A 12-kb structural variation in progressive myoclonic epilepsy was newly identified by long-read whole-genome sequencing.

We report a family with progressive myoclonic epilepsy who underwent whole-exome sequencing but was negative for pathogenic variants. Similar clinical courses of a devastating neurodegenerative phenotype of two affected siblings were highly suggestive of a genetic etiology, which indicates that the survey of genetic variation by whole-exome sequencing was not comprehensive. To investigate the presence of a variant that remained unrecognized by standard genetic testing, PacBio long-read sequencing was performed. Structural variant (SV) detection using low-coverage (6×) whole-genome sequencing called 17,165 SVs (7,216 deletions and 9,949 insertions). Our SV selection narrowed down potential candidates to only five SVs (two deletions and three insertions) on the genes tagged with autosomal recessive phenotypes. Among them, a 12.4-kb deletion involving the CLN6 gene was the top candidate because its homozygous abnormalities cause neuronal ceroid lipofuscinosis. This deletion included the initiation codon and was found in a GC-rich region containing multiple repetitive elements. These results indicate the presence of a causal variant in a difficult-to-sequence region and suggest that such variants that remain enigmatic after the application of current whole-exome sequencing technology could be uncovered by unbiased application of long-read whole-genome sequencing.

Clinical and genetic diversities of Charcot-Marie-Tooth disease with MFN2 mutations in a large case study.

Charcot-Marie-Tooth disease (CMT) constitutes a heterogeneous group affecting motor and sensory neurons in the peripheral nervous system. MFN2 mutations are the most common cause of axonal CMT. We describe the clinical and mutational spectra of CMT patients harboring MFN2 mutations in Japan. We analyzed 1,334 unrelated patients with clinically suspected CMT referred by neurological and neuropediatric departments throughout Japan. We conducted mutation screening using a DNA microarray, targeted resequencing, and whole-exome sequencing. We identified pathogenic or likely pathogenic MFN2 variants from 79 CMT patients, comprising 44 heterozygous and 1 compound heterozygous variants. A total of 15 novel variants were detected. An autosomal dominant family history was determined in 43 cases, and the remaining 36 cases were reported as sporadic with no family history. The mean onset age of CMT in these patients was 12 ± 14 (range 0-59) years. We observed neuropathic symptoms in all patients. Some had optic atrophy, vocal cord paralysis, or spasticity. We detected a compound heterozygous MFN2 mutation in a patient with a severe phenotype and the co-occurrence of MFN2 and PMP22 mutations in a patient with an uncommon phenotype. MFN2 is the most frequent causative gene of CMT2 in Japan. We present 15 novel variants and broad clinical and mutational spectra of Japanese MFN2-related CMT patients. Regardless of the onset age and inheritance pattern, MFN2 gene analysis should be performed. Combinations of causative genes should be considered to explain the phenotypic diversity.

A combination of genetic and biochemical analyses for the diagnosis of PI3K-AKT-mTOR pathway-associated megalencephaly.

BACKGROUND: Constitutive activation of the PI3K-AKT-mTOR pathway (mTOR pathway) underlies megalencephaly in many patients. Yet, prevalence of the involvement of the PI3K-AKT-mTOR pathway in patients with megalencephaly remains to be elucidated, and molecular diagnosis is challenging. Here, we have successfully established a combination of genetic and biochemical methods for diagnosis of mTOR pathway-associated megalencephaly, and have attempted to delineate the clinical characteristics of the disorder. METHODS: Thirteen patients with an increased head circumference and neurological symptoms participated in the study. To evaluate the activation of the mTOR pathway, we performed western blot analysis to determine the expression levels of phosphorylated S6 ribosomal protein (phospho-S6 protein) in lymphoblastoid cell lines from 12 patients. Multiplex targeted sequencing analysis for 15 genes involved in the mTOR pathway was performed on 12 patients, and whole-exome sequencing was performed on one additional patient. Clinical features and MRI findings were also investigated. RESULTS: We identified pathogenic mutations in six (AKT3, 1 patient; PIK3R2, 2 patients; PTEN, 3 patients) of the 13 patients. Increased expression of phospho-S6 protein was demonstrated in all five mutation-positive patients in whom western blotting was performed, as well as in three mutation-negative patients. Developmental delay, dysmorphic facial features were observed in almost all patients. Syndactyly/polydactyly and capillary malformations were not observed, even in patients with AKT3 or PIK3R2 mutations. There were no common phenotypes or MRI findings among these patients. CONCLUSIONS: A combination of genetic and biochemical methods successfully identified mTOR pathway involvement in nine of 13 (approximately 70%) patients with megalencephaly, indicating a major contribution of the pathway to the pathogenesis of megalencephaly. Our combined approach could be useful to identify patients who are suitable for future clinical trials using an mTOR inhibitor.

Arts syndrome with a novel missense mutation in the PRPS1 gene: A case report.

Arts syndrome is characterized by early-onset hypotonia, ataxia, intellectual disability, sensorineural hearing impairment, progressive optic atrophy, and a tendency to develop infections. Arts syndrome is an X-linked disorder caused by a loss-of-function mutation in the PRPS1 gene, which encodes phosphoribosylpyrophosphate synthetase 1. Only three families have been reported. Here, we report another family with Arts syndrome. The initial symptoms of the 1-year-old proband were hypotonia and ataxia, worsening recurrent infection-triggered muscle weakness, motor and intellectual developmental delay, and hearing loss. Both central nervous system involvement and peripheral neuropathy were demonstrated. His three maternal uncles had died before the age of 3years. A genetic analysis of PRPS1 revealed a novel missense mutation, c.367C>G (p.His123Asp). PRPS enzymatic activity was markedly reduced in the patient. His mother was supposed to be an asymptomatic carrier. Arts syndrome should be included in the differential diagnosis of infantile hypotonia and weakness aggravated by recurrent infection with a family history of X-linked inheritance.

Thalamic lesions in acute encephalopathy with biphasic seizures and late reduced diffusion.

BACKGROUND: We aimed to assess the characteristics of thalamic lesions in children with acute encephalopathy with biphasic seizures and late reduced diffusion. METHODS: Using the Tokai Pediatric Neurology Society database, we identified and enrolled 18 children with acute encephalopathy with biphasic seizures and late reduced diffusion from 2008 to 2010. Using diffusion-weighted images, we identified patients with thalamic lesions and compared their clinical factors with those of patients without thalamic lesions. We analyzed the time sequence of thalamic, sucortical, and cortical lesions. To study the topography of thalamic lesions, we divided the thalamus into five sections: anterior, medial, anterolateral, posterolateral, and posterior. Subsequently, we analyzed the relationship between the topography of thalamic lesions and the presence of central-sparing. RESULTS: Seven children presented with symmetrical thalamic lesions associated with bilateral subcortical or cortical lesions. No statistical difference in the clinical features was observed between individuals with and without thalamic lesions. These lesions were observed only when subcortical or cortical lesions were present. In 5 children, thalamic lesions were present in bilateral anterior or anterolateral sections and were associated with subcortical or cortical lesions in bilateral frontal lobes with central-sparing. In the other two children, thalamic lesions were extensive and accompanied by diffuse subcortical and cortical lesions without central-sparing. CONCLUSION: Thalamic lesions in patients with acute encephalopathy with biphasic seizures and late reduced diffusion involve the anterior sections. The thalamocortical network may play a role in development of thalamic lesions in patients with acute encephalopathy with biphasic seizures and late reduced diffusion.

SLC16A2 mutations in two Japanese patients with Allan-Herndon-Dudley syndrome.

Allan-Herndon-Dudley syndrome (AHDS) is a neurodevelopmental disorder that manifests as intellectual disability and motor developmental delay. Thyroid hormone transporter dysfunction due to SLC16A2 mutation is the underlying cause of this disorder. We identified a novel (P537del) and a recurrent (A150V) SLC16A2 mutation in Japanese AHDS patients from two different families. A150V co-segregated with S33P. Both patients showed similar clinical features including severe neurological features and delayed myelination. Thyroid function showed a common finding of elevated T3 levels. No clear genotype-phenotype correlation was observed in patients with SLC16A2 alterations.

Morphology design of porous coordination polymer crystals by coordination modulation.

The design of crystal morphology, or exposed crystal facets, has enabled the development (e.g., catalytic activities, material attributes, and oriented film formation) of porous coordination polymers (PCPs) without changing material compositions. However, because crystal growth mechanisms are not fully understood, control of crystal morphology still remains challenging. Herein, we report the morphology design of [Cu(3)(btc)(2)](n) (btc = benzene-1,3,5-tricarboxylate) by the coordination modulation method (modulator = n-dodecanoic acid or lauric acid). A morphological transition (octahedron-cuboctahedron-cube) in the [Cu(3)(btc)(2)](n) crystal was observed with an increase in concentration of the modulator. By suitably defining a coarse-grained standard unit of [Cu(3)(btc)(2)](n) as its cuboctahedron main pore and determining its attachment energy on crystal surfaces, Monte Carlo coarse-grain modeling revealed the population and orientation of carboxylates and elucidated an important role of the modulator in determining the <100>- and <111>-growth throughout the crystal growth process. This comprehension, in fact, successfully led to designed crystal morphologies with oriented growth on bare substrates. Because selective crystal orientations on the bare substrates were governed by crystal morphology, this contribution also casts a new light on the unexplored issue of the significance of morphology design of PCPs.

Unstitching the nanoscopic mystery of zeolite crystal formation.

A molecular-scale understanding of crystal growth is critical to the development of important materials such as pharmaceuticals, semiconductors and catalysts. Only recently has this been possible with the advent of atomic force microscopy that permits observation of nanoscopic features on solid surfaces under a liquid or solution environment. This allows in situ measurement of important chemical transformations such as crystal growth and dissolution. Further, the microscope can access not only an accurate height measurement of surface topography, important to deduce structural elements, but also the forces involved during nanoscopic processes. We have discovered that it is possible to use these features to "illuminate" critical nanoscopic chemical events at crystal surfaces and at the same time extract the associated energies and unstitch the details of the stepwise mechanism of growth and dissolution. This approach has been developed using nanoporous crystals of the heterogeneous catalyst zeolite L; however, in principle the approach could be adapted to many crystal growth problems.