RNA-seq analysis, targeted long-read sequencing and in silico prediction to unravel pathogenic intronic events and complicated splicing abnormalities in dystrophinopathy.

Dystrophinopathy is caused by alterations in DMD. Approximately 1% of patients remain genetically undiagnosed, because intronic variations are not detected by standard methods. Here, we combined laboratory and in silico analyses to identify disease-causing genomic variants in genetically undiagnosed patients and determine the regulatory mechanisms underlying abnormal DMD transcript generation. DMD transcripts from 20 genetically undiagnosed dystrophinopathy patients in whom no exon variants were identified, despite dystrophin deficiency on muscle biopsy, were analyzed by transcriptome sequencing. Genome sequencing captured intronic variants and their effects were interpreted using in silico tools. Targeted long-read sequencing was applied in cases with suspected structural genomic abnormalities. Abnormal DMD transcripts were detected in 19 of 20 cases; Exonization of intronic sequences in 15 cases, exon skipping in one case, aberrantly spliced and polyadenylated transcripts in two cases and transcription termination in one case. Intronic single nucleotide variants, chromosomal rearrangements and nucleotide repeat expansion were identified in DMD gene as pathogenic causes of transcript alteration. Our combined analysis approach successfully identified pathogenic events. Detection of diseasing-causing mechanisms in DMD transcripts could inform the therapeutic options for patients with dystrophinopathy.

A Neonatal Case of Mild Encephalopathy/Encephalitis with a Reversible Splenial Lesion.

The neurological symptoms of pediatric mild encephalopathy/encephalitis with a reversible splenial lesion (MERS) are mild and have a good prognosis. However, some aspects of neonatal MERS are unclear due to a lack of clinical knowledge. We present a neonatal case of MERS with features of poor activity and prolonged poor oxygenation after birth without asphyxia. He was diagnosed with MERS by brain magnetic resonance imaging (MRI) on day10, because the diffusion restriction of the splenium of the corpus callosum (SCC) seen on diffusion-weighted MRI on day 5 was attenuating. He was discharged due to good progress on day 26, but growth issues and developmental delay were observed in the follow up from 1-10 months. In rare neonatal cases, many aspects of the clinical course and prognosis are thus unclear. MERS should be considered in newborns who show unexplained non-neural or other encephalopathic symptoms.

Additional findings of tibial dysplasia in a male with orofaciodigital syndrome type XVI.

We describe the case of a male patient with orofaciodigital (OFD) syndrome type XVI with a homozygous variant of TMEM107 (p.Phe106del) and the additional findings of tibial dysplasia, which is a pivotal finding of OFD syndrome type IV. His family history included two fetuses with anencephaly with or without cleft lip/palate and polydactyly with no genetic information. Careful attention should be given to the interpretation of this rare pattern.

A severe case of status dystonicus caused by a de novo KMT2B missense mutation.

Here, we present the case of a 15-year-old Japanese girl with Dystonia 28, childhood-onset; DYT28 (MIM#606834) showing early-onset generalized progressive dystonia and status dystonicus. The patient was genetically undiagnosed and had not responded to various medications. By trio-based whole exome sequencing and in silico analyses, we identified a de novo heterozygous variant of KMT2B: NM_014727.2: c.7828C > T, p(Arg2610Cys). Globus pallidus internus deep brain stimulation (GPi-DBS) therapy was considered; however, the therapy could not be performed due to the patient's poor nutritional status and repeated infections. GPi-DBS is considered to be an effective treatment for patients with KMT2B mutations, and genetic diagnosis is important before progression to status dystonicus.

Simple and reliable method to simultaneously determine urinary 1- and 2-naphthol using in situ derivatization and gas chromatography-mass spectrometry for biological monitoring of naphthalene exposure in occupational health practice.

OBJECTIVES: The aim of this study was to develop and validate a simple and reliable gas chromatography-mass spectrometry (GC-MS) method to simultaneously determine urinary 1-naphthol (1-NAP) and 2-naphthol (2-NAP) for biological monitoring of occupational exposure to naphthalene. METHODS: NAPs were derivatized in situ with acetic anhydride after enzymatic hydrolysis, extracted with n-hexane, and analyzed using GC-MS. Validation of the proposed method was conducted in accordance with US Food and Drug Administration guidance. A final validation was performed by analyzing a ClinChek® -Control for phenolic compounds. RESULTS: The linearity of calibration curves was indicated by a high correlation coefficient (>0.999) in the concentration range 1-100 µg/L for each NAP. The limits of detection and quantification for each NAP were 0.30 and 1.00 µg/L, respectively. The recovery was 90.8%-98.1%. The intraday and interday accuracies, expressed as the deviation from the nominal value, were 92.2%-99.9% and 93.4%-99.9%, respectively. The intraday and interday precision, expressed as the relative standard deviation, was 0.3%-3.9% and 0.4%-4.1%, respectively. The ClinChek® values obtained using our method were sufficiently accurate. CONCLUSIONS: The proposed method is simple, reliable, and appropriate for routine analyses, and is useful for biological monitoring of naphthalene exposure in occupational health practice.

A novel homozygous missense SLC25A20 mutation in three CACT-deficient patients: clinical and autopsy data.

Carnitine-acylcarnitine translocase (CACT) deficiency is a fatty acid ß-oxidation disorder of the carnitine shuttle in mitochondria, with a high mortality rate in childhood. We evaluated three patients, including two siblings, with neonatal-onset CACT deficiency and revealed identical homozygous missense mutations of p.Arg275Gln within the SLC25A20 gene. One patient died from hypoglycemia and arrhythmia at 26 months; his pathological autopsy revealed increased and enlarged mitochondria in the heart but not in the liver.

A novel nonsense SMC1A mutation in a patient with intractable epilepsy and cardiac malformation.

Cornelia de Lange syndrome (CdLS) is a cohesinopathy caused by genetic variations. We present a female with SMC1A-associated CdLS with a novel SMC1A truncation mutation (p. Arg499Ter), transposition of the great arteries, and periodic intractable seizures from 40 months of age. A review of the literature revealed that a seizure-free period after birth of at least 15 months is required for these patients to be able to walk, irrespective of the epileptic course.

Mild prominence of the Sylvian fissure in a Bainbridge-Ropers syndrome patient with a novel frameshift variant in ASXL3.

A Japanese boy aged 7 years with Bainbridge-Ropers syndrome (BRPS) had a prominent domed forehead without metric ridge, mild prominence of the Sylvian fissure with bitemporal hollowing, and a heterozygous de novo novel variant "p.P1010Lfs*14" in ASXL3 gene in addition to typical findings of BRPS.

A new mutation found in newborn screening for Fabry disease evaluated by plasma globotriaosylsphingosine levels.

A pilot study of newborn screening for Fabry disease was performed in Okinawa, Japan. A total of 2,443 neonates were screened using dried blood spot samples over 7 years starting in 2007. Of 13 neonates determined to have low α-galactosidase A (GLA) activity, one boy had a new missense mutation, p.G144D of the GLA gene. This mutation was considered to be a late-onset type, as evaluated based on plasma globotriaosylsphingosine levels and family history.

Isovaleric acidemia: Therapeutic response to supplementation with glycine, l-carnitine, or both in combination and a 10-year follow-up case study.

Isovaleric acidemia (IVA) is an organic acid disease caused by a deficiency of isovaleryl-CoA dehydrogenase. Deficiency of this enzyme leads to accumulation of organic acids, such as isovalerylcarnitine and isovalerylglycine. The proposed IVA treatments include leucine restriction and l-carnitine and/or glycine supplementation, which convert isovaleric acid into non-toxic isovalerylcarnitine and isovalerylglycine, respectively. We examined the therapeutic response using the leucine load test and performed a 10-year follow-up in the patient. METHODS: We evaluated the patient with IVA beginning at 5 years of age, when he presented with a mild to intermediate metabolic phenotype. Ammonia, free carnitine, isovalerylcarnitine, and isovalerylglycine were analyzed in the urine and blood after a meal consisting of 1600 mg leucine with glycine alone (250 mg/kg/day), l-carnitine alone (100 mg/kg/day), or both glycine and l-carnitine for four days each. RESULTS: (Leucine load test) Three hours after the meal, serum ammonia levels increased most dramatically with glycine treatment alone, then with both in combination, and least with l-carnitine alone. Urinary isovalerylglycine levels increased 2-fold more with glycine supplementation than those following supplementation with both agents or with l-carnitine alone. Treatment with both agents resulted in a gradual increase in urinary acylcarnitine levels during the 6-h period following the leucine load, reaching concentrations comparable to those observed with l-carnitine alone. (Clinical course) After initiation of both glycine (200 mg/kg/day) and l-carnitine (100 mg/kg/day) supplementation at 5 years of age, doses were gradually reduced to 111.7 mg/kg/day and 55.8 mg/kg/day, respectively, at 15 years of age. His mind and body had developed without any sequelae. DISCUSSION: We concluded that l-carnitine conjugated isovaleric acid earlier than glycine. Additionally, during the 10-year follow-up period, the patient displayed no clinical deterioration.

[Anti-MOG + neuromyelitis optica spectrum disorders treated with plasmapheresis].

A 10-year-old boy developed bilateral optic neuritis and myelitis after a suspected viral infection and appendicitis. Magnetic resonance imaging (MRI) showed multiple lesions in both optic nerves, the optic chiasm, and the spinal cord. Several small lesions were also observed in the cerebellum and cerebral white matter. The serum tested negative for anti-aquaporin (AQP)-4 antibody and positive for anti-myelin oligodendrocyte glycoprotein (MOG) antibody. The diagnosis was neuromyelitis optica spectrum disorder (NMOSD). Two courses of high-dose methylprednisolone were administered; however, only a small improvement in his visual acuity was achieved. He underwent 3 courses of plasma exchange to achieve sufficient visual acuity. After the serum anti-MOG antibody titer decreased to the cut-off level, oral prednisolone and azathioprine administration were also stopped, 10 months after onset. Recently, NMO and NMOSD cases positive for anti-MOG antibodies have been reported, which showed clinical features different from those of NMO cases positive for anti-AQP4 antibody. Although most of the reported cases responded to steroid therapy, plasma exchange was required in our case. Further analysis on larger numbers of cases is needed to establish treatments for anti-MOG antibody-positive NMO and NMOSD.

Correlation of augmented startle reflex with brainstem electrophysiological responses in Tay-Sachs disease.

AIM: To clarify the evolution of an augmented startle reflex in Tay-Sachs disease and compare the temporal relationship between this reflex and brainstem evoked potentials. SUBJECTS AND METHODS: Clinical and electrophysiological data from 3 patients with Tay-Sachs disease were retrospectively collected. RESULTS: The augmented startle reflex appeared between the age of 3 and 17 months and disappeared between the age of 4 and 6 years. Analysis of brainstem auditory evoked potentials revealed that poor segregation of peak I, but not peak III, coincided with the disappearance of the augmented startle reflex. A blink reflex with markedly high amplitude was observed in a patient with an augmented startle reflex. CONCLUSION: The correlation between the augmented startle reflex and the preservation of peak I but not peak III supports the theory that the superior olivary nucleus is dispensable for this reflex. The blink reflex with high amplitudes may represent augmented excitability of reticular formation at the pontine tegmentum in Tay-Sachs disease, where the pattern generators for the augmented startle and blink reflexes may functionally overlap.

Matrix behavior during sample preparation using metabolomics analysis approach for pesticide residue analysis by GC-MS in agricultural products.

The detailed matrices and their behaviors during pesticide residue analyses were clarified using a metabolomics analysis approach. The matrix profile was investigated using two different extraction solvents, acetone and acetonitrile. Acetone extracted the matrix components with a wide range of log P(O/W) values. Components with log P(O/W) values >10, such as sterols and tocopherols, and components with log P(O/W) values <3.2 were more extracted by acetone than by acetonitrile. In contrast, components with log P(O/W) values in the range from 3.2 to 10 were extracted by both acetone and acetonitrile at the same concentration level. The study also examined the difference in the column cleanup efficiency using a solid phase extraction (SPE). Florisil, silica gel, NH(2), PSA, and GCB were selected as representative columns for pesticide residue analysis, and acetone extraction of brown rice was selected in this experiment. Most of the matrix components were removed by either column, whereas monoacylglycerols, which are the components causing the matrix effect, were not removed by any column. Understanding such a detailed matrix behavior helps to develop a better analytical method for pesticide analysis using GC-MS.

Deoxidation of fenthion sulfoxide, fenthion oxon sulfoxide and fensulfothion in gas chromatograph/mass spectrometer, and the prevention of sulfoxide deoxidation by polyethylene glycol 300.

Fenthion, fenthion sulfoxide, fenthion oxon sulfoxide and fensulfothion showed two different mass spectra in GC/MS, depending on their concentrations. The base peaks shifted to lower levels by 1 m/z at lower concentration, and no retention time shifts were observed. The "shifted base peaks" were not obtained by a general EI fragmentation. The product ion scan spectra of the "shifted base peaks" were coincident with those of molecular ions of their corresponding sulfides. These phenomena can be ascribed to the conversion of sulfoxide into sulfide by the dominant deoxidation reaction than EI fragmentation in an ion source. Adding polyethylene glycol 300 (PEG300) into a test solution prevented sulfoxide deoxidation.

Fast screening of pesticide multiresidues in aqueous samples by dual stir bar sorptive extraction-thermal desorption-low thermal mass gas chromatography-mass spectrometry.

A method for fast screening of pesticide multiresidues in aqueous samples using dual stir bar sorptive extraction-thermal desorption-low thermal mass gas chromatography-mass spectrometry (dual SBSE-TD-LTM-GC-MS) has been developed. Recovery of 82 pesticides - organochlorine, carbamate, organophosphorous, pyrethroid and others - for the SBSE was evaluated as a function of octanol-water distribution coefficients (log K(o/w): 1.7-8.35), sample volume (2-20 mL), salt addition (0-30% NaCl), and methanol addition (0-20%). The optimized method consists of a dual SBSE performed simultaneously on respectively a 20-mL sample containing 30% NaCl and a 20-mL sample without modifier (100% sample solution). One extraction with 30% NaCl is mainly targeting solutes with low K(o/w) (log K(o/w)<3.5) and another extraction with unmodified sample solution is targeting solutes with medium and high K(o/w) (log K(o/w)>3.5). After extraction, the two stir bars are placed in a single glass desorption liner and are simultaneously desorbed. The desorbed compounds are analyzed by use of LTM-GC-MS with fast temperature programming (75 degrees C min(-1)) using a 0.18 mm i.d. narrow-bore capillary column and fast scanning (10.83 scan s(-1)) using quadrupole MS. The method showed good linearity (r(2)>0.9900) and high sensitivity (limit of detection: <10 ng L(-1)) for most of the target pesticides. The method was applied to the determination of pesticides at nanograms per liter levels in river water and brewed green tea.

Simultaneous determination of 64 pesticides in river water by stir bar sorptive extraction and thermal desorption-gas chromatography-mass spectrometry.

A method for determining 68 pesticides in river water using stir bar sorptive extraction (SBSE)-thermal desorption (TD)-gas chromatography-mass spectrometry (GC-MS) is described. SBSE sampling was optimized for sample solution pH, salting-out and methanol addition. Although salting-out enhanced the ability of the method to extract most of the pesticides with low absolute recoveries, the absolute recoveries of four pesticides were not improved by salting-out. The detection limits of the method for the pesticides ranged from 0.2 to 20 ng/l. Analyte recoveries from a river water sample spiked with standards at 10 and 100 ng/l were 58.5-132.0% (RSD: 1.8-15.8%) and 61.0-121.3% (RSD: 1.4-20.2%), respectively.

Determination of 2-methylisoborneol and geosmin in aqueous samples by static headspace-gas chromatography-mass spectrometry with ramped inlet pressure.

A method for determining the earthy and musty odors 2-methylisoborneol (2-MIB) and geosmin in drinking water using static headspace-GC-MS is described. To achieve lower detection limits, split ratio was optimized with ramped inlet pressure for large headspace sampling volume. The ramped inlet pressure, which held higher pressure (higher column flow rate) only during injection, allowed us to inject 3-mL volume to GC with very low split ratio (2:1). Although sequential analysis with a stainless steel ion source often changed the mass spectrum of 2-MIB, this spectral change was eliminated by using an inert ion source with a 6 mm drawout plate. The detection limits of this method were 0.36 and 0.14 ng/L, respectively, for 2-MIB and geosmin. The repeatabilities (n = 30) were 6.6 and 4.8%, respectively, at 1 ng/L for 2-MIB and geosmin.

Simultaneous determination of alkylphenols and bisphenol A in river water by stir bar sorptive extraction with in situ acetylation and thermal desorption-gas chromatography-mass spectrometry.

A method for the determination of seven alkylphenols and bisphenol A by stir bar sorptive extraction (SBSE) with in situ derivatization-thermal desorption (TD)-gas chromatography (GC)-mass spectrometry (MS) is described. SBSE was performed with in situ acetylation and without derivatization for comparison. For 4-tert-butylphenol and bisphenol A, in situ acetylation improved the responses in SBSE-TD-GC-MS. The method detection limits ranged from 0.1 to 3.2 ng/l. The recoveries of the analytes from a river water sample spiked with standards at 10 and 100 ng/l were 85.3-105.9% (R.S.D., 3.0-11.0%) and 88.3-105.8% (R.S.D., 1.6-8.3%), respectively.