A novel STK11 germline mutation in two siblings with Peutz-Jeghers syndrome complicated by primary gastric cancer.

Patients with Peutz-Jeghers syndrome (PJS) are known to be at risk of gastric cancer (GC), and the STK11 gene is a susceptibility gene for PJS. However, as no cases of PJS with GC in which a STK11 germline mutation has been identified have ever been reported and other susceptibility genes have also been suggested to be involved in PJS, the relation between STK11 germline mutations and GC in PJS is still unknown. In this study, we used sequencing analysis to investigate the STK11, CDH1, and TP53 loci for a germline mutation in two siblings with PJS with primary GC. A novel type of the STK11 germline mutation, c.890delG, encoding a truncated protein (p.Arg297fsX38) was identified, but no germline mutations of the CDH1 and TP53 genes were detected. No inactivation of the wild-type allele by somatic mutation or chromosomal deletion or hypermethylation at the 5'-CpG site of STK11 was detected in the GC. This is the first report of a STK11 germline mutation in a PJS patient with GC and should contribute to establishing correlations between the STK11 germline mutations and GC in PJS patients.

Isolation and characterization of the genes up-regulated in isolated neurons by aged garlic extract (AGE).

Aged garlic extract (AGE) produces neurotrophic effects on cultured fetal rat hippocampal neurons. These studies examined the molecular events triggered by AGE that might account for a suppression of neuronal cell death. Genes differentially expressed by the addition of AGE in primary cultured hippocampal neurons isolated from fetal rat brain were screened using mRNA differential display. Four cDNA clones were significantly enhanced at their transcriptional level; they were designated as #24, #110, #153 and #155. Quantitative reverse transcription-polymerase chain reaction (RT-PCR), as well as dot-blot hybridization combined with RT-PCR, confirmed that the transcription from these four genes was elevated at least twofold, particularly the mRNA of #153, which was increased >20 times 72 h after the addition of AGE. A homology search of the respective cDNA sequences in the DNA database revealed that #153 is an alpha 2-microglobulin-related protein (alpha 2MRP) gene. The others genes were not identified. Induction of the alpha 2MRP gene expression occurred within 24 h after addition of AGE. These findings suggest a possible mechanism by which AGE may regulate gene expression and bring about a neurotrophic effect. Further, our results suggest that alpha 2MRP may function at the initial step of the molecular events triggered by AGE and play an important role in the survival of hippocampal neurons.

Complete nucleotide sequences of garlic viruses A and C, members of the newly ratified genus Allexivirus.

Complete genomic sequences of garlic viruses A (Gar V-A) and C (Gar V-C), members of an unassigned virus group recently identified in garlic plants, were determined. Their respective genomes consist of 8 660 and 8 405 nucleotides. The genomic structure and organization of these viruses are similar to shallot virus X (ShVX) which is the type species of the newly ratified genus Allexivirus. Phylogenetic analysis based on the amino acid sequences of the putative proteins including RNA-dependent RNA polymerase (RdRP), DNA helicase, or viral coat protein showed that the GarV-type viruses should be included in the genus Allexivirus. Furthermore, the amino acid sequence in the RdRP hypervariable region is highly divergent among the viruses in the genus Allexivirus, suggesting that they evolved independently from a hypothetical ancestor virus(es).

Differentiation of Allium carlaviruses isolated from different parts of the world based on the viral coat protein sequence.

Common primers which amplify the 3' terminal genomic RNAs of Allium carlaviruses were designed based on the nucleotide sequence of shallot latent virus (SLV), garlic latent virus (GLV) and garlic common latent virus (GCLV). A total of fifteen cDNAs encoding the coat protein (CP) of the carlaviruses, including the biologically identified isolates SLV, GLV and GCLV as well as viruses from infected Allium plants cultivated in different parts of the world, were amplified by RT-PCR with the common primers. The cDNAs were then cloned and sequenced. The predicted viral CP amino acid sequence as well as the nucleotide sequence revealed that SLV and GLV, previously considered as separate viruses on the basis of their biological and physical properties, belong to the same species of the genus Carlavirus. Both viruses are clearly differentiated from GCLV. In addition, every SLV and GLV isolate from the Allium plants in Taiwan showed characteristic and common variations in their CP sequences, suggesting the possible presence of geographical variants. However, no apparent sequence variations of SLV and GLV related to their host plant species, including A. sativum, A. wakegi, A. chinense, A. fistulosum, A. cepa and A. ampeloprasum, were observed. These findings suggested that the sequence variations observed in the respective virus isolates do not correlate with the specificity of their infectivities for Allium species.

Piroxicam and acarbose as chemopreventive agents for spontaneous intestinal adenomas in APC gene 1309 knockout mice.

The use of nonsteroidal anti-inflammatory drugs has been suggested to have a chemopreventive effect against colon carcinoma, through the inhibition of cyclooxygenases 1 and 2, in patients with familial adenomatous polyposis and in animal models. Acarbose, an alpha-glycosidase inhibitor, may also be chemopreventive. In order to examine the effects of these drugs we employed APC gene knockout mice randomized into 3 groups, one for treatment with piroxicam (0.05% concentration in drinking water), one for acarbose (0.04% concentration in food) and another for the control. After 14 weeks of treatment, mice were killed for quantitation of gastric and intestinal adenomas. Tumor multiplicity in the whole gastrointestinal tract decreased from 33.89 +/- 13.07 tumors/mouse in the control group to 17.05 +/- 7 tumors/mouse in the piroxicam-treated group (P < 0.001). The decrease in the acarbose-treated group (29.68 +/- 12.86 tumors/mouse) was not significant (P < 0.05). The number of tumors > or = 3 mm in diameter was also quantified in all gastrointestinal segments. The number of such tumors in the piroxicam group was decreased to 0.56 +/- 1.2 tumors/mouse from the control value of 3.78 +/- 1.17 tumors/mouse (P < 0.001), while in the acarbose-treated group the number decreased to 2.36 +/- 1.7 tumors/mouse (P < 0.01). Thus, piroxicam decreases the size and number of gastrointestinal adenomas in APC 1309 knockout mice, while acarbose decreases only the size.

Nucleotide sequence analysis of virus isolates indicates the presence of three potyvirus species in Allium plants.

cDNAs of potyviruses from Allium plants cultivated in different parts of the world were cloned by RT-PCR with a common primer for amplifying the 3' terminal genomic RNAs of onion yellow dwarf virus (OYDV), leek yellow stripe virus (LYSV) and, probably, of closely related potyviruses. Their nucleotide sequences bearing the viral coat protein (CP) gene and the 3' non-coding sequence were determined and compared. The degree of their sequence similarities clearly differentiated the respective viruses into 3 groups, namely OYDV "garlic-type", "wakegi-type" and LYSV group. The "garlic-type" included all the garlic isolates and two Indonesian shallot isolates. The "wakegi-type" group consisted of the isolates from Indonesian shallot and previously reported ones from Japanese Allium plants excluding garlic. The LYSV group was represented by LYSV isolates from garlic and leek. The CP sequences of LYSV group viruses differed from those of OYDV "garlic-type" and "wakegi-type" viruses (less than 60% similarities). In contrast, the sequence similarities between the OYDV "wakegi-type" and "garlic-type" isolates were 73.5 to 76.7%, suggesting they were closely related but should be discriminated as distinct species. These findings indicate that at least three distinct potyviruses, clearly distinguishable by the viral CP sequence, are present in Allium species. Finally, we concluded that the "garlic-type" viruses correspond to the typical OYDV and the "wakegi-type" viruses represent the viruses previously identified as Welsh onion yellow stripe virus (WoYSV) and shallot yellow stripe virus (SYSV). We propose the name wakegi yellow dwarf virus (WYDV) for the "wakegi-type" viruses.

Mass spectrometric gene diagnosis of one-base substitution from polymerase chain reaction amplified human DNA.

One-base substitution has been detected on the polymerase chain reaction (PCR) products amplified from human mutated DNA for the first time by using mass spectrometry. PCR fragments of 52 base pairs were produced on a collagen gene of an osteogenesis imperfecta patient's heterozygous DNAs. The products were digested with EcoRI restriction enzyme to liberate 3'-end adducts and purified by phenol + chloroform extraction, ammonium acetate addition and ethanol precipitation to remove sodium ions from the phosphoric acid backbone of the DNAs. Purified products were examined using an electrospray ionization mass spectrometer. Mass spectra showed four groups of fragment peaks with the expected molecular masses, which originate from the sense and antisense strands of the heterozygous DNAs.

Nucleotide sequences of the 3' terminal region of onion yellow dwarf virus isolates from Allium plants in Japan.

The 2032 nucleotide sequence of the 3' terminal region of onion yellow dwarf virus (OYDV) isolated from Allium wakegi, bearing the genes for viral coat protein (CP) and a truncated RNA-dependent RNA polymerase, has been determined. Respective homologies of the nucleotide sequence in the corresponding region and the deduced amino acid sequence of CP with the equivalents of leek yellow stripe virus (LYSV) from garlic were 68.0 and 59.3%. Variation in the nucleotide sequence is concentrated in the boundary region between the putative RNA-dependent RNA polymerase gene and the CP gene as well as in the 3' noncoding region. These sequence divergencies, including the deletion of 79 nucleotides, resulted both in alterations to the amino acid sequence and the absence of 28 amino acid residues in the amino terminal region of OYDV CP in comparison with LYSV CP. In addition, the length of the 3' noncoding sequence of OYDV was one-third that of LYSV. Comparison of the 3' terminal 1197 nucleotides sequence of OYDV with sequences of the respective cDNAs cloned by RT-PCR directly from the total RNA of infected Allium plants that included two varieties of A. fistulosum, "Wakenegi" and "Shimonita-negi", and A. chinense, showed 90.7% overall identities, even though they have long been cultivated in locally restricted area in Japan. These findings appear to suggest that a single strain of OYDV invaded Japanese Allium plants long ago and spread throughout them.

Molecular mass measurement of polymerase chain reaction products amplified from human blood DNA by electrospray ionization mass spectrometry.

We report here on the first analysis of polymerase chain reaction (PCR) products amplified from a small amount of human blood DNA by electrospray ionization mass spectrometry (ESI-MS). Adenomatous polyposis coli (APC) gene fragment of about 50 base pairs (bp) with a relative molecular mass (M(r)) of approximately 15,000 u was amplified from human blood DNA by PCR. The accurate molecular mass of the PCR products was determined with an accuracy of approximately 0.005% by ESI-MS. The amount of DNA used was only 100 ng (approximately 50 zmol; the theoretically required amount of blood is therefore less than 1 microliter for PCR). The ESI-MS measurement of the PCR products proved to be a new accurate, sensitive and fast tool for gene diagnosis.

Mutational heterogeneity among individual tumors in a case of multiple primary malignancy of the colon.

c-Ki-ras mutations were analyzed from quintuple colon tumors in a 75-year-old patient with no family history of colon cancer. Polymerase chain reaction-amplified DNA was sequenced for mutations in c-Ki-ras exon 1. Detected mutations were confirmed with allele-specific PCR which amplified only mutant sequences. Five tumors were histopathologically diagnosed as: adenoma with moderate atypia, adenoma with moderate atypia bearing a focal cancer, adenoma with severe atypia bearing a focal cancer, intramucosal carcinoma, well differentiated adenocarcinoma (advanced). Transitions, G-A, were found at the second base of codon 12 for the adenoma with severe atypia bearing a focal cancer and for the well- differentiated adenocarcinoma. The same substitution was found at the second base of codon 13 in the adenoma with mild atypia bearing a focal cancer. No base substitution at codon 12 or 13 was found for the intramucosal carcinoma nor for the adenoma with moderate atypia. These findings demonstrated there to be heterogeneous genetic and histopathological alterations in the individual tumors of the present case of synchronous malignancy of the colon.

Novel rod-shaped viruses isolated from garlic, Allium sativum, possessing a unique genome organization.

Rod-shaped flexuous viruses were partially purified from garlic plants (Allium sativum) showing typical mosaic symptoms. The genome was shown to be composed of RNA with a poly(A) tail of an estimated size of 10 kb as shown by denaturing agarose gel electrophoresis. We constructed cDNA libraries and screened four independent clones, which were designated GV-A, GV-B, GV-C and GV-D, using Northern and Southern blot hybridization. Nucleotide sequence determination of the cDNAs, two of which correspond to nearly one-third of the virus genomic RNA, shows that all of these viruses possess an identical genomic structure and that also at least four proteins are encoded in the viral cDNA, their M(r)s being estimated to be 15K, 27K, 40K and 11K. The 15K open reading frame (ORF) encodes the core-like sequence of a zinc finger protein preceded by a cluster of basic amino acid residues. The 27K ORF probably encodes the viral coat protein (CP), based on both the existence of some conserved sequences observed in many other rod-shaped or flexuous virus CPs and an overall amino acid sequence similarity to potexvirus and carlavirus CPs. The 11K ORF shows significant amino acid sequence similarities to the corresponding 12K proteins of the potexviruses and carlaviruses. On the other hand, the 40K ORF product does not resemble any other plant virus gene products reported so far. The genomic organization in the 3' region of the garlic viruses resembles, but clearly differs from, that of carlaviruses. Phylogenetic analysis based upon the amino acid sequence of the viral capsid protein also indicates that the garlic viruses have a unique and distinct domain different from those of the potexvirus and carlavirus groups. The results suggest that the garlic viruses described here belong to an unclassified and new virus group closely related to the carlaviruses.

Substitutions for glycine alpha 1-637 and glycine alpha 2-694 of type I procollagen in lethal osteogenesis imperfecta. The conformational strain on the triple helix introduced by a glycine substitution can be transmitted along the helix.

Two substitutions for glycine in the triple-helical domain were found in type I procollagen synthesized by skin fibroblasts from two probands with lethal osteogenesis imperfecta. One was a substitution of valine for glycine alpha 1-637, and the other was a substitution of arginine for glycine alpha 2-694. The effects of the mutations on the zipper-like folding of the collagen triple helix were similar, since there was post-translational overmodification of the collagenase A fragments (amino acids 1-775) but not of more COOH-terminal fragments of the protein. The mutations differed markedly, however, on their effects on thermal unfolding of the triple helix. The collagenase A fragment from the collagen containing the arginine alpha 2-694 substitution was cleaved at about amino acid 700 when incubated with trypsin at 30-35 degrees C. Therefore, there was micro-unfolding of the triple helix at a site close to the glycine substitution. Surprisingly, however, the collagenase A fragment with the valine alpha 1-637 substitution was also cleaved at about amino acid 700 under the same conditions. The results, therefore, demonstrated that although most glycine substitutions delay folding of the triple helix in regions that are NH2-terminal to the site of the substitution, the effects on unfolding can be transmitted to regions that are COOH-terminal to the site of the glycine substitution.