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1.
Sci Rep ; 13(1): 20619, 2023 Nov 27.
Article in English | MEDLINE | ID: mdl-38012284

ABSTRACT

The liquid water around the Antarctic Ice Sheet plays a key role in modulating both the vulnerability of ice shelves to hydrofracturing and ice discharge from outlet glaciers. Therefore, it needs to be adequately constrained for precise future projections of ice-mass loss and global sea-level rise. Although glacial lake outburst floods (GLOFs) pose one of the greatest risks in glacierized mountainous regions, any long-term monitoring of Antarctic ice-marginal lakes and their associated potential for GLOFs has been neglected until recently owing to the limited number of such events reported in Antarctica. Here we present direct evidence of repeated GLOFs from Lake Kaminotani-Ike, an ice-sheet-dammed lake in East Antarctica, via an analysis of historical aerial photographs and recent satellite data. Two GLOFs occurred in 1969-1971 and 2017, with discharge volumes of (8.6 ± 1.5) × 107 and (7.1 ± 0.4) × 107 m3, respectively, making them two of the largest GLOFs in Antarctica. A southerly oceanward pathway beneath the ice sheet is the most likely drainage route of these GLOF events based on the available surface- and bed-elevation datasets. Furthermore, the 2017 event occurred during the austral winter, thereby implying the possibility of year-round active subglacial networks in Antarctica. Our results highlight that studies on Antarctic ice-marginal lakes provide an opportunity to better understand Antarctic hydrological processes and emphasize the need for both detailed monitoring of ice-marginal lakes and detailed surveying of the subglacial environments of the Antarctic Ice Sheet.

2.
Annu Int Conf IEEE Eng Med Biol Soc ; 2022: 4179-4182, 2022 07.
Article in English | MEDLINE | ID: mdl-36086589

ABSTRACT

High-frequency sounds above 20 kHz presented via bone conduction can be heard clearly and transmit speech information using amplitude modulation. Additionally, bone-conducted ultrasound (BCU) can be perceived even when the vibrator is presented to body parts distant from the head, such as the neck, arm, and trunk. To evaluate this previously presented BCU hearing, word intelligibility and monosyllable articulation tests were conducted in Japanese. The results suggested that a practical speech transmission, comparable to ordinary BCUs presented onto the head, can be obtained by distantly presented BCU.


Subject(s)
Speech Perception , Acoustic Stimulation/methods , Bone Conduction , Hearing , Hearing Tests
3.
Geophys J Int ; 229(3): 1914-1926, 2022 Jun.
Article in English | MEDLINE | ID: mdl-35250356

ABSTRACT

Here we qualitatively analyse the mass change patterns across Antarctica via independent component analysis (ICA), a statistics-based blind source separation method to extract signals from complex data sets, in an attempt to reduce uncertainties in the glacial isostatic adjustment (GIA) effects and improve understanding of Antarctic Ice Sheet (AIS) mass-balance. We extract the six leading independent components from gravimetric data acquired during the Gravity Recovery and Climate Experiment (GRACE) and GRACE Follow-On (GRACE-FO) missions. The results reveal that the observed continental-scale mass changes can be effectively separated into several spatial patterns that may be dominated by different physical processes. Although the hidden independent physical processes cannot be completely isolated, some significant signals, such as glacier melt, snow accumulation, periodic climatic signals, and GIA effects, can be determined without introducing any external information. We also observe that the time period of the analysed data set has a direct impact on the ICA results, as the impacts of extreme events, such as the anomalously large snowfall events in the late 2000s, may cause dramatic spatial and temporal changes in the ICA results. ICA provides a unique and informative approach to obtain a better understanding of both AIS-scale mass changes and specific regional-scale spatiotemporal signal variations.

4.
J Hum Genet ; 66(3): 237-241, 2021 Mar.
Article in English | MEDLINE | ID: mdl-32920598

ABSTRACT

Loss-of-function (LoF) variants in NEK1 have recently been reported to be associated with amyotrophic lateral sclerosis (ALS). In this study, we investigated the association of NEK1 LoF variants with an increased risk of sporadic ALS (SALS) and the clinical characteristics of patients with SALS carrying LoF variants in a Japanese case series. Whole-exome sequencing analysis was performed for a series of 446 SALS patients in whom pathogenic variants in familial ALS-causative genes have not been identified and 1163 healthy control subjects in our Japanese series. We evaluated LoF variants, defined as nonsense, splice-site disrupting single-nucleotide variants (SNVs), or short insertion/deletion (indel) variants predicted to cause frameshifts in NEK1. We identified seven NEK1 LoF variants in patients with SALS (1.57%), whereas only one was identified in control subjects (0.086%) (P = 0.00073, Fisher's exact test). This finding is consistent with those in recent reports from other regions in the world. In conclusion, we demonstrated that NEK1 LoF variants are also associated with an increased risk of SALS in the Japanese population.


Subject(s)
Amyotrophic Lateral Sclerosis/genetics , Asian People/genetics , Loss of Function Mutation , NIMA-Related Kinase 1/deficiency , Age of Onset , Aged , Amyotrophic Lateral Sclerosis/ethnology , Amyotrophic Lateral Sclerosis/psychology , Codon, Nonsense , Cognition Disorders/genetics , Female , Genetic Association Studies , Genetic Predisposition to Disease , Humans , INDEL Mutation , Male , Middle Aged , Mutation , NIMA-Related Kinase 1/genetics , NIMA-Related Kinase 1/physiology , Polymorphism, Single Nucleotide , Protein Isoforms/genetics , RNA Splice Sites/genetics , Exome Sequencing
5.
Neurogenetics ; 22(1): 11-17, 2021 03.
Article in English | MEDLINE | ID: mdl-32815063

ABSTRACT

Our objective was to investigate the frequency of KIF5A variants in amyotrophic lateral sclerosis (ALS) and the clinical characteristics of familial ALS (FALS) associated with variants in KIF5A. Whole-exome sequence analysis was performed for a Japanese series of 43 families with FALS and 444 patients with sporadic ALS (SALS), in whom causative variants had not been identified. We compared the frequencies of rare variants (MAF < 0.01) in KIF5A, including missense and loss of function (LoF) variants, between ALS and control subjects (n = 1163). Clinical characteristics of patients with FALS carrying pathogenic variants in KIF5A were also described. LoF variants were identified only in the probands of two families with FALS, both of which were 3' splice-site variants leading to exon skipping and an altered C-terminal domain, located in the mutational hotspot causing FALS, and were considered to be pathogenic for FALS. Rare missense variants in KIF5A were identified in five patients with SALS (1.13%) and 11 control subjects (0.95%, carrier frequency), which were not significantly different. Consequently, the pathogenic LoF variants in KIF5A accounted for 2.1% of all FALS families in this study. These patients suffered from ALS characteristically associated with the predominant involvement of upper motor neuron. In conclusion, we identified two pathogenic splice-site variants in KIF5A in the probands in two Japanese families with FALS, which altered the C-terminal region of KIF5A. Our findings broaden the phenotype spectrum of ALS associated with variants in KIF5A in the Japanese series.


Subject(s)
Amyotrophic Lateral Sclerosis/genetics , Genetic Predisposition to Disease/genetics , Kinesins/genetics , Mutation/genetics , Adult , Amyotrophic Lateral Sclerosis/diagnosis , Asian People/genetics , Female , Genetic Association Studies , Humans , Japan , Male , Middle Aged
6.
Annu Int Conf IEEE Eng Med Biol Soc ; 2020: 3877-3880, 2020 07.
Article in English | MEDLINE | ID: mdl-33018847

ABSTRACT

Ultrasound can be clearly perceived by bone-conduction, and this "bone-conducted ultrasound (BCU)" can transmit speech information by using amplitude modulation (AM). Further, BCU can be perceived not only on the head but also on the distal parts of the body like the neck, trunk and arms. This "distantly-presented BCU" can be applied to the novel interface that can transmit sound information selectively to specific users who touches the vibrator. However, the ability to transmit sound information of distantly-presented BCU is unclear. First, to assess frequency discrimination ability, difference limens for frequency (DLFs) of the distantly-presented AM-BCU were measured with/without a low-pass masking noise that masked the self-demodulated components generated by the nonlinearity of biological tissues. DLFs comparable to that of air-conducted sounds were observed, whereas DLFs significantly increased above 1 kHz under the masking condition. These results suggest that practical frequency discrimination ability can be obtained even when BCUs were presented to distal body parts. Additionally, it is indicated that the demodulated components may contribute to transmitting frequency information above 1 kHz. Second, monosyllable articulation and word intelligibility tests were conducted in Japanese. The intelligibility and articulation at the neck were 55% and 38% respectively, whereas they decreased as the stimulus placement gets farther from the head. The results suggest the distantly-presented BCU device can be applied to transmission of speech information.


Subject(s)
Bone Conduction , Speech , Acoustic Stimulation , Differential Threshold , Ultrasonography
7.
Sci Rep ; 10(1): 11942, 2020 07 20.
Article in English | MEDLINE | ID: mdl-32686731

ABSTRACT

Intracranial artery stenosis (ICAS) is the most common cause of ischemic stroke worldwide. RNF213 single nucleotide variant c.14429G > A (p.Arg4810Lys, rs112735431) was recently reported to be associated with ICAS in East Asians. However, the disease susceptibility of other RNF213 variants has not been clarified. This study comprehensively investigated ICAS-associated RNF213 variants in a pool of 168 Japanese ICAS patients and 1,194 control subjects. We found 138 nonsynonymous germline variants by target resequencing of all coding exons in RNF213. Association study between ICAS patients and control subjects revealed that only p.Arg4810Lys had significant association with ICAS (P = 1.5 × 10-28, odds ratio = 29.3, 95% confidence interval 15.31-56.2 [dominant model]). Fourteen of 138 variants were rare variants detected in ICAS patients not harboring p.Arg4810Lys variant. Two of these rare variants (p.Cys118Arg and p.Leu2356Phe) consistent with variants previously reported in moyamoya disease patients characterized by stenosis of intracranial artery and association with RNF213, and three rare variants (p.Ser193Gly, p.Val1817Leu, and p.Asp3329Tyr) were found neither in control subjects and Single Nucleotide Polymorphism Database. The present findings may improve our understanding of the genetic background of intracranial artery stenosis.


Subject(s)
Adenosine Triphosphatases/genetics , Constriction, Pathologic/etiology , Constriction, Pathologic/pathology , Genetic Predisposition to Disease , Genetic Variation , Intracranial Arterial Diseases/genetics , Intracranial Arterial Diseases/pathology , Ubiquitin-Protein Ligases/genetics , Adolescent , Adult , Aged , Aged, 80 and over , Alleles , Amino Acid Substitution , Female , Genetic Association Studies , Genotype , Humans , Intracranial Arterial Diseases/diagnostic imaging , Male , Middle Aged , Mutation, Missense , Polymorphism, Single Nucleotide , Sequence Analysis, DNA , Young Adult
8.
Nat Genet ; 51(8): 1222-1232, 2019 08.
Article in English | MEDLINE | ID: mdl-31332380

ABSTRACT

Noncoding repeat expansions cause various neuromuscular diseases, including myotonic dystrophies, fragile X tremor/ataxia syndrome, some spinocerebellar ataxias, amyotrophic lateral sclerosis and benign adult familial myoclonic epilepsies. Inspired by the striking similarities in the clinical and neuroimaging findings between neuronal intranuclear inclusion disease (NIID) and fragile X tremor/ataxia syndrome caused by noncoding CGG repeat expansions in FMR1, we directly searched for repeat expansion mutations and identified noncoding CGG repeat expansions in NBPF19 (NOTCH2NLC) as the causative mutations for NIID. Further prompted by the similarities in the clinical and neuroimaging findings with NIID, we identified similar noncoding CGG repeat expansions in two other diseases: oculopharyngeal myopathy with leukoencephalopathy and oculopharyngodistal myopathy, in LOC642361/NUTM2B-AS1 and LRP12, respectively. These findings expand our knowledge of the clinical spectra of diseases caused by expansions of the same repeat motif, and further highlight how directly searching for expanded repeats can help identify mutations underlying diseases.


Subject(s)
Ataxia/genetics , Brain/pathology , Fragile X Syndrome/genetics , Genetic Markers , High-Throughput Nucleotide Sequencing/methods , Muscular Dystrophies/genetics , Neurodegenerative Diseases/genetics , Tremor/genetics , Trinucleotide Repeat Expansion/genetics , Adult , Ataxia/pathology , Brain/metabolism , Case-Control Studies , Female , Fragile X Mental Retardation Protein/genetics , Fragile X Syndrome/pathology , Genome-Wide Association Study , Humans , Intranuclear Inclusion Bodies/genetics , Intranuclear Inclusion Bodies/pathology , Linkage Disequilibrium , Low Density Lipoprotein Receptor-Related Protein-1/genetics , Male , Middle Aged , Muscular Dystrophies/pathology , Mutation , Neurodegenerative Diseases/pathology , Neuroimaging/methods , Pedigree , Tremor/pathology
9.
Parkinsonism Relat Disord ; 61: 57-63, 2019 04.
Article in English | MEDLINE | ID: mdl-30528172

ABSTRACT

INTRODUCTION: Glucocerebrosidase gene (GBA) variants are associated with Parkinson's disease (PD) and dementia with Lewy bodies (DLB). The molecular mechanisms underlying these diseases with GBA variants, however, are not well understood. In order to determine the effect of a deletion mutation in GBA, we performed a neuroimaging, genetic, and enzymatic study in a Japanese family with a gross deletion of exons 3 to 11 in GBA. METHODS: We performed [123I] FP-CIT SPECT and [123I] N-isopropyl-p-iodoamphetamine SPECT (IMP-SPECT), and determined GBA expression and glucocerebrosidase (GCase) activity in leukocytes in two GBA-associated PD patients and nine unaffected individuals (including four mutation carriers) in a Japanese family with a heterozygous gross deletion mutation in the GBA gene. RESULTS: The two PD patients and two of the four clinically unaffected carriers showed decreased [123I] FP-CIT uptake. IMP-SPECT showed a pattern like that in DLB in one patient. When we compared PD patients with GBA mutations with clinically unaffected carriers, there was a poor correlation between the development of PD and the expression level of GBA or GCase activity. CONCLUSION: We confirmed the gross deletion mutation in the GBA gene, which appeared to be associated with the PD or reduced [123I] FP-CIT in this family. However, since we cannot conclude whether a reduction of GCase activity is directly correlated with the pathogenesis of PD or not, longitudinal follow-up of this family is needed.


Subject(s)
Brain/diagnostic imaging , Glucosylceramidase/genetics , Parkinson Disease/genetics , Aged , Aged, 80 and over , Asian People , Exons , Family , Female , Gene Deletion , Glucosylceramidase/metabolism , Humans , Iofetamine , Japan , Leukocytes , Male , Middle Aged , Neuroimaging , Parkinson Disease/diagnostic imaging , Parkinson Disease/enzymology , Pedigree , Radiopharmaceuticals , Reverse Transcriptase Polymerase Chain Reaction , Tomography, Emission-Computed, Single-Photon , Tropanes
10.
J Neurol Neurosurg Psychiatry ; 90(5): 537-542, 2019 05.
Article in English | MEDLINE | ID: mdl-30355605

ABSTRACT

OBJECTIVES: To evaluate the burden of rare variants in the causative genes for amyotrophic lateral sclerosis (ALS) on the age at onset of ALS in a Japanese case series. METHODS: We conducted whole-exome sequencing analysis of 89 families with familial ALS (FALS) and 410 patients with sporadic ALS (SALS) to identify known pathogenic mutations or rare functionally predicted deleterious variants in the causative genes for ALS. Rare variants (minor allele frequency <1%) with scaled Combined Annotation-Dependent Depletion score >20 were defined as rare functionally predicted deleterious variants. The patients with ALS were classified on the basis of the number of pathogenic and/or rare functionally predicted deleterious variants, and the age at onset was compared among the classified groups. RESULTS: Whole-exome sequencing analysis revealed known pathogenic mutations or rare functionally predicted deleterious variants in causative genes for ALS in 56 families with FALS (62.9%) and 87 patients with SALS (21.2%). Such variants in multiple genes were identified in seven probands with FALS and eight patients with SALS. The ages at onset in the patients with ALS with multiple variants were significantly earlier than those in other patients with ALS. Even when the patients with known pathogenic mutations were excluded, a significantly earlier onset of the disease was still observed in patients with multiple rare functionally predicted deleterious variants. CONCLUSIONS: A substantial number of patients carried rare variants in multiple genes, and the burden of rare variants in the known causative genes for ALS affects the age at onset in the Japanese ALS series.


Subject(s)
Amyotrophic Lateral Sclerosis/genetics , Mutation/genetics , Adult , Age of Onset , Case-Control Studies , Female , Humans , Japan , Male , Middle Aged , Exome Sequencing
11.
Brain ; 141(6): 1622-1636, 2018 06 01.
Article in English | MEDLINE | ID: mdl-29718187

ABSTRACT

Several genes related to mitochondrial functions have been identified as causative genes of neuropathy or ataxia. Cytochrome c oxidase assembly factor 7 (COA7) may have a role in assembling mitochondrial respiratory chain complexes that function in oxidative phosphorylation. Here we identified four unrelated patients with recessive mutations in COA7 among a Japanese case series of 1396 patients with Charcot-Marie-Tooth disease (CMT) or other inherited peripheral neuropathies, including complex forms of CMT. We also found that all four patients had characteristic neurological features of peripheral neuropathy and ataxia with cerebellar atrophy, and some patients showed leukoencephalopathy or spinal cord atrophy on MRI scans. Validated mutations were located at highly conserved residues among different species and segregated with the disease in each family. Nerve conduction studies showed axonal sensorimotor neuropathy. Sural nerve biopsies showed chronic axonal degeneration with a marked loss of large and medium myelinated fibres. An immunohistochemical assay with an anti-COA7 antibody in the sural nerve from the control patient showed the positive expression of COA7 in the cytoplasm of Schwann cells. We also observed mildly elevated serum creatine kinase levels in all patients and the presence of a few ragged-red fibres and some cytochrome c oxidase-negative fibres in a muscle biopsy obtained from one patient, which was suggestive of subclinical mitochondrial myopathy. Mitochondrial respiratory chain enzyme assay in skin fibroblasts from the three patients showed a definitive decrease in complex I or complex IV. Immunocytochemical analysis of subcellular localization in HeLa cells indicated that mutant COA7 proteins as well as wild-type COA7 were localized in mitochondria, which suggests that mutant COA7 does not affect the mitochondrial recruitment and may affect the stability or localization of COA7 interaction partners in the mitochondria. In addition, Drosophila COA7 (dCOA7) knockdown models showed rough eye phenotype, reduced lifespan, impaired locomotive ability and shortened synaptic branches of motor neurons. Our results suggest that loss-of-function COA7 mutation is responsible for the phenotype of the presented patients, and this new entity of disease would be referred to as spinocerebellar ataxia with axonal neuropathy type 3.


Subject(s)
Electron Transport Complex IV/genetics , Hereditary Sensory and Motor Neuropathy/complications , Hereditary Sensory and Motor Neuropathy/genetics , Mutation/genetics , Spinocerebellar Ataxias/complications , Spinocerebellar Ataxias/genetics , Adolescent , Animals , Animals, Genetically Modified , Brain/diagnostic imaging , Cells, Cultured , Drosophila , Drosophila Proteins/genetics , Drosophila Proteins/metabolism , Family Health , Female , Fibroblasts/drug effects , Fibroblasts/metabolism , Fibroblasts/pathology , Genetic Predisposition to Disease/genetics , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/metabolism , HeLa Cells , Hereditary Sensory and Motor Neuropathy/diagnostic imaging , Humans , Imaginal Discs/metabolism , Imaginal Discs/ultrastructure , Locomotion/drug effects , Locomotion/genetics , Male , Middle Aged , Motor Neurons/pathology , Neuromuscular Junction/genetics , Neuromuscular Junction/pathology , Neuromuscular Junction/ultrastructure , Psychomotor Performance/physiology , RNA Interference/physiology , Spinal Cord/diagnostic imaging , Spinocerebellar Ataxias/diagnostic imaging , Young Adult
12.
Nat Genet ; 50(4): 581-590, 2018 04.
Article in English | MEDLINE | ID: mdl-29507423

ABSTRACT

Epilepsy is a common neurological disorder, and mutations in genes encoding ion channels or neurotransmitter receptors are frequent causes of monogenic forms of epilepsy. Here we show that abnormal expansions of TTTCA and TTTTA repeats in intron 4 of SAMD12 cause benign adult familial myoclonic epilepsy (BAFME). Single-molecule, real-time sequencing of BAC clones and nanopore sequencing of genomic DNA identified two repeat configurations in SAMD12. Intriguingly, in two families with a clinical diagnosis of BAFME in which no repeat expansions in SAMD12 were observed, we identified similar expansions of TTTCA and TTTTA repeats in introns of TNRC6A and RAPGEF2, indicating that expansions of the same repeat motifs are involved in the pathogenesis of BAFME regardless of the genes in which the expanded repeats are located. This discovery that expansions of noncoding repeats lead to neuronal dysfunction responsible for myoclonic tremor and epilepsy extends the understanding of diseases with such repeat expansion.


Subject(s)
DNA Repeat Expansion , Epilepsies, Myoclonic/genetics , Microsatellite Repeats , Nerve Tissue Proteins/genetics , Sterile Alpha Motif/genetics , Adult , Age of Onset , Autoantigens/genetics , Base Sequence , Epilepsies, Myoclonic/etiology , Epilepsies, Myoclonic/pathology , Female , Genomic Instability , Guanine Nucleotide Exchange Factors/genetics , Humans , Introns , Male , Pedigree , Purkinje Cells/pathology , RNA-Binding Proteins/genetics , Sequence Analysis, DNA
13.
Neurobiol Aging ; 64: 158.e15-158.e19, 2018 04.
Article in English | MEDLINE | ID: mdl-29398122

ABSTRACT

Amyotrophic lateral sclerosis (ALS) is a devastating neurological disease, and the etiology of sporadic ALS is generally unknown. The TANK-binding kinase 1 (TBK1) gene was identified as an ALS gene contributing to a predisposition toward ALS. To reveal the frequency and characteristics of variants of the TBK1 gene in sporadic ALS patients in Japan, we analyzed the TBK1 gene by exome sequencing in a large Japanese cohort of 713 sporadic ALS patients and 800 controls. We identified known or potentially toxic rare variants of TBK1 gene in 9 patients (1.26%) with sporadic ALS, including 4 novel missense variants (p.V23I, p.H322R, p.R358C, and p.T478I) and 3 loss-of-function variants (p.R357X, p.P378_I379del, and p.T419_G420del). The odds ratio between sporadic ALS patients and controls was 10.2 (p = 0.008, 95% confidence interval = 1.67-62.47). These findings support the contribution of TBK1 to the etiology of sporadic ALS in Japanese patients.


Subject(s)
Amyotrophic Lateral Sclerosis/etiology , Amyotrophic Lateral Sclerosis/genetics , Gene Frequency/genetics , Genetic Association Studies , Genetic Variation/genetics , Loss of Function Mutation/genetics , Mutation, Missense/genetics , Protein Serine-Threonine Kinases/genetics , Asian People/genetics , Cohort Studies , Genetic Predisposition to Disease/genetics , Humans , Exome Sequencing
14.
Neurobiol Aging ; 61: 255.e9-255.e16, 2018 01.
Article in English | MEDLINE | ID: mdl-29033165

ABSTRACT

To elucidate the genetic epidemiology of familial amyotrophic lateral sclerosis (FALS) in the Japanese population, we conducted whole-exome sequencing analysis of 30 FALS families in whom causative mutations have not been identified in previous studies. Consequently, whole-exome sequencing analysis revealed novel mutations in HNRNPA1, TBK1, and VCP. Taken together with our previous results of mutational analyses by direct nucleotide sequencing analysis, a microarray-based resequencing method, or repeat-primed PCR analysis, causative mutations were identified in 41 of the 68 families (60.3%) with SOD1 being the most frequent cause of FALS (39.7%). Of the mutations identified in this study, a novel c.862/1018C>G (p.P288A/340A) mutation in HNRNPA1 located in the nuclear localization signal domain of hnRNPA1, enhances the recruitment of mutant hnRNPA1 into stress granules, indicating that an altered nuclear localization signal activity plays an essential role in amyotrophic lateral sclerosis pathogenesis.


Subject(s)
Amyotrophic Lateral Sclerosis/epidemiology , Amyotrophic Lateral Sclerosis/genetics , Asian People/genetics , Exome Sequencing/methods , Genetic Association Studies , Heterogeneous Nuclear Ribonucleoprotein A1/genetics , Mutation/genetics , DNA Mutational Analysis/methods , Female , Humans , Japan/epidemiology , Male , Protein Serine-Threonine Kinases/genetics , Valosin Containing Protein/genetics
15.
Cerebellum ; 17(2): 237-242, 2018 Apr.
Article in English | MEDLINE | ID: mdl-28895081

ABSTRACT

Spinocerebellar ataxia 19/22 (SCA19/22) is a rare type of autosomal dominant SCA that was previously described in 11 families. We report the case of a 30-year-old Japanese man presenting with intellectual disability, early onset cerebellar ataxia, myoclonus, and dystonia without a family history. MRI showed cerebellar atrophy, and electroencephalograms showed paroxysmal sharp waves during hyperventilation and photic stimulation. Trio whole-exome sequencing analysis of DNA samples from the patient and his parents revealed a de novo novel missense mutation (c.1150G>A, p.G384S) in KCND3, the causative gene of SCA19/22, substituting for evolutionally conserved glycine. The mutation was predicted to be functionally deleterious by bioinformatic analysis. Although pure cerebellar ataxia is the most common clinical feature in SCA19/22 families, extracerebellar symptoms including intellectual disability and myoclonus are reported in a limited number of families, suggesting a genotype-phenotype correlation for particular mutations. Although autosomal recessive diseases are more common in patients with early onset sporadic cerebellar ataxia, the present study emphasizes that such a possibility of de novo mutation should be considered.


Subject(s)
Cerebellar Ataxia/genetics , Dystonia/genetics , Intellectual Disability/genetics , Mutation/genetics , Myoclonus/genetics , Shal Potassium Channels/genetics , Adolescent , Cerebellar Ataxia/complications , Cerebellar Ataxia/diagnostic imaging , Dystonia/complications , Dystonia/diagnostic imaging , Electroencephalography , Family Health , Humans , Intellectual Disability/complications , Intellectual Disability/diagnostic imaging , Magnetic Resonance Imaging , Male , Models, Molecular , Myoclonus/complications , Myoclonus/diagnostic imaging , Spinocerebellar Degenerations/genetics , Exome Sequencing
16.
Nat Commun ; 8(1): 1833, 2017 11 28.
Article in English | MEDLINE | ID: mdl-29184138

ABSTRACT

Centromeres and large-scale structural variants evolve and contribute to genome diversity during vertebrate speciation. Here, we perform de novo long-read genome assembly of three inbred medaka strains that are derived from geographically isolated subpopulations and undergo speciation. Using single-molecule real-time (SMRT) sequencing, we obtain three chromosome-mapped genomes of length ~734, ~678, and ~744Mbp with a resource of twenty-two centromeric regions of length 20-345kbp. Centromeres are positionally conserved among the three strains and even between four pairs of chromosomes that were duplicated by the teleost-specific whole-genome duplication 320-350 million years ago. The centromeres do not all evolve at a similar pace; rather, centromeric monomers in non-acrocentric chromosomes evolve significantly faster than those in acrocentric chromosomes. Using methylation sensitive SMRT reads, we uncover centromeres are mostly hypermethylated but have hypomethylated sub-regions that acquire unique sequence compositions independently. These findings reveal the potential of non-acrocentric centromere evolution to contribute to speciation.


Subject(s)
Centromere/genetics , CpG Islands , Genetic Speciation , Vertebrates/genetics , Animals , Base Sequence , Centromere/classification , Chromosome Mapping , Evolution, Molecular , Genetic Association Studies , Genetic Markers , Genetic Variation , Genome , Methylation , Models, Theoretical , Molecular Sequence Annotation , Mutation , Oryzias/genetics , Phylogeny , Polymorphism, Single Nucleotide , Telomere/genetics
17.
Am J Med Genet B Neuropsychiatr Genet ; 174(7): 712-723, 2017 Oct.
Article in English | MEDLINE | ID: mdl-28608572

ABSTRACT

Tourette Syndrome (TS) is a neurodevelopmental disorder characterized by chronic motor and vocal tics. Although there is a large genetic contribution, the genetic architecture of TS remains unclear. Exome sequencing has successfully revealed the contribution of de novo mutations in sporadic cases with neuropsychiatric disorders such as autism and schizophrenia. Here, using exome sequencing, we investigated de novo mutations in individuals with sporadic TS to identify novel risk loci and elucidate the genetic background of TS. Exome analysis was conducted for sporadic TS cases: nine trio families and one quartet family with concordant twins were investigated. Missense mutations were evaluated using functional prediction algorithms, and their population frequencies were calculated based on three public databases. Gene expression patterns in the brain were analyzed using the BrainSpan Developmental Transcriptome. Thirty de novo mutations, including four synonymous and four missense mutations, were identified. Among the missense mutations, one in the rapamycin-insensitive companion of mammalian target of rapamycin (RICTOR)-coding gene (rs140964083: G > A, found in one proband) was predicted to be hazardous. In the three public databases analyzed, variants in the same SNP locus were absent, and variants in the same gene were either absent or present at an extremely low frequency (3/5,008), indicating the rarity of hazardous RICTOR mutations in the general population. The de novo variant of RICTOR may be implicated in the development of sporadic TS, and RICTOR is a novel candidate factor for TS etiology.


Subject(s)
Exome , Mutation, Missense , Rapamycin-Insensitive Companion of mTOR Protein/genetics , Sequence Analysis, DNA/methods , Tourette Syndrome/genetics , Adolescent , Adult , Child , Family , Female , Follow-Up Studies , Genetic Markers , Genetic Predisposition to Disease , Humans , Male , Middle Aged , Prognosis , Young Adult
18.
J Neurol Sci ; 375: 424-429, 2017 Apr 15.
Article in English | MEDLINE | ID: mdl-28320181

ABSTRACT

Peroxisome biogenesis factor 10 (PEX10) is involved in the import of peroxisomal matrix proteins, and the mutation of this gene causes 3 subtypes of peroxisome biogenesis disorders, namely Zellweger syndrome (severe), neonatal adrenoleukodystrophy (moderate) and an ataxic form (mild). Here, we report 3 siblings of the ataxic form with cerebellar ataxia, mild mental retardation, and 3 additional characteristic features: mydriasis, hyperreflexia and involuntary head movement. All 3 siblings are compound heterozygous for a previously reported mutation, c.2T>C (p.M1T), and a novel mutation, c.920G>A, causing a missense change (p.C307Y) located in the RING finger domain of PEX10. The present cases suggest that these PEX10 mutations involve not only cerebellar but also more multiple nervous systems including pupillary autonomic, pyramidal and extrapyramidal systems.


Subject(s)
Cerebellar Ataxia/genetics , Family Health , Mutation/genetics , Peroxisomal Disorders/genetics , Receptors, Cytoplasmic and Nuclear/genetics , Adult , Cerebellar Ataxia/complications , Cerebellar Ataxia/diagnostic imaging , DNA Mutational Analysis , Female , Humans , Magnetic Resonance Imaging , Male , Peroxins , Peroxisomal Disorders/complications , Peroxisomal Disorders/diagnostic imaging , Phenotype
19.
J Hum Genet ; 62(4): 473-480, 2017 Apr.
Article in English | MEDLINE | ID: mdl-27928163

ABSTRACT

Spinal muscular atrophy (SMA) is an autosomal recessive neurodegenerative disorder caused by survival motor neuron gene mutations. Variant forms of SMA accompanied by additional clinical presentations have been classified as atypical SMA and are thought to be caused by variants in as yet unidentified causative genes. Here, we presented the clinical findings of two siblings with an SMA variant followed by progressive cerebral atrophy, and the results of whole-exome sequencing analyses of the family quartet that was performed to identify potential causative variants. We identified two candidate homozygous missense variants, R942Q in the tubulin-folding cofactor D (TBCD) gene and H250Q in the bromo-adjacent homology domain and coiled-coil containing 1 (BAHCC1) gene, located on chromosome 17q25.3 with an interval of 1.4 Mbp. The in silico analysis of both variants suggested that TBCD rather than BAHCC1 was likely the pathogenic gene (TBCD sensitivity, 0.68; specificity, 0.97; BAHCC1 sensitivity, 1.00; specificity, 0.00). Thus, our results show that TBCD is a likely novel candidate gene for atypical SMA with progressive cerebral atrophy. TBCD is predicted to have important functions on tubulin integrity in motor neurons as well as in the central nervous system.


Subject(s)
Brain Diseases/genetics , Microtubule-Associated Proteins/genetics , Proteins/genetics , Spinal Muscular Atrophies of Childhood/genetics , Brain Diseases/physiopathology , Child , Female , Genetic Association Studies , Genetic Predisposition to Disease , Homozygote , Humans , Motor Neurons/pathology , Mutation, Missense , Pedigree , Spinal Muscular Atrophies of Childhood/physiopathology
20.
J Neurol Sci ; 372: 6-10, 2017 Jan 15.
Article in English | MEDLINE | ID: mdl-28017249

ABSTRACT

d-Bifunctional protein (DBP) deficiency is an autosomal recessive disorder of peroxisomal fatty acid oxidation caused by mutations in HSD17B4. It is typically fatal by the age of two years with symptom onset during the neonatal period, and survival until late childhood is rare. We herein report the case of a patient with DBP deficiency surviving until adulthood, who showed severe sensorineural deafness, disturbances in language acquisition, slowly progressive cerebellar ataxia, and peripheral neuropathy. This patient, in whom findings of prior investigations were nondiagnostic, had been followed up as having an early-onset spinocerebellar degeneration of unknown etiology. Whole-exome sequencing analysis at the age of 36 showed two heterozygous variants in the gene HSD17B4, which encodes DBP in this patient. A panel of peroxisomal investigations showed normal levels of very long chain fatty acids (VLCFAs) in plasma and elevated serum phytanic acid levels. Recently, an increasing number of patients with DBP deficiency surviving until adolescence/adulthood have been reported, in whom abnormalities in the levels of VLCFAs and other peroxisomal metabolites are marginal or nonexistent. Genetic analysis of HSD17B4 should be considered in adult patients with cerebellar ataxia, peripheral neuropathy, and pyramidal signs in addition to sensorineural auditory disturbance since childhood.


Subject(s)
Peroxisomal Multifunctional Protein-2/deficiency , Peroxisomal Multifunctional Protein-2/genetics , Protein Deficiency/diagnosis , Protein Deficiency/genetics , Adult , DNA Mutational Analysis , Disease Progression , Humans , Male , Mutation , Peroxisomal Multifunctional Protein-2/blood , Protein Deficiency/mortality
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