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Deleterious mutations in the essential mRNA metabolism factor, hGle1, in amyotrophic lateral sclerosis.
Kaneb HM, Folkmann AW, Belzil VV, Jao LE, Leblond CS, Girard SL, Daoud H, Noreau A, Rochefort D, Hince P, Szuto A, Levert A, Vidal S, André-Guimont C, Camu W, Bouchard JP, Dupré N, Rouleau GA, Wente SR, Dion PA
(2015) Hum Mol Genet 24: 1363-73
MeSH Terms: Amyotrophic Lateral Sclerosis, Animals, Arthrogryposis, Codon, Nonsense, DNA-Binding Proteins, Disease Models, Animal, Haploinsufficiency, HeLa Cells, Humans, Microscopy, Confocal, Motor Neurons, Mutation, Missense, Nuclear Pore, Nucleocytoplasmic Transport Proteins, Pedigree, Protein Processing, Post-Translational, RNA Splicing, RNA, Messenger, Zebrafish
Show Abstract · Added February 19, 2015
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder characterized by the selective death of motor neurons. Causative mutations in the global RNA-processing proteins TDP-43 and FUS among others, as well as their aggregation in ALS patients, have identified defects in RNA metabolism as an important feature in this disease. Lethal congenital contracture syndrome 1 and lethal arthrogryposis with anterior horn cell disease are autosomal recessive fetal motor neuron diseases that are caused by mutations in another global RNA-processing protein, hGle1. In this study, we carried out the first screening of GLE1 in ALS patients (173 familial and 760 sporadic) and identified 2 deleterious mutations (1 splice site and 1 nonsense mutation) and 1 missense mutation. Functional analysis of the deleterious mutants revealed them to be unable to rescue motor neuron pathology in zebrafish morphants lacking Gle1. Furthermore, in HeLa cells, both mutations caused a depletion of hGle1 at the nuclear pore where it carries out an essential role in nuclear export of mRNA. These results suggest a haploinsufficiency mechanism and point to a causative role for GLE1 mutations in ALS patients. This further supports the involvement of global defects in RNA metabolism in ALS.
© The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
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19 MeSH Terms
Whole-exome sequencing in familial atrial fibrillation.
Weeke P, Muhammad R, Delaney JT, Shaffer C, Mosley JD, Blair M, Short L, Stubblefield T, Roden DM, Darbar D, National Heart, Lung, and Blood Institute (NHLBI) GO Exome Sequencing Project
(2014) Eur Heart J 35: 2477-83
MeSH Terms: Adolescent, Adult, Aged, Atrial Fibrillation, Codon, Nonsense, Exome, Female, Gene Frequency, Genetic Predisposition to Disease, Genetic Variation, Humans, Male, Middle Aged, Mutation, Missense, Pedigree, RNA Splice Sites, Registries, Sequence Analysis, DNA, Young Adult
Show Abstract · Added June 26, 2014
AIMS - Positional cloning and candidate gene approaches have shown that atrial fibrillation (AF) is a complex disease with familial aggregation. Here, we employed whole-exome sequencing (WES) in AF kindreds to identify variants associated with familial AF.
METHODS AND RESULTS - WES was performed on 18 individuals in six modestly sized familial AF kindreds. After filtering very rare variants by multiple metrics, we identified 39 very rare and potentially pathogenic variants [minor allele frequency (MAF) ≤0.04%] in genes not previously associated with AF. Despite stringent filtering >1 very rare variants in the 5/6 of the kindreds were identified, whereas no plausible variants contributing to familial AF were found in 1/6 of the kindreds. Two candidate AF variants in the calcium channel subunit genes (CACNB2 and CACNA2D4) were identified in two separate families using expression data and predicted function.
CONCLUSION - By coupling family data with exome sequencing, we identified multiple very rare potentially pathogenic variants in five of six families, suggestive of a complex disease mechanism, whereas none were identified in the remaining AF pedigree. This study highlights some important limitations and challenges associated with performing WES in AF including the importance of having large well-curated multi-generational pedigrees, the issue of potential AF misclassification, and limitations of WES technology when applied to a complex disease.
Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2014. For permissions please email: journals.permissions@oup.com.
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19 MeSH Terms
Trafficking-deficient mutant GABRG2 subunit amount may modify epilepsy phenotype.
Kang JQ, Shen W, Macdonald RL
(2013) Ann Neurol 74: 547-59
MeSH Terms: Animals, Cell Line, Transformed, Codon, Nonsense, Disease Models, Animal, Endoplasmic Reticulum, Epilepsy, Gene Expression Regulation, Genotype, Glycosylation, Humans, Mice, Mice, Transgenic, Models, Molecular, Mutagenesis, Phenotype, Protein Subunits, Protein Transport, Receptors, GABA-A, Transcription Factor CHOP, Transfection, Ubiquitin
Show Abstract · Added January 24, 2015
OBJECTIVE - Genetic epilepsies and many other human genetic diseases display phenotypic heterogeneity, often for unknown reasons. Disease severity associated with nonsense mutations is dependent partially on mutation gene location and resulting efficiency of nonsense-mediated mRNA decay (NMD) to eliminate potentially toxic proteins. Nonsense mutations in the last exon do not activate NMD, thus producing truncated proteins. We compared the protein metabolism and the impact on channel biogenesis, function, and cellular homeostasis of truncated γ2 subunits produced by GABRG2 nonsense mutations associated with epilepsy of different severities and by a nonsense mutation in the last exon unassociated with epilepsy.
METHODS - γ-Aminobutyric acid type A receptor subunits were coexpressed in non-neuronal cells and neurons. NMD was studied using minigenes that support NMD. Protein degradation rates were determined using (35) S radiolabeling pulse chase. Channel function was determined by whole cell recordings, and subunits trafficking and cellular toxicity were determined using flow cytometry, immunoblotting, and immunohistochemistry.
RESULTS - Although all GABRG2 nonsense mutations resulted in loss of γ2 subunit surface expression, the truncated subunits had different degradation rates and stabilities, suppression of wild-type subunit biogenesis and function, amounts of conjugation with polyubiquitin, and endoplasmic reticulum stress levels.
INTERPRETATION - We compared molecular phenotypes of GABRG2 nonsense mutations. The findings suggest that despite the common loss of mutant allele function, each mutation produced different intracellular levels of trafficking-deficient subunits. The concentration-dependent suppression of wild-type channel function and cellular disturbance resulting from differences in mutant subunit metabolism may contribute to associated epilepsy severities and by implication to phenotypic heterogeneity in many inherited human diseases.
© 2013 American Neurological Association.
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21 MeSH Terms
mRNA surveillance and endoplasmic reticulum quality control processes alter biogenesis of mutant GABAA receptor subunits associated with genetic epilepsies.
Macdonald RL, Kang JQ
(2012) Epilepsia 53 Suppl 9: 59-70
MeSH Terms: Animals, Channelopathies, Codon, Nonsense, Endoplasmic Reticulum, Epilepsy, Epilepsy, Generalized, Frameshift Mutation, Humans, Ion Channels, Mutation, Proteostasis Deficiencies, RNA Splicing, RNA, Messenger, Receptors, GABA-A
Show Abstract · Added January 24, 2015
Previous studies from our and other groups have demonstrated that the majority of γ-aminobutyric acid (GABA)(A) receptor subunit mutations produce mutant subunits with impaired biogenesis and trafficking. These GABA(A) receptor mutations include missense, nonsense, deletion, or insertion mutations that result in a frameshift with premature translation-termination codons (PTCs) and splice-site mutations. Frameshift or splice-site mutations produce mutant proteins with PTCs, thus generating nonfunctional truncated proteins. All of these mutant GABA(A) receptor subunits are subject to cellular quality control at the messenger RNA (mRNA) or protein level. These quality-control checkpoints shape the cell's response to the presence of the mutant subunits and attempt to reduce the impact of the mutant subunit on GABA(A) receptor expression and function. The check points prevent nonfunctioning or malfunctioning GABA(A) receptor subunits from trafficking to the cell surface or to synapses, and help to ensure that the receptor channels trafficked to the membrane and synapses are indeed functional. However, if and how these quality control or check points impact the posttranslational modifications of functional GABA(A) receptor channels such as receptor phosphorylation and ubiquitination and their involvement in mediating GABAergic inhibitory synaptic strength needs to be investigated in the near future.
Wiley Periodicals, Inc. © 2012 International League Against Epilepsy.
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14 MeSH Terms
The GABRG2 nonsense mutation, Q40X, associated with Dravet syndrome activated NMD and generated a truncated subunit that was partially rescued by aminoglycoside-induced stop codon read-through.
Huang X, Tian M, Hernandez CC, Hu N, Macdonald RL
(2012) Neurobiol Dis 48: 115-23
MeSH Terms: Aminoglycosides, Codon, Nonsense, Codon, Terminator, Epilepsies, Myoclonic, HEK293 Cells, Humans, Nonsense Mediated mRNA Decay, Protein Subunits, Receptors, GABA-A
Show Abstract · Added January 24, 2015
The GABRG2 nonsense mutation, Q40X, is associated with the severe epilepsy syndrome, Dravet syndrome, and is predicted to generate a premature translation-termination codon (PTC) in the GABA(A) receptor γ2 subunit mRNA in a position that codes for the first amino acid of the mutant subunit. We determined the effects of the mutation on γ2 subunit mRNA and protein synthesis and degradation, as well as on α1β2γ2 GABA(A) receptor assembly, trafficking and surface expression in HEK cells. Using bacterial artificial chromosome (BAC) constructs, we found that γ2(Q40X) subunit mRNA was degraded by nonsense mediated mRNA decay (NMD). Undegraded mutant mRNA was translated to a truncated peptide, likely the signal peptide, which was cleaved further. We also found that mutant γ2(Q40X) subunits did not assemble into functional receptors, thus decreasing GABA-evoked current amplitudes. The GABRG2(Q40X) mutation is one of several epilepsy-associated nonsense mutations that have the potential to be rescued by reading through the PTC, thus restoring full-length protein translation. As a first approach, we investigated the use of the aminoglycoside, gentamicin, to rescue translation of intact mutant subunits by inducing mRNA read-through. In the presence of gentamicin, synthesis of full length γ2 subunits was partially restored, and surface biotinylation and whole cell recording experiments suggested that rescued γ2 subunits could corporate into functional, surface GABA(A) receptors, indicating a possible direction for future therapy.
Copyright © 2012 Elsevier Inc. All rights reserved.
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9 MeSH Terms
The intronic GABRG2 mutation, IVS6+2T->G, associated with childhood absence epilepsy altered subunit mRNA intron splicing, activated nonsense-mediated decay, and produced a stable truncated γ2 subunit.
Tian M, Macdonald RL
(2012) J Neurosci 32: 5937-52
MeSH Terms: Analysis of Variance, Animals, Brain, Cell Line, Transformed, Cells, Cultured, Cerebral Cortex, Chromosomes, Artificial, Bacterial, Codon, Nonsense, Embryo, Mammalian, Flow Cytometry, Gene Expression Regulation, Humans, Immunoprecipitation, Introns, Membrane Potentials, Mice, Mice, Inbred C57BL, Mice, Transgenic, Microscopy, Confocal, Models, Molecular, Mutation, Neurons, Nonsense Mediated mRNA Decay, Patch-Clamp Techniques, Protein Subunits, Protein Transport, RNA Splicing, RNA, Messenger, RNA, Small Interfering, Rats, Rats, Sprague-Dawley, Receptors, GABA-A, Transfection, gamma-Aminobutyric Acid
Show Abstract · Added December 5, 2013
The intronic GABRG2 mutation, IVS6+2T→G, was identified in an Australian family with childhood absence epilepsy and febrile seizures (Kananura et al., 2002). The GABRG2 intron 6 splice donor site was found to be mutated from GT to GG. We generated wild-type and mutant γ2 subunit bacterial artificial chromosomes (BACs) driven by a CMV promoter and expressed them in HEK293T cells and expressed wild-type and mutant γ2 subunit BACs containing the endogenous hGABRG2 promoter in transgenic mice. Wild-type and mutant GABRG2 mRNA splicing patterns were determined in both BAC-transfected HEK293T cells and transgenic mouse brain, and in both, the mutation abolished intron 6 splicing at the donor site, activated a cryptic splice site, generated partial intron 6 retention, and produced a frameshift in exon 7 that created a premature translation termination codon (PTC). The resultant mutant mRNA was either degraded partially by nonsense-mediated mRNA decay or translated to a stable, truncated subunit (the γ2-PTC subunit) containing the first six GABRG2 exons and a novel frameshifted 29 aa C-terminal tail. The γ2-PTC subunit was homologous to the mollusk AChBP (acetylcholine binding protein) but was not secreted from cells. It was retained in the ER and not expressed on the surface membrane, but it did oligomerize with α1 and β2 subunits. These results suggested that the GABRG2 mutation, IVS6+2T→G, reduced surface αβγ2 receptor levels, thus reducing GABAergic inhibition, by reducing GABRG2 transcript level and producing a stable, nonfunctional truncated subunit that had a dominant-negative effect on αβγ2 receptor assembly.
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34 MeSH Terms
Loss-of-function mutations in Notch receptors in cutaneous and lung squamous cell carcinoma.
Wang NJ, Sanborn Z, Arnett KL, Bayston LJ, Liao W, Proby CM, Leigh IM, Collisson EA, Gordon PB, Jakkula L, Pennypacker S, Zou Y, Sharma M, North JP, Vemula SS, Mauro TM, Neuhaus IM, Leboit PE, Hur JS, Park K, Huh N, Kwok PY, Arron ST, Massion PP, Bale AE, Haussler D, Cleaver JE, Gray JW, Spellman PT, South AP, Aster JC, Blacklow SC, Cho RJ
(2011) Proc Natl Acad Sci U S A 108: 17761-6
MeSH Terms: Base Sequence, Carcinoma, Squamous Cell, Cell Communication, Codon, Nonsense, Electrophoretic Mobility Shift Assay, Humans, Lod Score, Lung Neoplasms, Molecular Sequence Data, Receptor, Notch1, Receptor, Notch2, Sequence Analysis, DNA, Signal Transduction, Skin Neoplasms
Show Abstract · Added March 10, 2014
Squamous cell carcinomas (SCCs) are one of the most frequent forms of human malignancy, but, other than TP53 mutations, few causative somatic aberrations have been identified. We identified NOTCH1 or NOTCH2 mutations in ~75% of cutaneous SCCs and in a lesser fraction of lung SCCs, defining a spectrum for the most prevalent tumor suppressor specific to these epithelial malignancies. Notch receptors normally transduce signals in response to ligands on neighboring cells, regulating metazoan lineage selection and developmental patterning. Our findings therefore illustrate a central role for disruption of microenvironmental communication in cancer progression. NOTCH aberrations include frameshift and nonsense mutations leading to receptor truncations as well as point substitutions in key functional domains that abrogate signaling in cell-based assays. Oncogenic gain-of-function mutations in NOTCH1 commonly occur in human T-cell lymphoblastic leukemia/lymphoma and B-cell chronic lymphocytic leukemia. The bifunctional role of Notch in human cancer thus emphasizes the context dependency of signaling outcomes and suggests that targeted inhibition of the Notch pathway may induce squamous epithelial malignancies.
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14 MeSH Terms
Zebrafish model of tuberous sclerosis complex reveals cell-autonomous and non-cell-autonomous functions of mutant tuberin.
Kim SH, Speirs CK, Solnica-Krezel L, Ess KC
(2011) Dis Model Mech 4: 255-67
MeSH Terms: Animals, Brain, Cell Size, Codon, Nonsense, Disease Models, Animal, Embryo, Nonmammalian, Gene Expression Regulation, Developmental, Hepatocytes, Humans, Liver, Mutant Proteins, Neurons, Sirolimus, Transcription Factors, Tuberous Sclerosis, Tuberous Sclerosis Complex 2 Protein, Tumor Suppressor Proteins, Zebrafish
Show Abstract · Added September 24, 2013
Tuberous sclerosis complex (TSC) is an autosomal dominant disease caused by mutations in either the TSC1 (encodes hamartin) or TSC2 (encodes tuberin) genes. Patients with TSC have hamartomas in various organs throughout the whole body, most notably in the brain, skin, eye, heart, kidney and lung. To study the development of hamartomas, we generated a zebrafish model of TSC featuring a nonsense mutation (vu242) in the tsc2 gene. This tsc2(vu242) allele encodes a truncated Tuberin protein lacking the GAP domain, which is required for inhibition of Rheb and of the TOR kinase within TORC1. We show that tsc2(vu242) is a recessive larval-lethal mutation that causes increased cell size in the brain and liver. Greatly elevated TORC1 signaling is observed in tsc2(vu242/vu242) homozygous zebrafish, and is moderately increased in tsc2(vu242/+) heterozygotes. Forebrain neurons are poorly organized in tsc2(vu242/vu242) homozygous mutants, which have extensive gray and white matter disorganization and ectopically positioned cells. Genetic mosaic analyses demonstrate that tsc2 limits TORC1 signaling in a cell-autonomous manner. However, in chimeric animals, tsc2(vu242/vu242) mutant cells also mislocalize wild-type host cells in the forebrain in a non-cell-autonomous manner. These results demonstrate a highly conserved role of tsc2 in zebrafish and establish a new animal model for studies of TSC. The finding of a non-cell-autonomous function of mutant cells might help explain the formation of brain hamartomas and cortical malformations in human TSC.
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18 MeSH Terms
Topoisomerase IIalpha binding domains of adenomatous polyposis coli influence cell cycle progression and aneuploidy.
Wang Y, Coffey RJ, Osheroff N, Neufeld KL
(2010) PLoS One 5: e9994
MeSH Terms: Adenomatous Polyposis Coli, Adenomatous Polyposis Coli Protein, Aneuploidy, Antigens, Neoplasm, Binding Sites, Cell Cycle, Cell Line, Tumor, Codon, Nonsense, DNA Topoisomerases, Type II, DNA-Binding Proteins, Epithelial Cells, G2 Phase, Humans, Repetitive Sequences, Nucleic Acid, beta Catenin
Show Abstract · Added August 12, 2010
BACKGROUND - Truncating mutations in the tumor suppressor gene APC (Adenomatous Polyposis Coli) are thought to initiate the majority of colorectal cancers. The 15- and 20-amino acid repeat regions of APC bind beta-catenin and have been widely studied for their role in the negative regulation of canonical Wnt signaling. However, functions of APC in other important cellular processes, such as cell cycle control or aneuploidy, are only beginning to be studied. Our previous investigation implicated the 15-amino acid repeat region of APC (M2-APC) in the regulation of the G2/M cell cycle transition through interaction with topoisomerase IIalpha (topo IIalpha).
METHODOLOGY/PRINCIPAL FINDINGS - We now demonstrate that the 20-amino acid repeat region of APC (M3-APC) also interacts with topo IIalpha in colonic epithelial cells. Expression of M3-APC in cells with full-length endogenous APC causes cell accumulation in G2. However, cells with a mutated topo IIalpha isoform and lacking topo IIbeta did not arrest, suggesting that the cellular consequence of M2- or M3-APC expression depends on functional topoisomerase II. Both purified recombinant M2- and M3-APC significantly enhanced the activity of topo IIalpha. Of note, although M3-APC can bind beta-catenin, the G2 arrest did not correlate with beta-catenin expression or activity, similar to what was seen with M2-APC. More importantly, expression of either M2- or M3-APC also led to increased aneuploidy in cells with full-length endogenous APC but not in cells with truncated endogenous APC that includes the M2-APC region.
CONCLUSIONS/SIGNIFICANCE - Together, our data establish that the 20-amino acid repeat region of APC interacts with topo IIalpha to enhance its activity in vitro, and leads to G2 cell cycle accumulation and aneuploidy when expressed in cells containing full-length APC. These findings provide an additional explanation for the aneuploidy associated with many colon cancers that possess truncated APC.
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15 MeSH Terms
Transcripts from a novel BMPR2 termination mutation escape nonsense mediated decay by downstream translation re-initiation: implications for treating pulmonary hypertension.
Hamid R, Hedges LK, Austin E, Phillips JA, Loyd JE, Cogan JD
(2010) Clin Genet 77: 280-6
MeSH Terms: Aminoglycosides, Bone Morphogenetic Protein Receptors, Type II, Codon, Nonsense, Female, Humans, Hypertension, Pulmonary, Lymphocytes, Male, Mutation, Pedigree
Show Abstract · Added March 5, 2014
Bone morphogenetic protein receptor type 2 (BMPR2) gene mutations are a major risk factor for heritable pulmonary arterial hypertension (HPAH), an autosomal dominant fatal disease. We have previously shown that BMPR2 transcripts that contain premature termination codon (PTC) mutations are rapidly and nearly completely degraded through nonsense mediated decay (NMD). Here we report a unique PTC mutation (W13X) that did not behave in the predicted manner. We found that patient-derived cultured lymphocytes (CLs) contained readily detectable levels of the PTC-containing transcript. Further analysis suggested that this transcript escaped NMD by translational re-initiation at a downstream Kozak sequence, resulting in the omission of 173 amino acids. Treatment of CLs containing the PTC with an aminoglycoside decreased the truncated protein levels, with a reciprocal increase in full-length BMPR2 protein and, importantly, BMPR-II signaling. This is the first demonstration of aminoglycoside-mediated 'repair' of a BMPR2 mutation at the protein level in patient-derived cells and has obvious implications for treatment of HPAH where no disease-specific treatment options are available. Our data also suggest the need for a more thorough characterization of mutations prior to labeling them as haploinsufficient or dominant negative based simply on sequencing data.
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10 MeSH Terms