Impact of five SNPs in dopamine-related genes on executive function.

OBJECTIVES: Dopamine neurotransmission is a critical factor for executive function, which is controlled by the prefrontal cortex in humans. Although the contribution of genetic factors to the regulation of brain dopaminergic activity is widely acknowledged, identification of a genotype-phenotype association has not yet been clearly established. In this study, we therefore evaluated the effects of five functional single-nucleotide polymorphisms (SNPs) in specific genes related to dopamine neurotransmission on executive function in a general population. MATERIALS AND METHODS: Participants of the health examination at the Shimane Institute of Health Science were recruited for this study (n = 964). To evaluate executive function, the Frontal Assessment Battery (FAB) was administered. SNPs were genotyped using the TaqMan method. RESULTS: A significant association was found between an SNP in the catechol-O-methyltransferase (COMT) gene (rs4680) encoding the low-activity Met allele and FAB score (P = 0.003). Of note, the flexibility subset of the FAB was associated with the SNP in COMT (P = 0.003) after adjustment for confounding factors. The generalized multifactor dimensionality reduction method identified that the combination of two SNPs in the COMT gene (rs4680) and the dopamine D4 receptor gene (rs1800955) had a significant effect on FAB score. CONCLUSIONS: Our study indicates a contribution of rs4680 in the COMT gene to the variability in executive function, as assessed by the FAB. In addition, we have indicated that a complex gene-gene interaction between SNPs in the genes related to dopamine neurotransmission may influence executive function in a general population.

Expansion of human CMV-specific cytotoxic T lymphocytes to a clinical scale: a simple culture system using tetrameric HLA-peptide complexes.

BACKGROUND: Recipients of allogeneic stem cell transplants (SCT) are at risk of human CMV infection during their immunocompromised period. The increasing number of reports of CMV isolates resistant to ganciclovir after transplantation has led us to attempt to develop alternative strategies for preventing or treating CMV infection. This study describes a system for generating sufficient numbers of CMV-specific cytotoxic T lymphocytes (CTL) for adoptive immunotherapy after SCT. METHODS: CMV-specific CTL were isolated from a single blood draw of a CMV-seropositive donor using PE-labeled HLA-A*0201/pp65(495-503) tetramers and anti-PE magnetic beads. A mixture of a tetramer-positive population and CD4(+) T lymphocytes was expanded to sufficient numbers for clinical application with IL-2 and immobilized anti-CD3 stimulation. RESULT: Starting from 50 mL of blood, we generated >10(7)/m(2) tetramer-positive CTL within 2 weeks. Flow cytometric analysis of expanded lymphocytes showed that purity of CMV peptide-specific CTL was >75%. Upon stimulation of HLA-A*0201-restricted CMV peptide, expanded CD8 T lymphocytes produced intracellular IFN-gamma. Purified CTL exhibited cytotoxic activity against CMV peptide-pulsed T2 cells and CMV-infected HLA-A*0201-positive fibroblasts, but not against HLA mismatched or uninfected target cells. Alloreactivity could be excluded in MLC. DISCUSSION: This simple, rapid culture system can be useful for adoptive immunotherapy after allogeneic SCT. We are now trying to adapt our laboratory scale study to a clinical scale study under good manufacturing practices (GMP) conditions.

Identification of tumor suppressor candidate genes by physical and sequence mapping of the TSLC1 region of human chromosome 11q23.

Loss of heterozygosity for a locus on human chromosome 11q22-23 is observed at high frequency in non-small cell lung carcinoma (NSCLC). Introduction of a 1.1 Mb fragmented yeast artificial chromosome (YAC) mapping to this region completely suppresses the tumorigenic properties of a human NSCLC cell line, A549. Smaller fragmented YACs give partial but not complete suppression. To further localize the gene(s) responsible for this partial suppression, a bacterial artificial chromosome (BAC) and P1-based artificial chromosome (PAC) contig was constructed, completely spanning the candidate region. End sequence generated in the construction of the BAC/PAC contig identified a previously unmapped EST and served to order genomic sequence contigs from the publicly available Celera Genomics (CG) and Human Genome Project (HGP) efforts. Comparison showed that CG provided larger contigs, while HGP provided more coverage. Neither CG nor HGP provided complete sequence coverage, alone or in combination. The sequence was used to map 110 ESTs and to predict new genes, including two GenScan gene predictions that overlapped ESTs and were shown to be differentially expressed in tumorigenic and suppressed A549 cell lines.

TSLC1 is a tumor-suppressor gene in human non-small-cell lung cancer.

The existence of tumor-suppressor genes was originally demonstrated by functional complementation through whole-cell and microcell fusion. Transfer of chromosome 11 into a human non-small-cell lung cancer (NSCLC) cell line, A549, suppresses tumorigenicity. Loss of heterozygosity (LOH) on the long arm of chromosome 11 has been reported in NSCLC and other cancers. Several independent studies indicate that multiple tumor-suppressor genes are found in this region, including the gene PPP2R1B at 11q23-24 (ref. 7). Linkage studies of NSCLC are precluded because no hereditary forms are known. We previously identified a region of 700 kb on 11q23.2 that completely suppresses tumorigenicity of A549 human NSCLC cells. Most of this tumor-suppressor activity localizes to a 100-kb segment by functional complementation. Here we report that this region contains a single confirmed gene, TSLC1, whose expression is reduced or absent in A549 and several other NSCLC, hepatocellular carcinoma (HCC) and pancreatic cancer (PaC) cell lines. TSLC1 expression or suppression is correlated with promoter methylation state in these cell lines. Restoration of TSLC1 expression to normal or higher levels suppresses tumor formation by A549 cells in nude mice. Only 2 inactivating mutations of TSLC1 were discovered in 161 tumors and tumor cell lines, both among the 20 primary tumors with LOH for 11q23.2. Promoter methylation was observed in 15 of the other 18 primary NSCLC, HCC and PaC tumors with LOH for 11q23.2. Thus, attenuation of TSLC1 expression occurred in 85% of primary tumors with LOH. Hypermethylation of the TSLC1 promoter would seem to represent the 'second hit' in NSCLC with LOH.

Molecular cloning and characterization of two novel genes on chromosome 8p21.3.

Through large-scale sequencing of genomic DNA from human chromosome 8p22-p21.3 we have isolated two novel genes, designated GK1 and G5. Their predicted products showed no significant similarity to any known proteins in public databases. A comparison of GK1 cDNA sequences, which encode a 1270-amino-acid protein, with corresponding genomic DNA sequences revealed that this gene consists of 15 exons and spans an approximately 113-kb genomic region. Northern blot analysis revealed ubiquitous expression of 7.0- and 4.4-kb transcripts; in addition, we detected a 5.0-kb skeletal muscle-specific transcript and a 4.0-kb transcript specifically expressed in heart and pancreas. Computer and immunocytochemical analyses of a GK1 Green fluolesent protein (GFP) fused construct indicated that the gene product, which contains putative leucine-zipper domains, was likely to be a mitochondrial protein. The other novel gene, G5, expressed four transcripts (4.2, 2.2, 1.7, and 1.0-kb) ubiquitously; the longer three transcripts, which differed only in the 3'-non coding region, encoded identical 397-amino-acid peptides. The G5 gene consists of 14 exons and spans approximately 52 kb of genomic DNA; its deduced 397-amino acid product appears to contain coiled-coil domains and a proline-rich region, and to be located in cytoplasm.

Development of a highly sensitive enzyme immunoassay for human calcitonin using solid phase coupled with multiple antibodies.

We have developed a highly sensitive chemiluminescent enzyme immunoassay for human calcitonin using three different mouse monoclonal antibodies that recognize the N-terminal, C-terminal and central portions of a human calcitonin molecule. The assay signal in a two-step sandwich enzyme immunoassay for human calcitonin using a solid phase coupled with a mixture of monoclonal antibodies. CT08 and OCT1, was 3.7-fold higher than when using either or both solid phases coupled with CT08 or OCT1, respectively. This enhancement is the result of improved avidity of immobilized antibodies and greater stability of the complex of immobilized antibodies and calcitonin in the first reaction, which resulted in greater reactivity of the immunocomplex with alkaline phosphatase-conjugate in the second reaction. The present assay showed a linear response up to 2.5 micrograms/L of human calcitonin and a high specificity for human calcitonin, but not for rat calcitonin, human calcitonin gene-related peptide and rat calcitonin gene-related peptide. The detection limit of human calcitonin was estimated to be 0.29 ng/L at zero (assay blank) + 3 SD. Interbatch coefficients of variation ranged from 2.2-26.7%.

Cloning and characterization of human and mouse PROSC (proline synthetase co-transcribed) genes.

Large-scale DNA sequencing, coupled with in silico gene trapping, is a robust approach to identifying unknown genes in selected genomic regions. Using this approach we have isolated a novel human gene, PROSC (for proline synthetase co-transcribed [bacterial homolog]), from human chromosome 8p11.2, and its mouse counterpart. The human PROSC gene spanned 17 kb of genomic DNA; its cDNA was 2530 bp long, with 8 exons that included an open reading frame of 825 bp (275 amino acids). The mouse cDNA (Prosc), 1995 bp long, was predicted to encode 274 amino acids. PROSC is ubiquitously expressed in human tissues and has been highly conserved among divergent species from bacteria to mammals, suggesting its important cellular function. The gene product is likely to be a soluble cytoplasmic protein, but its function remains to be determined.

Significant differences in the frequency of transcriptional units, types and numbers of repetitive elements, GC content, and the number of CpG islands between a 1010-kb G-band genomic segment on chromosome 9q31.3 and a 1200-kb R-band genomic segment on chromosome 3p21.3.

We determined the nucleotide sequence of the entire 1,010,525-bp insert contained in CEPH YAC clone 867e8. This human genomic segment was derived from chromosome 9q31.3 and corresponds to a G-band region. We compared this segment, in terms of structure, with a previously characterized 1,201,033-bp sequence in CEPH YAC936c1 that had come from a portion of human chromosome 3p21.3 corresponding to an R-band region. The two segments were significantly different with respect to the frequency of transcriptional units, the types and numbers of repetitive elements present, their GC content, and the number of CpG islands. Alu elements, GC content, and CpG islands all showed positive correlations with the abundance of exons, but the distribution of LINE1s did not. These observations might reflect an influence of the first three of these features on the functions or expression of genes in the respective regions. In addition to a novel gene (F36) lying at the centromeric end of the 9q segment, we found a cluster of placenta-specific genes within a small section (about 400 kb) on the telomeric side of YAC867e8. This cluster consisted of four apparently unrelated ESTs and two genes, pregnancy-associated plasma protein-A (PAPP-A) and a novel gene (tentatively named EST-YD1). Our characterization of the two chromosomal regions provided evidence that genes are not evenly distributed throughout the human genome, and that gene richness is correlated with the GC content and with the frequency of either Alu elements or CpG islands.

Cloning and characterization of a novel gene (C8orf2), a human representative of a novel gene family with homology to C. elegans C42.C1.9.

Large-scale sequencing of selected genomic regions, coupled with in silico gene trapping, is a robust approach to identifying previously unknown genes. In this way we have found a gene (C8orf2) that is highly homologous to C. elegans C42C1.9. C8orf2 was situated on 8p11. 2 between STS markers NIB1979 (proximal) and AFMA295ZD5 (distal), oriented toward the centromere. C8orf2 consisted of 16 exons spanning more than 16.5 kb of genomic DNA, and was expressed ubiquitously in human tissues. The gene encoded 339-and 152-amino acid polypeptides by alternative splicing; the larger variant contained a region extremely rich in charged amino acids, in particular lysine and glutamic acid. C8orf2 also bore sequence homology to the human KE04p gene. Its conservation among highly divergent species suggests that C8orf2 belongs to a novel gene family.

Cloning of translocation breakpoints associated with Shwachman syndrome and identification of a candidate gene.

Shwachman syndrome is an autosomal-recessive disorder characterized by exocrine pancreatic insufficiency, bone-marrow dysfunction, and metaphyseal chondrodysplasia. A de novo balanced translocation was recently documented in a patient with this disease. Toward isolating the gene(s) responsible for Shwachman syndrome, we cloned and sequenced the translocation breakpoints in the DNA of this patient. The nucleotide sequences around the breakpoints contained neither repetitive elements nor motifs reported to be implicated in recombination events, although we did detect gains or losses of oligonucleotides at the translocation junctions. By large-scale genomic sequencing and in silico gene trapping, we identified two novel transcripts in the vicinity of the breakpoints that might represent candidate genes for Shwachman syndrome, one on chromosome 6 and the other on chromosome 12. The gene on chromosome 12 was actually disrupted by the translocation.

Cloning and characterization of ASH2L and Ash2l, human and mouse homologs of the Drosophila ash2 gene.

Drosophila ash2 belongs to the trithorax (trx) gene family. The ash2 product positively regulates expression of homeotic selector genes, and is implicated in early development and formation of various disc patterns in the fruit fly. Through large-scale sequencing of human genomic DNA coupled with in silico gene trapping, we identified a gene (ASH2L) on chromosome 8p11.2 whose predicted product was highly homologous to ash2, characterized it, and identified its mouse counterpart. The human ash2 cDNA is 2368 bp long, encoding 628 amino acids. The 16-exon gene spans more than 34 kb of genomic DNA between STS markers WI-9207 (centromere) and AFMA295ZD5 (telomere) on chromosome 8, with transcription oriented telomere to centromere. The ash2 genes are highly conserved among different species, including C. elegans and yeast. The presence of a conserved bipartite nuclear localization signal and a PHD finger motif in the human ash2 gene suggests that the gene product would function as a transcriptional regulator in humans, as its homologue does in Drosophila.

Removal of Formaldehyde by Activated Carbons Containing Amino Groups.

Formaldehyde has been used for disinfection and antisepsis in hospitals due to its bactericidal action, but it is toxic to humans. Hence, we developed adsorbates for the removal of formaldehyde. The adsorbate was prepared by the amination of an activated carbon surface. The removal efficiency and the adsorption mechanism of formaldehyde onto the aminated activated carbon were studied. The concentrated sulfuric acid and nitric acid treatment introduced nitro groups onto the surface of the activated carbon. The nitro groups were reduced by the reaction of powdered iron and hydrochloric acid to the amino groups. The amount of formaldehyde adsorbed onto the activated carbon increased with the amination of the activated carbon because of the increasing interaction between the surface of the activated carbon and the formaldehyde. Copyright 1999 Academic Press.

Characterization of a 1200-kb genomic segment of chromosome 3p22-p21.3.

We previously determined the nucleotide sequence and characterized the 685-kb proximal half of CEPH YAC936c1, which corresponds to a portion of human chromosome 3p21.3. In the study reported here, we characterized the remaining 515-kb of this YAC clone corresponding to the telomeric half of its human insert. The newly sequenced region contained a total of ten genes including six reported previously: phospholipase C delta 1 (PLCD1), human activin receptor type IIB (hActR-IIB), organic cation transporter-like 1 (OCTL1), organic cation transporter-like 2 (OCTL2), oxidative stress response 1 (OSR1), and human xylulokinase-like protein (XYLB). The remaining four genes present in the telomeric region included two known genes, MyD88 and ACAA, and two novel genes. One (designated ENGL) of the novel sequences was found to encode an amino-acid sequence homologous to the family of DNA/RNA endonucleases, especially endonuclease G. The other gene F56 revealed no significant homology to any known genes. These results disclosed complete physical and transcriptional maps of the 1200-kb region of 3p present in YAC 936c1.

Sequence analysis of an 800-kb genomic DNA region on chromosome 8q21 that contains the Nijmegen breakage syndrome gene, NBS1.

An 800-kb region on chromosome 8q21, which complements the phenotype of cells from Nijmegen breakage syndrome patients, is a candidate for the locus of the underlying gene, termed NBS1. The sequence of this 800-kb region of DNA indicated that the size of this segment is 755,832 bp with an additional 36-kb gap. From this region, we identified four genes including NBS1, a gene coding for a 27-kDa vitamin D-dependent calcium-binding protein (27-kDa calbindin), the mitochondrial 2,4-dienoyl-CoA reductase gene, and a novel gene, C8orf1/hT41. All four genes were aligned in a 250-kb centromeric portion of the region, and no gene was found in the remaining telomeric portion containing 500 kb. The genomic organization of the C8orf1/hT41 and NBS1 genes has been analyzed using the computer programs GRAIL 2 and GENSCAN. They predicted and successfully found more than 93% of the exons, even a small 54-bp exon, indicating that one or more exons in any gene can be identified by these programs. GENSCAN was more efficient at locating the four genes than GRAIL 2 and identified 15 of the 16 exons of the NBS1 gene. This 800-kb region contained repetitive sequences, including 179 copies of the Alu sequence (1 copy/4.2 kb), 123 copies of the L1 sequence (1 copy/6.1 kb), 107 copies of the LTR sequence (1 copy/7.1 kb), and 63 copies of the MER sequence (1 copy/12 kb). There was a slight but not significant difference in the repetitive content of the gene-rich region and the remaining noncoding region. Our results indicate that computer-assisted methods are useful and powerful for identifying exons of both known and novel genes.

Sequence analysis of a total of three megabases of DNA in two regions of chromosome 8p.

Large-scale sequencing of genomic regions and in silico gene trapping together represent a highly efficient and powerful approach for identifying novel genes. We performed megabase-level sequence analyses of two genomic regions on human chromosome 8p (8p11.2 and 8p22-->p21.3), after covering those segments with sequence-ready contigs composed of 74 cosmids, 14 BACs, and three PAC clones. We determined continuous nucleotide sequences of 1,856,753 bases on 8p11.2 and 1,210,381 bases on 8p22-->p21.3 by combining the shotgun and primer-walking methods. In silico gene trapping identified four novel genes in the 8p11.2 region and, in the 8p22-->p21.3 region, six known genes (PRLTS, PCM1, MTAMR7, HCAT2, HFREP-1 and PHP) and three novel genes. The distribution of Alu and LINE1 repetitive elements and the densities of predicted exons were different in each region, and Alu-rich portions contained more exonic sequences than LINE1-rich areas.

Heterozygosities and allelic frequencies of 358 dinucleotide-repeat marker loci in the Japanese population.

We examined 64 normal Japanese chromosomes to determine the heterozygosities and allelic frequencies of 358 dinucleotide-repeat marker loci spanning the whole human genome. Comparisons of the data for each marker in the Japanese population sample with data for the same markers among Caucasian samples in the Genome Database (GDB) revealed a slightly lower average of heterozygosity in Japanese (71% vs 79%). Although the majority of the markers were as informative as in Caucasians, some in our sample were uninformative due to low heterozygosity; 38 loci revealed heterozygosities lower than 50% and 11 of these were less than 30%. Furthermore, allelic distributions at many of the marker loci were quite different in the two racial groups. Since such differences will influence statistical analyses between markers and disease loci, our data will be essential for linkage analyses, sib-ship pair analyses, and association studies involving the Japanese population. Therefore we have archived this database on a home page on the Internet (http:@www.ims.u-tokyo.ac.jp/nakamura/Yamane.html++ +).

Positional cloning of the gene for Nijmegen breakage syndrome.

Nijmegen breakage syndrome (NBS), also known as ataxia-telangiectasia (AT) variant, is an autosomal recessive disorder characterized by microcephaly, growth retardation, severe combined immunodeficiency and a high incidence of lymphoid cancers. Cells from NBS patients display chromosome instability, hypersensitivity to ionizing radiation and abnormal cell-cycle regulation after irradiation, all of which are characteristics shared with AT. Recently, the NBS locus was mapped at 8q21 by two independent approaches, complementation studies and linkage analysis. Here, we report the positional cloning of the NBS gene, NBS1, from an 800-kb candidate region. The gene comprises 50 kb and encodes a protein of 754 amino acids. The amino-terminal region of the protein shows weak homology to the yeast XRS2, MEK1, CDS1 and SPK1 proteins. The gene is expressed at high levels in the testes, suggesting that it might be involved in meiotic recombination. We detected the same 5-bp deletion in 13 individuals, and conclude that it is likely to be a founder mutation.

The yhhP gene encoding a small ubiquitous protein is fundamental for normal cell growth of Escherichia coli.

H-NS is a major constituent of the Escherichia coli nucleoid, whereas sigmaS is a stress-induced sigma factor. An hns null mutation affects the cellular content of sigmaS in such a way that a remarkable accumulation of sigmaS is observed in the logarithmic growth phase, which results in enhanced expression of a number of sigmaS-dependent genes, including the katE gene. We isolated an extragenic mutation that affects the expression of the katE-lacZ fusion gene in the deltahns background. The relevant gene was identified as yhhP, which encodes a small polypeptide of 81 amino acids. Lesion of this gene seemed to affect the stability of sigmaS. A deletion analysis of yhhP revealed that this small protein plays a fundamental role in the general physiology of E. coli. The yhhP-deficient cell is not capable of growing in standard laboratory rich medium (i.e., Luria broth), resulting in the formation of filamentous cells. Homologs of this intriguing protein occur in a wide variety of bacterial species, including archaeal species.

Enzymatic synthesis of oligosaccharides containing Gal beta-->4Gal disaccharide at the non-reducing end using beta-galactanase from Penicillium citrinum.

The transglycosylation reaction was done with a beta-galactanase from Penicillium citrinum. The regioselectivity in the transglycosylation reaction was studied using soy bean arabinogalactan as a donor and mono- or disaccharide derivatives containing beta-galactosyl residue as acceptors. We also synthesized oligosaccharides containing Gal beta 1-->4Gal sequence such as Gal beta 1-->4Gal beta1-->4Glc, Gal beta 1-->4Gal beta 1-->3GlcNac, Gal beta 1-->4Gal beta 1-->4GlcNAc, Gal beta 1-->4Gal beta 1-->6GlcNAc, and Gal beta 1-->4Gal beta 1-->3GalNAc for use in the total synthesis of complex sugar chains.

No evidence of mutation in the human PTC gene, responsible for nevoid basal cell carcinoma syndrome, in human primary squamous cell carcinomas of the esophagus and lung.

The high frequency of loss of heterozygosity that has been observed on the distal region of the long arm of chromosome 9 in squamous cell carcinomas of esophagus, lung, uterus, and head and neck indicates the presence of a tumor suppressor gene(s) in this region. To investigate the possible role of the PTC gene on chromosome 9q22.3, that was identified as the cause of nevoid basal cell carcinoma syndrome, during carcinogenesis in esophagus and lung, we examined 20 esophageal squamous cell carcinomas and 10 squamous cell carcinomas of the lung for mutations in any coding exon of PTC. Using single-strand conformation polymorphism and direct sequencing, we detected no mutations other than two non-deleterious polymorphisms. Our results suggest that inactivation of some tumor suppressor gene(s) on 9q other than PTC contributes to the development of squamous cell carcinomas in these tissues.