Detection of copy number variations in epilepsy using exome data.

Epilepsies are common neurological disorders and genetic factors contribute to their pathogenesis. Copy number variations (CNVs) are increasingly recognized as an important etiology of many human diseases including epilepsy. Whole-exome sequencing (WES) is becoming a standard tool for detecting pathogenic mutations and has recently been applied to detecting CNVs. Here, we analyzed 294 families with epilepsy using WES, and focused on 168 families with no causative single nucleotide variants in known epilepsy-associated genes to further validate CNVs using 2 different CNV detection tools using WES data. We confirmed 18 pathogenic CNVs, and 2 deletions and 2 duplications at chr15q11.2 of clinically unknown significance. Of note, we were able to identify small CNVs less than 10 kb in size, which might be difficult to detect by conventional microarray. We revealed 2 cases with pathogenic CNVs that one of the 2 CNV detection tools failed to find, suggesting that using different CNV tools is recommended to increase diagnostic yield. Considering a relatively high discovery rate of CNVs (18 out of 168 families, 10.7%) and successful detection of CNV with <10 kb in size, CNV detection by WES may be able to surrogate, or at least complement, conventional microarray analysis.

Novel biallelic SZT2 mutations in 3 cases of early-onset epileptic encephalopathy.

The seizure threshold 2 (SZT2) gene encodes a large, highly conserved protein that is associated with epileptogenesis. In mice, Szt2 is abundantly expressed in the central nervous system. Recently, biallelic SZT2 mutations were found in 7 patients (from 5 families) presenting with epileptic encephalopathy with dysmorphic features and/or non-syndromic intellectual disabilities. In this study, we identified by whole-exome sequencing compound heterozygous SZT2 mutations in 3 patients with early-onset epileptic encephalopathies. Six novel SZT2 mutations were found, including 3 truncating, 1 splice site and 2 missense mutations. The splice-site mutation resulted in skipping of exon 20 and was associated with a premature stop codon. All individuals presented with seizures, severe developmental delay and intellectual disabilities with high variability. Brain MRIs revealed a characteristic thick and short corpus callosum or a persistent cavum septum pellucidum in each of the 2 cases. Interestingly, in the third case, born to consanguineous parents, had unexpected compound heterozygous missense mutations. She showed microcephaly despite the other case and previous ones presenting with macrocephaly, suggesting that SZT2 mutations might affect head size.

Unique role of SNT-2/FRS2beta/FRS3 docking/adaptor protein for negative regulation in EGF receptor tyrosine kinase signaling pathways.

The membrane-linked docking protein SNT-2/FRS2beta/FRS3 becomes tyrosine phosphorylated in response to fibroblast growth factors (FGFs) and neurotrophins and serves as a platform for recruitment of multiple signaling proteins, including Grb2 and Shp2, to FGF receptors or neurotrophin receptors. We previously reported that SNT-2 is not tyrosine phosphorylated significantly in response to epidermal growth factor (EGF) but that it inhibits ERK activation via EGF stimulation by forming a complex with ERK2. In the present report, we show that expression of SNT-2 suppressed EGF-induced cell transformation and proliferation, and expression level of SNT-2 is downregulated in cancer. The activities of the major signaling molecules in EGF receptor (EGFR) signal transduction pathways, including autophosphorylation of EGFR, were attenuated in cells expressing SNT-2 but not in cells expressing SNT-2 mutants lacking the ERK2-binding domain. Furthermore, SNT-2 constitutively bound to EGFR through the phosphotyrosine binding (PTB) domain both with and without EGF stimulation. Treatment of cells with MEK inhibitor U0126 partially restored the phosphorylation levels of MEK and EGFR in cells expressing SNT-2. On the basis of these findings, we propose a novel mechanism of negative control of EGFR tyrosine kinase activity with SNT-2 by recruiting ERK2, which is the site of negative-feedback loop from ERK, ultimately leading to inhibition of EGF-induced cell transformation and proliferation.

Methylation of E-cadherin and hMLH1 genes in Indian sporadic breast carcinomas.

Hypermethylation of promoter regions leading to inactivation of tumor suppressor genes is a common event in the progression of several tumor types. We have employed a novel restriction digestion based multiplex PCR assay to analyse the methylation status of promoter regions of tumor suppressor genes (p16, hMLH1, MGMT and E-cadherin) in sporadic breast carcinomas of Indian women. The present results indicated the absence of hypermethylation in promoter region of p16 and MGMT genes. However, 6 of the 19 (31.6%) sporadic breast carcinomas showed hypermethylation in the promoters of two of the genes analysed; three in hMLH1 and another three in E-cad. Since our earlier studies have shown lack of genetic alterations such as missense mutations and deletions in the tumor associated genes-p16, ras and p14ARF in sporadic breast tumors, the epigenetic alterations of the two genes reported in the present study could be of interest and might be among the events in the genesis/progression of sporadic breast carcinomas.

Thermochemical stabilities and structures of the cluster ions OCS+, S2+, H+(OCS), and C2H5+ with OCS molecules in the gas phase.

The gas-phase clustering reactions of OCS+, S2+, H+(OCS), and C2H5+ ions with carbonyl sulfide (OCS) molecules were studied using a pulsed electron-beam high-pressure mass spectrometer and applying density functional theory (DFT) calculations. In the cluster ions OCS+(OCS)(n) and H+(OCS)(OCS)(n), a moderately strong, here referred to as "semi-covalent", bond was formed with n = 1. However, the nature of bonding changed from semi-covalent to electrostatic with n = 1 --> 2. The bond energy of S2(+)(OCS) was determined experimentally to be 12.9 +/- 1 kcal/mol, which is significantly smaller than that of the isovalent S2(+)(CS2) complex (30.9 +/- 1.5 kcal/mol). DFT based calculations predicted the presence of several isomeric structures for H+(OCS)(OCS)(n) complexes. The bond energies in the C2H5+(OCS)(n) clusters showed an irregular decrease for n = 1 --> 2 and 7 --> 8. The nonclassical bridge structure for the free C2H5+ isomerized to form a semi-covalent bond with one OCS ligand, [H3CCH2...SCO]+, i.e., reverted to classical structure. However, the nonclassical bridge structure of C2H5+ was preserved in the cluster ions C2H5+(OCS)(n) below 140 K attributable to the lack of thermal energy for the isomerization. DFT calculations revealed that stability orders of the geometric isomers of H+(OCS)(OCS)(n) and C2H5+(OCS)(n) changed with increasing n values.

Gas-phase ion/molecule reactions in C5F8.

Gas-phase ion-molecule reactions in octafluorocyclopentene (C5F8) were studied with a pulsed electron beam mass spectrometer. When a few Torr of major gas, CH4, Ar, or N2, containing approximately 10 mTorr C5F8 was ionized by 2 keV electrons, C5F8+, C5F7+, C4F6+, C4F5+, and C3F3+ were formed as major fragment ions. The interaction between those ions and C5F8 is found to be a weak electrostatic interaction. The cation...C5F8 bonding energies are around 10 kcal/mol, which were reproduced well by (U)B3LYP/6-311+G(d) calculations. The proton affinity of C5F8 (=148.6 kcal/mol by B3LYP/6-311+G(d)) was found to be smaller than that of C2H4 (=162.8 kcal/mol). In the negative mode of operation, the intense signal of C5F8- was observed during the electron pulse. This indicates that C5F8 has a positive electron affinity (1.27 eV by (U)B3LYP/6-311+G(d)). The C5F8- ion was quickly converted to a complex C10F16-. This complex did not react further with C5F8 down to 170 K. The theoretical calculation revealed that a C5F7-F-...C5F8 interaction mode in (C5F8)2- was converted to a C5F7*...C5F9- one via fluoride-ion transfer. The F- ion was found to form a strong covalent bond with C5F8, but the interaction in F-(C5F8)- - -C5F8 is a weak electrostatic interaction due to the charge dispersal in F-(C5F8). The halide ions except F- interact with C5F8 only weakly. Thermochemical stabilities for the cluster ions I-(CH3I)n (n = 1, 2) were also determined.

Upregulation of non-mutated H-ras and its upstream and downstream signaling proteins in colorectal cancer.

We analyzed H-ras protein expression in 38 human colon cancers and the paired normal tissues. H-ras levels were significantly higher in the malignant tumor (average 0.19+/-0.27) than in its normal adjacent tissues (average 0.06+/-0.15) (p<0.05). The H-ras protein expressed in colon carcinomas contained activated form of H-ras without mutation, based on the findings obtained by RBD-binding (ras binding domain of Raf protein) assay and PCR-SSCP analysis. In addition, we found that H-ras expression was higher in female patients than male, and in cancers with distant metastasis compared to those with non-distant metastasis. Good correlation between H-ras expression levels and those of the upstream and downstream signaling proteins of EGFR, MEK and ERK was found, suggesting that H-ras may play a significant role in carcinogenesis of colorectal cancer.

[Comparison between the short program and the long program of post-operative rehabilitation of hip fracture for making the critical path].

Patients receiving operative treatment for fracture are good candidate for critical path management. Recently, we have developed a Short Program (SP) for post-operative rehabilitation of hip fractures. The purpose of this study was to evaluate the effectiveness, the safety and the cost efficiency of this SP, by comparing it with the former Long Program (LP) in terms of choosing the better program for the critical path. The enrolled patients were over 65 years old, had been able to walk by themselves with or without canes, were free from neurological diseases like hemiplegia and Parkinson's disease, and without pathological fractures. We enrolled 101 patients (mean age: 83.1) for the LP and 143 patients (mean age: 82.8) for the SP. The operative procedure for these patients was internal fixation with a sliding hip screw or prosthetic replacement for a femoral head. Length of hospitalization, the rate of recovering walking ability, medical expenses during hospitalization, and the types and incidence of complications were investigated to determine differences between the SP and the LP. Length of hospitalization was significantly shorter in SP patients (p < 0.01). The ratio of recovering walking ability was equal in both programs, while that among the patients with dementia was lower in the SP group. Medical expenses were significantly less in SP (p < 0.01). The SP had fever complications than the LP group (p < 0.05). As a result, the SP was superior to the LP in terms of effectiveness, safety and cost efficiency, thus it was considered to be suitable for critical path management of hip fracture cases. However, because recovery of walking ability was harder for patients over 85 years old with the SP than with the LP, a modified program is necessary for such older patients.

S-myotrophin promotes the hypertrophy of myotube as insulin-like growth factor-I does.

We have reported previously that a novel muscle cell growth factor, having a structure of a peptide with sugar chains, was successfully purified from porcine skeletal muscle. It was named s-myotrophin. To determine the role of s-myotrophin in skeletal muscle growth, the effect of s-myotrophin on primary cultured chick skeletal muscle cells (composed almost totally of multinucleated myotubes) was investigated by comparing s-myotrophin with Insulin-like growth factor-I (IGF-I). Both s-myotrophin and IGF-I significantly increased creatine kinase activity of the cultures; both substances gave similar responses. Intracellar protein content was also increased by the addition of these factors. The content of myosin and actin in s-myotrophin treated culture in the differentiation medium was significantly higher than that of the control (unstimulated). The content of those proteins in IGF-I treated culture was also higher than that of control, but the differences were not statistically significant. Immunoblot analysis confirmed that the amounts of myosin and actin in the myocytes were greatly increased by s-myotrophin stimulation and also by IGF-I stimulation. Morphological observations using an anti-desmin antibody staining procedure demonstrated that the size of both s-myotrophin and IGF-I treated myotubes was appreciably larger than that of control myotubes. These results suggest that s-myotrophin is a potent mediator of skeletal muscle cell hypertrophy thorough the accumulations of muscle structural proteins.

Selective deletion of p14(ARF) exon 1beta of the INK4a locus in oral squamous cell carcinomas of Indians.

The tumor suppressor gene - p16 INK4/CDKN2/MTS1 and its alternate splice product p14 (ARF), constitute the INK4a locus. We have examined the integrity of exon 1beta of p14(ARF) gene of oral squamous cell carcinomas (n=58) in untreated Indian patients. No mutations were detected in this region by PCR-SSCP analysis of the tumor DNA's. Further, PCR-based analysis revealed homozygous deletions of exon 1beta in 14 of the 58 tumors; these results were confirmed by hybridization of tumor DNAs with exon 1beta specific probe. The deletions were limited to the exon 1beta while the exons coding p16/INK4 were not affected. Except in two cases these deletions were mutually exclusive to the p53 inactivating mutations. These observations suggest an alternate mechanism of loss of p14(ARF) in the genesis of oral squamous cell carcinomas.

Mutational analysis of the candidate tumor suppressor gene ING1 in Indian oral squamous cell carcinoma.

ING1, a recently identified candidate tumor suppressor gene, involved in the p53 signaling pathway is mapped at chromosome 13q34. Since loss of heterozygosity at 13q34 has been reported in squamous cell carcinoma of head and neck, we screened for mutations in ING1 by polymerase chain reaction-single strand conformation polymorphism in 71 oral squamous cell carcinomas (OSCC) from India, 15 of which were known to harbor p53 mutations. A single polymorphism (G to A) was detected in 14 (19.7%) of the tumors analyzed. No mutation was observed in any of the 71 OSCCs analyzed. These results suggest that ING1 is not a target for mutational inactivation in OSCC of Indians.

Caspase-dependent cytosolic release of cytochrome c and membrane translocation of Bax in p53-induced apoptosis.

Activation of p53 induces apoptosis in various cell types. However, the mechanism by which p53 induces apoptosis is still unclear. We reported previously that the activation of a temperature-sensitive mutant p53 (p53(138Val)) induced activation of caspase 3 and apoptosis in Jurkat cells. To elucidate the pathway linking p53 and downstream caspases, we examined the activation of caspases 8 and 9 in apoptotic cells. The results showed that both caspases were activated during apoptosis as judged by the appearance of cleavage products from procaspases and the caspase activities to cleave specific fluorogenic substrates. The significant inhibition of apoptosis by a tetrapeptide inhibitor of caspase 8 and caspase 9 suggested that both caspases are required for apoptosis induction. In addition, the membrane translocation of Bax and cytosolic release of cytochrome c, but not loss of mitochondrial membrane potential, were detected at an early stage of apoptosis. Moreover, Bax translocation, cytochrome c release, and caspase 9 activation were blocked by the broad-spectrum caspase inhibitor, Z-VAD-fmk and the caspase 8-preferential inhibitor, Ac-IETD-CHO, suggesting that the mitochondria might participate in apoptosis by amplifying the upstream death signals. In conclusion, our results indicated that activation of caspase 8 or other caspase(s) by p53 triggered the membrane translocation of Bax and cytosolic release of cytochrome c, which might amplify the apoptotic signal by activating caspase 9 and its downstream caspases.

P53 and MDM2 co-expression in tobacco and betel chewing-associated oral squamous cell carcinomas.

Oral cancers of tobacco and betel chewers represents a unique in-vivo model to understand the genotoxic effect of tobacco and betel carcinogens on oncogenes and tumor suppressor genes. Coordinated interactions of p53 and MDM2 play an important role in regulation of critical growth control gene following exposure to DNA damaging agents. The purpose of this study is to determine if the tumor suppressor function of p53 is inactivated by mutation or other alternative mechanisms in carcinogen-induced oral squamous cell carcinoma (SCC), and to investigate the clinicopathological significance of p53 and MDM2 expression. The p53 mutation in oral SCC of tobacco and betel chewers (n=40) was detected by polymerase chain reaction - single strand conformation polymorphism (PCR-SSCP) analysis and immunohistochemistry (IHC) was done to investigate p53 and MDM2 proteins overexpression. The incidence of p53 mutation was relatively low (17.5%), but there was a high prevalence of MDM2 overexpression (72.5%). In the total of 40 cases, IHC phenotype showed p53 positive immunostaining with MDM2 positive immunostaining (p53+/MDM2+) 62.5%, p53 negative immunostaining with MDM2 negative immunostaining (p53-/MDM2-) 15%, p53 positive immunostaining with MDM2 negative immunostaining (p53+/MDM2-) 12.5%, and p53 negative immunostaining with MDM2 positive immunostaining (p53-/MDM2+) 10%. A significant correlation was found between MDM2 and p53 overexpression (p=0.0289). Moreover, p53+/MDM2+ phenotype was significantly associated with poorly differentiated tumors (p= 0.0007). These results conclude that other factors than p53 mutation is likely to be the targets of tobacco/betel carcinogens and MDM2 may play an important role in tobacco/betel chewing-related oral SCCs. Overexpression of MDM2 protein may constitute an alternative mechanism for p53 inactivation.

Mutation profile of the p53, fhit, p16INK4a/p19ARF and H-ras genes in Indian breast carcinomas.

Breast cancer is the second most prevalent cancer affecting Indian women. Genetic alterations of oncogenes and tumor suppressor genes were attributed to the development of breast carcinomas. In the present study, human breast tumor DNAs from untreated, non-familial, Indian patients were analysed for the presence of mutations in p53, fhit, p16INK4a/p19ARF and H-ras genes. Polymerase chain reaction-single strand conformation polymorphism and sequencing analysis were used to detect point mutations. Exons 5-8 of p53, exons 1-2 of p16INK4a, exon 2 of p19ARF, exons 5-9 of fhit gene and exons 1-2 of H-ras genes were amplified and analysed individually using exon-flanking primers. Only 12% of the tumors had mutation in p53, 8% had mutation in fhit gene and none of the tumors showed evidence for mutation in p16INK4a/p19ARF and H-ras genes. Tumor B18 exhibited two novel mutations in the p53 gene, ATGright curved arrow GTG (Metright curved arrow Val) at codon 237 and AATright curved arrow GAT (Asnright curved arrow Asp) at codon 263. Both of these mutations are hitherto unreported in breast carcinomas. Tumor B20 had a non-sense mutation CGAright curved arrow TGA (Argright curved arrow Stop) at codon 306 of p53 gene. In fhit gene, tumor B1 exhibited TTCTright curved arrow TACT mutation at intron 8 and tumor B15 had a silent mutation GAGright curved arrow GAA (Gluright curved arrow Glu) at codon 123. Our results indicate that, among the genes analysed, the p53 gene was more frequently mutated than fhit, p16INK4a/p19ARF and H-ras genes in Indian mammary tumors. Transcribable point mutations of fhit gene were found to be extremely uncommon in these tumors. Mutations in the above genes are mutually exclusive and are infrequent in fhit, p16INK4a/p19ARF and H-ras genes suggesting that these genes may not play a major role in Indian breast carcinomas. However, the significant frequency of mutations in the p53 gene suggest that p53 could be one of the genes involved in the genesis of sporadic breast carcinomas in Indian women.

Defining a common region of DNA amplification at 22q11.2-12 in head and neck squamous cell carcinomas by quantitative FISH analysis.

By comparative genomic hybridization (CGH) with 17 head and neck squamous cell carcinoma (HNSCC) cell lines, we previously detected an amplified region as a distinct peak at 22q11.2-12 in 3 cell lines. Because the possible presence of an oncogene was strongly suggested, the region was mapped in more detail by defining the minimum region that was commonly amplified by using fluorescence in situ hybridization (FISH) with a series of cosmids. Eighteen cosmid clones on 22q11.2-12 were assigned to their locations as a fractional length map and hybridized to cells from three HNSCC cell lines. The three cosmid clones, cHKA-118, cHKAD-26, and D22S938, showed the highest levels of amplification, and the size of the amplicon was calculated to be approximately 1.7 Mb in the OM1 and HSC6 cell lines. Several genes related to oncogenesis, including PRKM1, map to this locus. Thus, the definition of the common region with the highest level of copy number increases by FISH provides a starting point for identifying the gene that may play an important role in the development of HNSCC.

Novel apoptosis-inducing activity in Bacteroides forsythus: a comparative study with three serotypes of Actinobacillus actinomycetemcomitans.

Bacteroides forsythus, which has been reported to be associated with periodontitis but has not been recognized as a key pathogen, was found to induce cytolytic activity against HL-60 and other human leukemic cells. This cytolytic activity was demonstrated according to three different criteria: (i) loss of both mitochondrial membrane potential and membrane integrity in cells treated with bacterial extracts and then with Rh123 and propidium iodide, respectively, as demonstrated by flow cytometry; (ii) damage to cytoplasmic membrane, as revealed by scanning electron microscopy (SEM); and (iii) DNA ladder formation and activation of caspase-3. These results indicate that B. forsythus produced an apoptosis-inducing factor(s) found to be composed of protein as judged by heat and trypsin sensitivity. In addition to extracts from B. forsythus, the culture supernatant of this bacterium has the ability to induce a cytolytic effect against peripheral white blood cells, especially lymphocytes. For comparison with B. forsythus, the same analyses were applied to two strains with different serotypes of Actinobacillus actinomycetemcomitans, serotypes a (ATCC 43717) and c (ATCC 43719), in addition to previously reported apoptosis-inducing serotype b (ATCC 43718), which was used as a positive control. The strains of A. actinomycetemcomitans serotypes a and b induced apoptosis in HL-60 cells as judged by the above three criteria but to a slightly lesser extent than did B. forsythus, while the serotype c strain produced apoptosis to a negligible extent. Detailed SEM images showed that the A. actinomycetemcomitans serotype a strain induced large-pore formation and the serotype b strain produced small pores with typical blebbing, while B. forsythus induced severe membrane ruffling. Further DNA ladder formation and caspase-3 activation were observed in the serotype a and b strains but not in the serotype c strain. The present paper is the first report of a protein factor(s) from B. forsythus and the A. actinomycetemcomitans serotype a strain which induces apoptotic cell death.

FHIT gene mutations and single nucleotide polymorphism in Indian oral and cervical squamous cell carcinomas.

Genetic alterations at the FHIT (fragile histidine triad) tumor suppressor gene have been found in various human cancers. We have made an attempt to find point mutations of this gene in two different cancers from India, with entirely different etiologic factors: oral cancer (55 samples) caused by chewing tobacco and cervical cancer (43 samples) caused mainly by HPV (human papilloma virus) infection. Analysis of tumor DNA by the polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) method was performed on each of FHIT exons 5-9 individually, using exon-flanking primers. Two different mutations were identified in both oral and cervical tumors: one at the second nucleotide 3' to the termination codon (TGA) in exon 9 and the other at the ninth nucleotide upstream to the beginning of exon 9. These results indicate that mutations in the FHIT gene are rare events in these tumors in India (approximately 4%). In addition, we found a single nucleotide FHIT gene polymorphism which is due to T/A replacement at 17 nucleotides upstream to exon 9 where the A allele is 0.6 of the population.