Targeted next-generation sequencing in the diagnosis of neurodevelopmental disorders

We developed a next-generation sequencing (NGS) based mutation screening strategy for neurodevelopmental diseases. Using this system, we screened 284 genes in 40 patients. Several novel mutations were discovered. Patient 1 had a novel mutation in ACTB. Her dysmorphic feature was mild for Baraitser-Winter syndrome. Patient 2 had a truncating mutation of DYRK1A. She lacked microcephaly, which was previously assumed to be a constant feature of DYRK1A loss of function. Patient 3 had a novel mutation in GABRD gene. She showed Rett syndrome like features. Patient 4 was diagnosed with Noonan syndrome with PTPN11 mutation. He showed complete agenesis of corpus callosum. We have discussed these novel findings.

Morphological and immunohistochemical analyses of soluble proteins in mucous membranes of living mouse intestines by cryotechniques

We have performed immunohistochemical or ultrastructural analyses of living mouse small intestines using Epon blocks prepared by 'in vivo cryotechnique' (IVCT). By electron microscopy, intracellular ultrastructures of epithelial cells were well preserved in tissue areas 5-10 μm away from cryogen-contact surface tissues. Their microvilli contained dynamically waving actin filaments, and highly electron-dense organelles, such as mitochondria, were seen under the widely organized terminal web. By quick-freezing of fresh resected tissues (FT-QF), many erythrocytes were congested within blood vessels due to loss of blood pressure. By immersion-fixation (IM-DH) and perfusion-fixation (PF-DH), small vacuoles were often seen in the cytoplasm of epithelial cells, and their intercellular spaces were also dilated. Moreover, actin filament bundles were irregular in cross sections of microvilli, compared with those with IVCT. Epon-embedded thick sections were treated with sodium ethoxide, followed by antigen retrieval and immunostained for immunoglobulin A (IgA), Ig kappa light chain (Igκ), J-chain and albumin. By cryotechniques, IgA immunoreactivity was detected as tiny dot-like patterns in cytoplasm of some epithelial cells. Both J-chain and Igκ immunoreactivities were detected in the same local areas as those of IgA. By FT-QF, however, the IgA immunoreactivity was more weakly detected, compared with that with IVCT. In thick sections prepared by IM-DH and PF-DH, it was rarely observed in both plasma and epithelial cells. Another albumin was diffusely immunolocalized in extracellular matrices of mucous membranes and also within blood vessels. Thus, IVCT was useful for preservation of soluble proteins and ultrastructural analyses of dynamically changing epithelial cells of living mouse small intestines.

Three-dimensional volume imaging with electron microscopy toward connectome

Ultrastructural analyses with electron microscopy have provided indispensable information to understand physiology and pathology of the nervous system. Recent advancement in imaging methodology paved the way for complete reconstruction of the neuronal connection map in the central nervous system, which is termed 'connectome' and would provide key insights to understand the functions of the brain. The critical advancement includes serial ultrastructural observation with scanning electron microscopy (SEM) instead of conventional serial sectioning transmission electron microscopy along with specific tissue preparation methods to increase heavy metal deposition for efficient SEM imaging. The advanced imaging methods using SEM have distinct advantages and disadvantages in multiple aspects, such as resolution and imaging speed, and should be selected depending on the observation conditions, such as target tissue sizes, required spatial resolution and necessity for re-observation. Dealing with the huge dataset remained to be a major obstacle, and automation in segmentation and 3D reconstruction would be critical to understand neuronal circuits in a larger volume of the brain. Future improvement in acquisition and analyses of the morphological data obtained with the advanced SEM imaging is awaited to elucidate the significance of whole connectome as the structural basis of the consciousness, intelligence and memory of a subject.

Long-term entecavir therapy results in falls in serum hepatitis B surface antigen levels and seroclearance in nucleos(t)ide-naïve chronic hepatitis B patients

Entecavir (ETV) is reported to result in suppression of hepatitis B virus DNA (HBV DNA) replication with minimal drug resistance. However, information on the long-term effect of such therapy on serum hepatitis B surface antigen (HBsAg) level and elimination of HBsAg is not available. ETV therapy was started in 553 nucleos(t)ide-naïve patients with chronic hepatitis B infection (HBeAg positive: 45%) in our hospital. Serum HBsAg levels were measured serially by the Architect assay. The median baseline HBsAg was 2180 IU/mL (0.12-243 000 IU/mL), and median follow-up period was 3.0 years, with 529, 475, 355, 247 and 163 patients followed-up for 1, 2, 3, 4 and 5 years, respectively. At year 5, the mean log HBsAg decline from baseline was -0.48 log IU/mL, and the cumulative HBsAg clearance rate was 3.5%. Multivariate analysis identified HBV DNA level at baseline (<3.0 log copies IU/mL, odd ratio = 10.2; 95% confidence interval = 1.87-55.5, P = 0.007) and HBsAg level (<500 IU/mL, odd ratio = 29.4; 95% confidence interval = 2.80-333, P = 0.005) as independent predictors of HBsAg seroclearance. These results indicate that although serum HBsAg level declines gradually during ETV therapy, HBsAg seroclearance remains a rare event.

Mutations in COG2 encoding a subunit of the conserved oligomeric golgi complex cause a congenital disorder of glycosylation

The conserved oligomeric Golgi (COG) complex is involved in intra-Golgi retrograde trafficking, and mutations in six of its eight subunits have been reported in congenital disorders of glycosylation (CDG). Here we report a patient showing severe acquired microcephaly, psychomotor retardation, seizures, liver dysfunction, hypocupremia, and hypoceruloplasminemia. Analysis of his serum glycoproteins revealed defects in both sialylation and galactosylation of glycan termini. Trio-based whole-exome sequencing identified two heterozygous mutations in COG2: a de novo frameshift mutation [c.701dup (p.Tyr234*)] and a missense mutation [c.1900T > G (p.Trp634Gly)]. Sequencing of cloned reverse-transcription polymerase chain reaction (RT-PCR) products revealed that both mutations were located on separate alleles, as expected, and that the mutant transcript harboring the frameshift mutation underwent degradation. The c.1900T > G (p.Trp634Gly) mutation is located in a domain highly conserved among vertebrates and was absent from both the public database and our control exomes. Protein expression of COG2, along with COG3 and COG4, was decreased in fibroblasts from the patient. Our data strongly suggest that these compound heterozygous mutations in COG2 are causative of CDG.

Distinct cell clusters touching islet cells induce islet cell replication in association with over-expression of Regenerating Gene (REG) protein in fulminant type 1 diabetes

BACKGROUND

Pancreatic islet endocrine cell-supporting architectures, including islet encapsulating basement membranes (BMs), extracellular matrix (ECM), and possible cell clusters, are unclear.

PROCEDURES

The architectures around islet cell clusters, including BMs, ECM, and pancreatic acinar-like cell clusters, were studied in the non-diabetic state and in the inflamed milieu of fulminant type 1 diabetes in humans.

RESULT

Immunohistochemical and electron microscopy analyses demonstrated that human islet cell clusters and acinar-like cell clusters adhere directly to each other with desmosomal structures and coated-pit-like structures between the two cell clusters. The two cell-clusters are encapsulated by a continuous capsule composed of common BMs/ECM. The acinar-like cell clusters have vesicles containing regenerating (REG) Iα protein. The vesicles containing REG Iα protein are directly secreted to islet cells. In the inflamed milieu of fulminant type 1 diabetes, the acinar-like cell clusters over-expressed REG Iα protein. Islet endocrine cells, including beta-cells and non-beta cells, which were packed with the acinar-like cell clusters, show self-replication with a markedly increased number of Ki67-positive cells.

CONCLUSION

The acinar-like cell clusters touching islet endocrine cells are distinct, because the cell clusters are packed with pancreatic islet clusters and surrounded by common BMs/ECM. Furthermore, the acinar-like cell clusters express REG Iα protein and secrete directly to neighboring islet endocrine cells in the non-diabetic state, and the cell clusters over-express REG Iα in the inflamed milieu of fulminant type 1 diabetes with marked self-replication of islet cells.

Exploration and characterization of genes involved in the synthesis of diterpene defence secretion in nasute termite soldiers

Nasutitermes takasagoensis soldiers defend their colonies using characteristic diterpenes. Diterpenes are thought to be synthesized in the frontal gland cells surrounding the gland reservoir. To identify the genes involved in diterpene synthesis, a cDNA library was prepared from the frontal gland cells and exhaustively sequenced using a 454 pyrosequencer (GS Junior; Roche, Branford, CT, USA). A total of 50,290 clean sequences were assembled into 1111 contigs, which were grouped into 774 genes (isogroups). Based on sequence similarity with known proteins, we identified seven genes encoding the following four enzymes associated with diterpene synthesis: 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) synthase (HMGS), HMG-CoA reductase (HMGR), farnesyl diphosphate synthase, and geranylgeranyl diphosphate synthases. The expression levels of two enzymes, HMGS and HMGR, involved in the mevalonate pathway were examined, assuming that the site of the defensive terpenoid synthesis strongly activates the mevalonate pathway, which produces a precursor of terpenoids. Real-time quantitative reverse-transcriptase PCR confirmed significantly higher expression of HMGS and HMGR in the heads of soldiers. We then divided the head into three parts and found that the expression levels of HMGS and HMGR were significantly higher in the part containing class 1 secretory cells of the frontal gland. Overall, the results suggested that the mevalonate pathway for diterpene synthesis occurs in class 1 cells around the frontal gland reservoir.

Visualization of ATP with luciferin-luciferase reaction in mouse skeletal muscles using an "in vivo cryotechnique"

Adenosine triphosphate (ATP) is a well-known energy source for muscle contraction. In this study, to visualize localization of ATP, a luciferin-luciferase reaction (LLR) was performed in mouse skeletal muscle with an "in vivo cryotechnique" (IVCT). First, to confirm if ATP molecules could be trapped and detected after glutaraldehyde (GA) treatment, ATP was directly attached to glass slides with GA, and LLR was performed. The LLR was clearly detected as an intentional design of the ATP attachment. The intensity of the light unit by LLR was correlated with the concentration of the GA-treated ATP in vitro. Next, LLR was evaluated in mouse skeletal muscles with IVCT followed by freeze-substitution fixation (FS) in acetone-containing GA. In such tissue sections the histological structure was well maintained, and the intensity of LLR in areas between muscle fibers and connective tissues was different. Moreover, differences in LLR among muscle fibers were also detected. For the IVCT-FS tissue sections, diaminobenzidine (DAB) reactions were clearly detected in type I muscle fibers and erythrocytes in capillaries, which demonstrated flow shape. Thus, it became possible to perform microscopic evaluation of the numbers of ATP molecules in the mouse skeletal muscles with IVCT, which mostly reflect living states.

Immunohistochemical analysis of various serum proteins in living mouse thymus with "in vivo cryotechnique"

It has been difficult to clarify the precise localizations of soluble serum proteins in thymic tissues of living animals with conventional immersion- or perfusion-fixation followed by alcohol dehydration owing to ischemia and anoxia. In this study, "in vivo cryotechnique" (IVCT) followed by freeze-substitution fixation was performed to examine the thymic structures of living mice and immunolocalizations of intrinsic or extrinsic serum proteins, which were albumin, immunoglobulin G1 (IgG1), IgA, and IgM, as well as intravenously injected bovine serum albumin (BSA). Mouse albumin was more clearly immunolocalized in blood vessels and interstitial matrices of the thymic cortex than in tissues prepared by the conventional methods. The immunoreactivities of albumin and IgG1 were stronger than those of IgA and IgM in the interstitium of subcapsular cortex. The injected BSA was time-dependently immunolocalized in blood vessels and the interstitium of corticomedullary areas at 3.5 h after its injection, and then gradually diffused into the interstitium of the whole cortex at 6 h and 12 h. Thus, IVCT revealed definite immunolocalizations of serum albumin and IgG1 in the interstitium of thymus of living mice, indicating different accessibility of serum proteins from the corticomedullary areas, not from the subcapsular cortex of living animals, depending on various molecular sizes and concentrations.

Immunohistochemical distribution of serum proteins in living mouse heart with In vivo cryotechnique

In vivo cryotechnique (IVCT), which immediately cryofixes target organs in situ, was used to clarify the morphological features of beating heart tissue of living mice. IVCT was performed for diastolic heart tissue under the condition of monitoring with electrocardiogram (ECG). Other mouse hearts were prepared with conventional perfusion-fixation (PF-DH) or immersion-fixation followed by dehydration (IM-DH), and quick-freezing of resected heart tissues (FQF). Immunolocalizations of albumin, immunoglobulin G1 (IgG1), intravenously injected bovine serum albumin (BSA), and connexin 43 were examined after different intervals of BSA injection. In the case of IVCT, the exact stop time of beating mouse hearts was recorded by ECG, and open blood vessels with flowing erythrocytes were observed with less artificial tissue shrinkage than with conventional preparation methods. Both albumin and BSA were well preserved in intercalated discs and t-tubules of cardiomyocytes in addition to blood vessels and interstitial matrices. IgG1 was immunolocalized in interstitial matrices of heart tissues in addition to their blood vessels. At 4 hr after BSA injection, it was immunolocalized in the intercalated discs of cardiomyocytes and lost later at 8 hr. IVCT should prove to be more useful for the morphofunctional examination of dynamically changing heart tissue than conventional preparation methods.

Histological study and LYVE-1 immunolocalization of mouse mesenteric lymph nodes with "In Vivo Cryotechnique"

The “in vivo cryotechnique” (IVCT) is a powerful tool to directly freeze living animal organs in order to maintain biological components in frozen tissues, reflecting their native states. In this study, mesenteric lymph nodes of living mice were directly frozen with IVCT, and we did morphological studies and immunohistochemical analyses on a hyaluronic acid receptor, LYVE-1. In lymph nodes, widely open lymphatic sinuses were observed, and many lymphocytes adhered to inner endothelial cells along subcapsular sinuses. The LYVE-1 was clearly immunolocalized at inner endothelial cells of subcapsular sinuses, as well as those of medullary sinuses. Conventional pre-embedding electron microscopy also showed LYVE-1 immunolocalization along both the apical and basal sides of cell membranes of inner endothelial cells. By triple-immunostaining for LYVE-1, smooth muscle actin, and type IV collagen, the LYVE-1 was immunolocalized only in the inner endothelial cells, but not in outer ones which were surrounded by collagen matrix and smooth muscle cells. Thus, the functional morphology of lymph nodes in vivo was demonstrated and LYVE-1 immunolocalization in inner endothelial cells of subcapsular sinuses suggests hyaluronic acid incorporation into lymph node parenchyma.

Determination of physical processes influencing Chl a distribution using remotely sensed images

In management of the Japanese scallop Mizuhopecten yessoensis culture, it is important to understand the phytoplankton bloom development in the coastal region of the Okhotsk Sea. Variations in food available to this benthic bivalve are a primary environmental factor affecting growth in nature. This paper determined the seasonal variability of Chlorophyll a (Chl a) at the scallop farming region in the Okhotsk Sea from 1998 to 2004 using satellite imageries. Satellite images were processed using default NASA coefficients and community-standard algorithms as implemented by Sea DAS. Spatial and temporal variation of Chl a was determined by EOF analysis. The Chl a concentration showed high seasonal and interannual variability. Peak of Chl a concentration occurred in spring followed by autumn and summer. This was evident in the Empirical Orthogonal Function (EOF) analysis. The spatial pattern of the first mode of EOF analysis of Chl a revealed intensified Chl a at the shelf and offshore areas in spring and autumn (51.8% of variance). The second mode explained 14.2% of the variance indicating enhancement of spring (April-May) Chl a pattern in the frontal area along the coast. Meanwhile, the third mode captured 9.0% of the variability demonstrating high Chl a extending seaward from the shelf area during late autumn. These seasonal variability of Chl a resulted from the variability in occurrences of physical processes associated with retreat of sea ice in spring, advection of Soya Warm Current in summer and intrusion of East Sakhalin Current in autumn.

Immunolocalization of membrane skeletal protein, 4.1G, in enteric glial cells in the mouse large intestine

4.1 family proteins are membrane skeletal proteins that interact with spectrin-actin networks and intramembraneous proteins. We reported that one of them, 4.1G, was immunolocalized in myelinated nerve fibers of the mouse peripheral nervous system, especially along cell membranes of paranodes and Schmidt-Lanterman incisures in Schwann cells. In this study, to examine 4.1G's appearance in unmyelinated peripheral nerve fibers, we focused on the enteric nervous system in mouse large intestines. In intestinal tissues prepared by an "in vivo cryotechnique" followed by freeze-substitution fixation, 4.1G was immunolocalized in Auerbach's myenteric plexus and connecting nerve fiber networks. Its immunostaining was mostly colocalized with glial fibrillar acidic protein, a marker of enteric glial cells, but not with c-Kit, a marker of interstitial cells of Cajal. Using whole-mount preparation after splitting inner and outer muscle layers, the nerve fiber networks including the plexus were clearly detected by the 4.1G immunostaining. By conventional pre-embedding immunoelectron microscopy, 4.1G was detected along cell membranes of enteric glial cells and their processes surrounding axons. These indicate that 4.1G may have some roles in adhesion and/or signal transduction in unmylinated PNS nerve fibers.

Three-dimensional reconstruction of living mouse liver tissues using cryotechniques with confocal laser scanning microscopy

Soluble proteins and glycogen particles are well preserved in paraffin-embedded sections prepared by in vivo cryotechnique (IVCT) and cryobiopsy followed by freeze substitution fixation. We performed confocal laser scanning microscopic analyses on the distributions of glycogen with periodic acid-Schiff (PAS) staining and serum proteins with immunostaining for mouse liver tissues. Livers of fully fed mice showed a strong fluorescence signal of PAS staining in all hepatocytes and immunofluorescence of immunoglobulin kappa light chain (Igκ) in blood vessels and bile canaliculi. However, some hepatocytes in mechanically damaged livers were PAS-negative and Igκ-immunopositive, showing extraction of glycogen particles and infiltration of serum proteins in hepatocytes. By three-dimensional (3D) reconstruction of serial optical sections, interconnecting hepatic sinusoids and bile canaliculi were detected with Igκ immunostaining between trabecular hepatocytes that were PAS stained. In PAS-stained samples under fasting conditions, interstitial structures along sinusoids were clarified in vivo by 3D reconstruction because of the lower PAS staining intensity of hepatocytes. In addition, 100-μm-thick eosin-stained slices provided 3D structural images more than 30 μm in thickness away from tissue surfaces, showing blood vessels with flowing erythrocytes and networks of bile ducts and canaliculi. IVCT and cryobiopsy with histochemical analyses enabled us to visualize native hepatocytic glycogen and 3D structures, such as vascular networks, reflecting their living states by confocal laser scanning microscopy.

Immunohistochemical detection of soluble immunoglobulins in living mouse small intestines using an in vivo cryotechnique

Some morphological changes are inevitable during immersion- or perfusion-fixation and following alcohol-dehydration for tissue preparations. Common immunostaining techniques for these specimens have some limitations to capture accurate localizations of soluble proteins in cells and tissues. In this study, to examine in situ distributions of immunoglobulins (Igs), small intestinal tissues of living mice were prepared with our "in vivo cryotechnique" (IVCT). Thin sections were first stained with hematoxylin-eosin for morphology, and then some immunostainings were performed on serial sections for IgA, Ig kappa light chain, IgG1 heavy chain (IgG1), and IgM. Living morphological states of small intestinal tissues, including flowing erythrocytes and opening blood vessels, were observed on paraffin sections prepared with IVCT. IgA was immunolocalized in many plasma cells of the lamina mucosa propria, intestinal matrices, and also in epithelial cells of the intestinal villi and crypts. Both IgG1 and IgM immunoreactivities were mainly detected in blood vessels, whereas only IgG1 was also immunolocalized in interstitial matrices of mucous membranes. By perfusion-fixation and alcohol-dehydration, however, IgA immunoreactivity was observed in plasma cells, but not in epithelial cells or the lamina mucosa propria. Thus, IVCT was more useful to examine in vivo immunolocalizations of soluble Igs in small intestines.

Parthenogenetic chimaerism/mosaicism with a Silver-Russell syndrome-like phenotype

Introduction

We report a 34-year-old Japanese female with a Silver-Russell syndrome (SRS)-like phenotype and a mosaic Turner syndrome karyotype (45,X/46,XX).

Methods/Results

Molecular studies including methylation analysis of 17 differentially methylated regions (DMRs) on the autosomes and the XIST-DMR on the X chromosome and genome-wide microsatellite analysis for 96 autosomal loci and 30 X chromosomal loci revealed that the 46,XX cell lineage was accompanied by maternal uniparental isodisomy for all chromosomes (upid(AC)mat), whereas the 45,X cell lineage was associated with biparentally derived autosomes and a maternally derived X chromosome. The frequency of the 46,XX upid(AC)mat cells was calculated as 84% in leukocytes, 56% in salivary cells, and 18% in buccal epithelial cells.

Discussion

The results imply that a parthenogenetic activation took place around the time of fertilisation of a sperm missing a sex chromosome, resulting in the generation of the upid(AC)mat 46,XX cell lineage by endoreplication of one blastomere containing a female pronucleus and the 45,X cell lineage by union of male and female pronuclei. It is likely that the extent of overall (epi)genetic aberrations exceeded the threshold level for the development of SRS phenotype, but not for the occurrence of other imprinting disorders or recessive Mendelian disorders.

Significance of 'in vivo cryotechnique' for morphofunctional analyses of living animal organs

Our final goal of morphological and immunohistochemical studies is that all findings examined in animal experiments should reflect the physiologically functional background. Therefore, the preservation of original components in cells and tissues of animals is necessary for describing the functional morphology of living animal organs. It is generally accepted that morphological findings of various organs were easily modified by stopping their blood supply. There had been a need to develop a new preparation technique for freezing the living animal organs in vivo and then obtaining acceptable morphology and also immunolocalization of original components in functioning cells and tissues. We already developed the 'in vivo cryotechnique' (IVCT) not only for their morphology, but also for immunohistochemistry of many soluble components in various living animal organs. All physiological processes of cells and tissues were immediately immobilized by IVCT, and every component in the cells and tissues was maintained in situ at the time of freezing. Thus, the ischaemic or anoxic effects on them could be minimized by IVCT. Our specially designed cryoknife with liquid cryogen has solved the morphological and immunohistochemical problems which are inevitable with the conventional preparation methods at a light or electron microscopic level. The IVCT will be extremely useful for arresting transient physiological processes and for maintaining any intracellular components in situ, such as rapidly changing signal molecules, membrane channels and receptors.

MERRF/MELAS overlap syndrome: a double pathogenic mutation in mitochondrial tRNA genes

BACKGROUND

Myoclonic epilepsy with ragged-red fibres (MERRF) and mitochondrial encephalopathy, lactic acidosis and stroke-like episodes (MELAS) are established phenotypes of mitochondrial encephalomyopathy. The m.8356T>C transition in the mitochondrial tRNA(Lys) gene is a pathogenic mutations of MERRF. The m.3243A>G transition in the mitochondrial tRNA(Leu) gene is detected in most MELAS patients. Although previous analyses of double mutations in mitochondrial DNA (mtDNA) were useful for discussing their nature, many unsolved questions remain.

OBJECTIVE

To describe the clinical and genetic features of a family with the above mtDNA double-point mutations and discuss the role of double mtDNA mutations in diverse clinical features in the family.

PATIENTS AND METHODS

The proband was a 23-year-old woman with MERRF harbouring m.8356T>C and m.3243A>G transitions in mitochondrial tRNA genes. We assessed clinical aspects of her and those of her three relatives and performed mutation analyses on their mtDNA.

RESULTS

Phenotypes of the four patients were MERRF, MERRF/MELAS overlap syndrome and asymptomatic carrier. We hypothesise that the course of the phenotype of this family begins with MERRF and is followed by MELAS. This double mutation was heteroplasmic in blood of all four patients but with different rates in each patient, while m.8356T>C appeared homoplasmic and m.3243A>G was heteroplasmic in muscle of the two examined cases. No other mutations were detected in the total mtDNA sequence in this family.

CONCLUSIONS

This is the first reported case of a double-point mutation in mtDNA, both of which were heteroplasmic and pathogenic for the established phenotypes.