target genes essential for inner ear function, suggesting genetic contribution to disease phenotype. This study expanded the phenotypic and genotypic spectrum of ESRRB in DFNB35 and revealed molecular mechanisms underlying ESRRB-associated DFNB35. These findings suggest that variants with high allele frequencies can also possess functional pathogenicity, providing a breakthrough for cases where VUS, previously unexplored, could be reinterpreted by elucidating their functional roles and disease-causing characteristics.
Assuntos
Perda Auditiva Neurossensorial , Receptores de Estrogênio , Feminino , Humanos , Masculino , Códon sem Sentido/genética , Frequência do Gene , Predisposição Genética para Doença , Perda Auditiva/genética , Perda Auditiva Neurossensorial/genética , Mutação de Sentido Incorreto , Linhagem , Splicing de RNA/genética , Receptores de Estrogênio/genéticaRESUMO
BACKGROUND: Defects in PPP1R12A can lead to genitourinary and/or brain malformation syndrome (GUBS). GUBS is primarily characterized by neurological or genitourinary system abnormalities, but a few reported cases are associated with neonatal seizures. Here, we report a case of a female newborn with neonatal seizures caused by a novel variant in PPP1R12A, aiming to enhance the clinical and variant data of genetic factors related to epilepsy in early life. METHODS: Whole-exome and Sanger sequencing were used for familial variant assessment, and bioinformatics was employed to annotate the variant. A structural model of the mutant protein was simulated using molecular dynamics (MD), and the free binding energy between PPP1R12A and PPP1CB was analyzed. A mutant plasmid was constructed, and mutant protein expression was analyzed using western blotting (WB), and the interaction between the mutant and PPP1CB proteins using co-immunoprecipitation (Co-IP) experiments. RESULTS: The patient experienced tonic-clonic seizures on the second day after birth. Genetic testing revealed a heterozygous variant in PPP1R12A, NM_002480.3:c.2533 C > T (p.Arg845Ter). Both parents had the wild-type gene. MD suggested that loss of the C-terminal structure in the mutant protein altered its structural stability and increased the binding energy with PPP1CB, indicating unstable protein-protein interactions. On WB, a low-molecular-weight band was observed, indicating that the protein was truncated. Co-IP indicated that the mutant protein no longer interacted with PPP1CB, indicating an effect on the structural stability of the myosin phase complex. CONCLUSION: The PPP1R12A c.2533 C > T variant may explain the neonatal seizures in the present case. The findings of this study expand the spectrum of PPP1R12A variants and highlight the potential significance of truncated proteins in the pathogenesis of GUBS.
Assuntos
Códon sem Sentido , Epilepsia , Fosfatase de Miosina-de-Cadeia-Leve , Feminino , Humanos , Recém-Nascido , Masculino , População do Leste Asiático/genética , Epilepsia/genética , Linhagem , Proteína Fosfatase 1/genética , Fosfatase de Miosina-de-Cadeia-Leve/genéticaRESUMO
Distal hereditary motor neuropathies (dHMN) are a group of heterogeneous diseases and previous studies have reported that the compound heterozygous recessive MME variants cause dHMN. Our study found a novel homozygous MME variant and a reported compound heterozygous MME variant in two Chinese families, respectively. Next-generation sequencing and nerve conduction studies were performed for two probands. The probands in two families presented with the muscle weakness and wasting of both lower limbs and carried a c.2122 A > T (p.K708*) and c.1342 C > T&c.2071_2072delinsTT (p.R448*&p.A691L) variant, respectively. Prominently axonal impairment of motor nerves and slight involvement of sensory nerves were observed in nerve conduction study. Our study reported a "novel" nonsense mutation and a missense variant of autosomal recessive late-onset dHMN and reviewed reported MME variants associated with dHMN phenotype.
Assuntos
Neuropatia Hereditária Motora e Sensorial , Neprilisina , Adulto , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Idade de Início , Alelos , China , Códon sem Sentido , População do Leste Asiático/genética , Genes Recessivos , Neuropatia Hereditária Motora e Sensorial/genética , Linhagem , Neprilisina/genéticaRESUMO
Infertility represents a significant health concern, with sperm quantity and quality being crucial determinants of male fertility. Oligoasthenoteratozoospermia (OAT) is characterized by reduced sperm motility, lower sperm concentration, and morphological abnormalities in sperm heads and flagella. Although variants in several genes have been implicated in OAT, its genetic etiologies and pathogenetic mechanisms remain inadequately understood. In this study, we identified a homozygous nonsense mutation (c.916C>T, p.Arg306*) in the coiled-coil domain containing 146 ( CCDC146) gene in an infertile male patient with OAT. This mutation resulted in the production of a truncated CCDC146 protein (amino acids 1-305), retaining only two out of five coiled-coil domains. To validate the pathogenicity of the CCDC146 mutation, we generated a mouse model ( Ccdc146 mut/mut ) with a similar mutation to that of the patient. Consistently, the Ccdc146 mut/mut mice exhibited infertility, characterized by significantly reduced sperm counts, diminished motility, and multiple defects in sperm heads and flagella. Furthermore, the levels of axonemal proteins, including DNAH17, DNAH1, and SPAG6, were significantly reduced in the sperm of Ccdc146 mut/mut mice. Additionally, both human and mouse CCDC146 interacted with intraflagellar transport protein 20 (IFT20), but this interaction was lost in the mutated versions, leading to the degradation of IFT20. This study identified a novel deleterious homozygous nonsense mutation in CCDC146 that causes male infertility, potentially by disrupting axonemal protein transportation. These findings offer valuable insights for genetic counseling and understanding the mechanisms underlying CCDC146 mutant-associated infertility in human males.
Assuntos
Astenozoospermia , Proteínas Associadas aos Microtúbulos , Animais , Humanos , Masculino , Camundongos , Astenozoospermia/genética , Códon sem Sentido , Homozigoto , Infertilidade Masculina/genética , Mutação , Oligospermia/genética , Motilidade dos Espermatozoides/genética , Espermatozoides , Proteínas Associadas aos Microtúbulos/genéticaRESUMO
BACKGROUND: Biotinidase deficiency (BD) is a rare, autosomal recessive metabolic disorder characterized by neurocutaneous symptoms. This study investigates a case of profound BD in an Indian infant and the underlying genetic basis. METHODS: A 10-month-old male presenting with seizures, hypotonia, ataxia, visual impairments, and developmental delay underwent biochemical and genetic analysis. Biotinidase activity was measured using an ELISA kit. Sanger sequencing of the biotinidase (BTD) gene was performed to identify genetic variations. In silico analysis was employed to assess the potential impact of the identified variants. RESULTS: The infant biotinidase activity was undetectable and its suggest profound biotinidase deficiency. Novel biallelic loss-of-function variations (c.903G > A and c.946 C > T) in the BTD gene were identified, leading to premature stop codons and truncated, non-functional protein fragments. CONCLUSION: This case expands our knowledge of BD genetic diversity and underscores the critical role of early diagnosis and newborn screening programs in managing this treatable condition.
Assuntos
Deficiência de Biotinidase , Biotinidase , Humanos , Deficiência de Biotinidase/genética , Deficiência de Biotinidase/diagnóstico , Masculino , Lactente , Biotinidase/genética , Índia , Mutação com Perda de Função/genética , Alelos , Códon sem Sentido/genéticaRESUMO
Abnormalities in MYO5B, which encodes an unconventional myosin Vb, not only cause microvillus inclusion disease but also cholestatic liver disease, including benign recurrent intrahepatic cholestasis (BRIC). However, MYO5B-related cholestasis has not yet been reported in Japan. In this study, we present the case of a female patient in her thirties, who had developed jaundice, without diarrhea, in the first year after birth. The jaundice spontaneously subsided and occasionally recurred. Whole-exome sequencing identified two pathogenic variants in MYO5B: a nonsense mutation (c. G1124A: p. W375X) and a missense mutation (c.C2470T: p.R824C). Therefore, the patient was diagnosed with MYO5B-associated BRIC. This is the first reported case of cholestasis with a defined MYO5B defect in Japan.
Assuntos
Colestase Intra-Hepática , Códon sem Sentido , Sequenciamento do Exoma , Mutação de Sentido Incorreto , Miosina Tipo V , Recidiva , Humanos , Miosina Tipo V/genética , Miosina Tipo V/deficiência , Feminino , Colestase Intra-Hepática/genética , Colestase Intra-Hepática/etiologia , Adulto , Cadeias Pesadas de Miosina/genética , Japão , Icterícia/etiologiaRESUMO
Neurofibromatosis type 1 (NF1) is a human genetic disorder caused by variants in the NF1 gene. Plexiform neurofibromas, one of many NF1 manifestations, are benign peripheral nerve sheath tumors occurring in up to 50% of NF1 patients. A substantial fraction of NF1 pathogenetic variants are nonsense mutations, which result in the synthesis of truncated non-functional NF1 protein (neurofibromin). To date, no therapeutics have restored neurofibromin expression or addressed the consequences of this protein's absence in NF1 nonsense mutation patients, but nonsense suppression is a potential approach to the problem. Ataluren is a small molecule drug that has been shown to stimulate functional nonsense codon readthrough in several models of nonsense mutation diseases, as well as in Duchenne muscular dystrophy patients. To test ataluren's potential applicability in nonsense mutation NF1 patients, we evaluated its therapeutic effects using three treatment regimens in a previously established NF1 patient-derived (c.2041C > T; p.Arg681X) nonsense mutation mouse model. Collectively, our experiments indicate that: i) ataluren appeared to slow the growth of neurofibromas and alleviate some paralysis phenotypes, ii) female Nf1-nonsense mutation mice manifested more severe paralysis and neurofibroma phenotypes than male mice, iii) ataluren doses with apparent effectiveness were lower in female mice than in male mice, and iv) age factors also influenced ataluren's effectiveness.
Assuntos
Códon sem Sentido , Modelos Animais de Doenças , Neurofibromatose 1 , Neurofibromina 1 , Animais , Códon sem Sentido/efeitos dos fármacos , Camundongos , Masculino , Feminino , Neurofibromatose 1/genética , Neurofibromatose 1/tratamento farmacológico , Neurofibromina 1/genética , Oxidiazóis/farmacologia , Oxidiazóis/uso terapêutico , Humanos , Camundongos Endogâmicos C57BL , Camundongos TransgênicosRESUMO
Recessive dystrophic epidermolysis bullosa (RDEB) is a rare genetic disease caused by loss of function mutations in the gene coding for collagen VII (C7) due to deficient or absent C7 expression. This disrupts structural and functional skin architecture, leading to blistering, chronic wounds, inflammation, important systemic symptoms affecting the mouth, gastrointestinal tract, cornea, and kidney function, and an increased skin cancer risk. RDEB patients have an extremely poor quality of life and often die at an early age. A frequent class of mutations in RDEB is premature termination codons (PTC), which appear in homozygosity or compound heterozygosity with other mutations. RDEB has no cure and current therapies are mostly palliative. Using patient-derived keratinocytes and a library of 8273 small molecules and 20,160 microbial extracts evaluated in a phenotypic screening interrogating C7 levels, we identified three active chemical series. Two of these series had PTC readthrough activity, and one upregulated C7 mRNA, showing synergistic activity when combined with the reference readthrough molecule gentamicin. These compounds represent novel potential small molecule-based systemic strategies that could complement topical-based treatments for RDEB.
Assuntos
Colágeno Tipo VII , Epidermólise Bolhosa Distrófica , Epidermólise Bolhosa Distrófica/genética , Epidermólise Bolhosa Distrófica/tratamento farmacológico , Colágeno Tipo VII/genética , Colágeno Tipo VII/metabolismo , Humanos , Regulação para Cima/efeitos dos fármacos , Queratinócitos/efeitos dos fármacos , Queratinócitos/metabolismo , Bibliotecas de Moléculas Pequenas/farmacologia , Códon sem Sentido , Gentamicinas/farmacologiaRESUMO
Many of the most highly conserved elements in the human genome are "poison exons," alternatively spliced exons that contain premature termination codons and permit post-transcriptional regulation of mRNA abundance through induction of nonsense-mediated mRNA decay (NMD). Poison exons are widely assumed to be highly conserved due to their presumed importance for organismal fitness, but this functional importance has never been tested in the context of a whole organism. Here, we report that a poison exon in Smndc1 is conserved across mammals and plants and plays a molecular autoregulatory function in both kingdoms. We generated mouse and A. thaliana models lacking this poison exon to find its loss leads to deregulation of SMNDC1 protein levels, pervasive alterations in mRNA processing, and organismal size restriction. Together, these models demonstrate the importance of poison exons for both molecular and organismal phenotypes that likely explain their extraordinary conservation.
Assuntos
Processamento Alternativo , Arabidopsis , Éxons , Degradação do RNAm Mediada por Códon sem Sentido , Animais , Humanos , Camundongos , Processamento Alternativo/genética , Arabidopsis/genética , Arabidopsis/crescimento & desenvolvimento , Códon sem Sentido/genética , Sequência Conservada , Éxons/genética , Degradação do RNAm Mediada por Códon sem Sentido/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismoRESUMO
Dystrophinopathies are a group of neuromuscular disorders, inherited in an X-linked recessive manner, caused by pathogenic variants in the DMD gene. Copy number variation detection and next generation sequencing allow the detection of around 99 % of the pathogenic variants. However, some patients require mRNA studies from muscle biopsies to identify deep intronic pathogenic variants. Here, we report a child suspected of having Duchenne muscular dystrophy, with a muscle biopsy showing dystrophin deficiency, and negative molecular testing for deletions, duplications, and small variants. mRNA analysis from muscle biopsy revealed a pseudoexon activation that introduce a premature stop codon into the reading frame. gDNA sequencing allowed to identified a novel variant, c.832-186 T>G, which creates a cryptic donor splice site, recognizing the underlying mechanism causing the pseudoexon insertion. This case highlights the usefulness of the mRNA analysis from muscle biopsy when routine genetic testing is negative and clinical suspicion of dystrophinopathies remains the main clinical diagnosis suspicion.
Assuntos
Códon sem Sentido , Distrofina , Íntrons , Distrofia Muscular de Duchenne , Humanos , Distrofia Muscular de Duchenne/genética , Distrofina/genética , Masculino , Éxons , Criança , RNA Mensageiro/genética , RNA Mensageiro/metabolismoRESUMO
BACKGROUND: This study aims to report the clinical characteristics of a child with autosomal recessive polycystic kidney disease (ARPKD) within a Chinese Zhuang ethnic family. METHODS: We used whole exome sequencing (WES) in the family to examine the genetic cause of the disease. Candidate pathogenic variants were validated by Sanger sequencing. RESULTS: We identified previously unreported mutations in the PKHD1 gene of the proband with ARPKD through WES: a splice site mutation c.6809-2Aâ >â T, a nonsense mutation c.4192Câ >â T(p.Gln1398Ter), and a missense mutation c.2181Tâ >â G(p.Asn727Lys). Her mother is a heterozygous carrier of c.2181Tâ >â G(p.Asn727Lys) mutation. Her father is a carrier of c.6809-2Aâ >â T mutation and c.4192Câ >â T(p.Gln1398Ter) mutation. CONCLUSIONS: The identification of novel mutations in the PKHD1 gene through WES not only expands the spectrum of known variants but also potentially enhances genetic counseling and prenatal diagnostic approaches for families affected by ARPKD.
Assuntos
Códon sem Sentido , Linhagem , Rim Policístico Autossômico Recessivo , Receptores de Superfície Celular , Humanos , Rim Policístico Autossômico Recessivo/genética , Receptores de Superfície Celular/genética , Feminino , China , Masculino , Sequenciamento do Exoma , Povo Asiático/genética , Sítios de Splice de RNA/genética , Mutação de Sentido Incorreto , Adulto , População do Leste AsiáticoRESUMO
Nonsense mutations in the coding region turn amino acid codons into termination codons, resulting in premature termination codons (PTCs). In the case of the in-frame PTC, if translation does not stop at the PTC but continues to the natural termination codon (NTC) with the insertion of an amino acid, known as readthrough, the full-length peptide is formed, albeit with a single amino acid mutation. We have previously developed the functionality-transfer oligonucleotide (FT-Probe), which forms a hybrid complex with RNA of a complementary sequence to transfer the functional group, resulting in modification of the 4-amino group of cytosine or the 6-amino group of adenine. In this study, the FT-Probe was used to chemically modify the adenosines of the PTC (UAA, UAG, and UGA) of mRNA, which were assayed for the readthrough in a reconstituted Escherichia coli translation system. The third adenosine-modified UAA produced three readthrough peptides incorporating tyrosine, glutamine and lysine at the UAA site. It should be noted that the additional modification with a cyclodextrin only induced glutamine incorporation. The adenosine modified UGA induced readthrough very efficiently with selective tryptophan incorporation. Readthrough of the modified UGA is caused by inhibition of the RF2 function. This study has demonstrated that the chemical modification of the adenosine 6-amino group of the PTC is a strategy for effective readthrough in a prokaryotic translation system.
Assuntos
Adenosina , Escherichia coli , Peptídeos , Escherichia coli/genética , Escherichia coli/efeitos dos fármacos , Escherichia coli/metabolismo , Adenosina/química , Adenosina/análogos & derivados , Peptídeos/química , Peptídeos/farmacologia , Códon sem Sentido , Códon de Terminação/genética , Biossíntese de Proteínas/efeitos dos fármacosRESUMO
BACKGROUND: Type III Bartter syndrome (BS) is an autosomal recessive renal tubular disease caused by the mutation of the chloride voltage-gated channel Kb (CLCNKB) gene. This condition is characterized by renal sodium loss, hypokalemia, metabolic alkaliosis, high renin, and high aldosterone levels. METHODS: We report a case of adult type III BS caused by a novel complex heterozygous mutation of the CLCNKB gene. The peripheral blood was extracted for whole genome DNA extraction, and the genome exon region of BS- related genes, was predicted by high-throughput sequencing and protein function prediction software. The selected mutation sites were verified by sequencing with Sanger method. RESULTS: The new complex heterozygous mutations of CLCNKB include heterozygous deletion of exon 2 - 20 of CLCNKB and nonsense mutation of exon 19, c.2010G>A (p.W670X). This complex heterozygous mutation has not been reported in humans. CONCLUSIONS: For patients with high clinical suspicion of BS, a clear diagnosis should be made through genetic test-ing to improve patients' quality of life and provide genetic guidance.
Assuntos
Síndrome de Bartter , Canais de Cloreto , Heterozigoto , Humanos , Síndrome de Bartter/genética , Síndrome de Bartter/diagnóstico , Canais de Cloreto/genética , Mutação , Adulto , Masculino , Feminino , Éxons/genética , Análise Mutacional de DNA , Códon sem SentidoRESUMO
Premature termination codons (PTCs) cause ~10-20% of inherited diseases and are a major mechanism of tumor suppressor gene inactivation in cancer. A general strategy to alleviate the effects of PTCs would be to promote translational readthrough. Nonsense suppression by small molecules has proven effective in diverse disease models, but translation into the clinic is hampered by ineffective readthrough of many PTCs. Here we directly tackle the challenge of defining drug efficacy by quantifying the readthrough of ~5,800 human pathogenic stop codons by eight drugs. We find that different drugs promote the readthrough of complementary subsets of PTCs defined by local sequence context. This allows us to build interpretable models that accurately predict drug-induced readthrough genome-wide, and we validate these models by quantifying endogenous stop codon readthrough. Accurate readthrough quantification and prediction will empower clinical trial design and the development of personalized nonsense suppression therapies.
Assuntos
Códon sem Sentido , Códon de Terminação , Humanos , Genoma Humano , Biossíntese de Proteínas/efeitos dos fármacos , Bibliotecas de Moléculas Pequenas/farmacologiaRESUMO
The nonsense-mediated RNA decay (NMD) pathway is a crucial mechanism of mRNA quality control. Current annotations of NMD substrate RNAs are rarely data-driven, but use generally established rules. We present a data set with four cell lines and combinations for SMG5, SMG6, and SMG7 knockdowns or SMG7 knockout. Based on this data set, we implemented a workflow that combines Nanopore and Illumina sequencing to assemble a transcriptome, which is enriched for NMD target transcripts. Moreover, we use coding sequence information (CDS) from Ensembl, Gencode consensus Ribo-seq ORFs, and OpenProt to enhance the CDS annotation of novel transcript isoforms. In summary, 302,889 transcripts were obtained from the transcriptome assembly process, out of which 24% are absent from Ensembl database annotations, 48,213 contain a premature stop codon, and 6433 are significantly upregulated in three or more comparisons of NMD active versus deficient cell lines. We present an in-depth view of these results through the NMDtxDB database, which is available at https://shiny.dieterichlab.org/app/NMDtxDB, and supports the study of NMD-sensitive transcripts. We open sourced our implementation of the respective web-application and analysis workflow at https://github.com/dieterich-lab/NMDtxDB and https://github.com/dieterich-lab/nmd-wf.
Assuntos
Anotação de Sequência Molecular , Degradação do RNAm Mediada por Códon sem Sentido , RNA Mensageiro , Humanos , Degradação do RNAm Mediada por Códon sem Sentido/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Transcriptoma , Bases de Dados Genéticas , Fases de Leitura Aberta/genética , Códon sem Sentido/genéticaRESUMO
RATIONALE: Allan-Herndon-Dudley syndrome (AHDS) results from a pathogenic variant in the hemizygous subunit of the SLC16A2 gene, which encodes monocarboxylate transporter 8 and follows an X-linked recessive pattern. AHDS manifests as neuropsychomotor developmental delay, intellectual disability, movement disorders, and thyroid hormone abnormalities. It is frequently misdiagnosed as cerebral palsy or hypothyroidism. PATIENT CONCERNS: A 9-month-old male infant exhibited poor head control, hypodynamia, motor retardation, hypertonic limbs, and thyroid abnormalities. Despite levothyroxine supplementation and rehabilitation therapy, no improvements were observed. Whole-exome sequencing identified a novel nonsense mutation in SLC16A2 (c.124Gâ >â T, p.E42X), which unequivocally established the diagnosis. DIAGNOSES: AHDS was confirmed. INTERVENTIONS: Levothyroxine treatment commenced early in infancy, followed by 3 months of rehabilitation therapy, starting at 5 months of age. The combined administration of levothyroxine and methimazole was initiated at 1 year and 10 months of age, respectively. OUTCOMES: While improvements were noted in thyroid hormone levels, neurological developmental delays persisted. LESSONS: AHDS should be considered in patients presenting with atypical neurological features and thyroid hormone abnormalities such as elevated triiodothyronine and decreased thyroxine levels. The early utilization of exome sequencing aids in prompt diagnosis. The identified SLC16A2 nonsense mutation correlates with severe neurological phenotypes and adds to the spectrum of genetic variations associated with AHDS.