[Large deletion in mismatch repair genes uncovered by quantitative multiplex PCR-high performance liquid chromatography system]

OBJECTIVE

Establishing a new method on the basis of multiplex PCR-high performance liquid chromatography (HPLC) for screening a large deletion in mismatch repair genes.

METHODS

Thirty-five pairs of primers were used to amplify all 16 exons of MSH2 and all 19 exons of MLH1 gene in 8 multiplex PCR. The products of multiplex PCR were analysed for the large deletion with Double Strand DNA Analysis System of HPLC. Firstly, validation of the method was tested on positive and negative controls in blind analysis. Secondly, 14 blood cell DNA samples from hereditary nonpolyposis colorectal cancer (HNPCC) patients and 13 colorectal cancer (CRC) tissues DNA samples from sporadic CRC patients were checked with the new developed method.

RESULTS

(1) the genomic deletions in all 4 of positive controls were identically uncovered with the new method; (2) a novel germline and a novel somatic large deletions were unveiled in 1/14 HNPCC patients and in 1/13 CRC tissues.

CONCLUSION

The method developed on multiplex PCR-HPLC is reliable for uncovering large genomic deletion in mismatch repair genes, and can be taken as a valuable addition to mutation screening system.

Abnormal vascular network complexity: a new phenotypic marker in hereditary non-polyposis colorectal cancer syndrome

BACKGROUND

Hereditary non-polyposis colorectal cancer (HNPCC) (Lynch cancer family syndrome I (LCFS1) and II (LCFS2)) is one of the most common hereditary cancer disorders. HNPCC results from dominantly inherited germline mutations in mismatch repair (MMR) genes, leading to genomic instability and cancer. No predictive physical signs of HNPCC are available to date.

AIMS

Increased complexity in tumour associated vascular growth has been reported. Here, we tested the hypothesis that an increased vascular network complexity is a phenotypic marker for LCFS2.

METHODS

Fourteen subjects from an LCFS2 kindred (gene carriers, n=5; non-carriers, n=9) and 30 controls were examined. Fractal dimension (D) at two scales (D (1-46), and D (1-15), tortuosity (minimum path dimension, Dmin), and relative Lempel-Ziev complexity (L-Z) of the vascular networks from the lower gingival and vestibular oral mucosa were measured.

RESULTS

LCFS2 networks exhibited a significantly increased overall complexity at both larger (D (1-46): 1.82 (0.04) v 1.68 (0.08); p<0.0001) and smaller (D (1-15): 1.51 (0.11) v 1.20 (0.09); p<0.0001) scales, increased destructured randomness (L-Z: 0.77 (0.09) v 0.56 (0.03); p<0.0001), and decreased vessel tortuosity (DMIN: 1.02 (0.03) v 1.07 (0.04); p=0.0005) compared with control patterns. The vascular networks of LCFS2 gene carriers showed higher complexity at the smaller scale (D (1-15): 1.59 (0.12) v 1.47 (0.07); p=0.034), and higher destructured randomness (L-Z: 0.85 (0.11) v 0.73 (0.05); p=0.013) than those of non-carriers.

CONCLUSIONS

Increased oral vascular network complexity is a previously unrecognised phenotypic marker for LCFS2, and is related to gene mutation carrier status.

Mismatch repair gene expression defects contribute to microsatellite instability in ovarian carcinoma

BACKGROUND

hMLH1, the human MutL homologue, has been linked to microsatellite instability (MSI) in gastrointestinal tumors. However, to the authors' knowledge, the role of hMLH1, the other mismatch repair genes (MMR), and MSI in ovarian carcinoma has not been well defined. The purpose of the current study was to determine the relation between MSI of ovarian carcinoma and MMR gene expression, hMLH1 and hMSH2 hypermethylation, and hMLH1 and hMSH2 null mutations.

METHODS

hMLH1 mRNA was detected by reverse transcriptase-polymerase chain reaction (RT-PCR) and amplification of cDNA using a housekeeping gene (glycerol 3-phosphate dehydrogenase) as a control for mRNA quality and quantity. Methylation-specific PCR (MS-PCR) was used to correlate methylation of the hMLH1 and hMSH2 CpG islands with mRNA expression status. Similar techniques were used to evaluate the concomitant expression of five other MMR: hMSH2, hMSH3, hMSH6, PMS1, and PMS2. Microsatellite instability was studied using the National Cancer Institute consensus markers (D2S123, D5S346, D17S250, BAT25, and BAT26) and NM23 as described previously.

RESULTS

One hundred twenty-five primary tumors were analyzed. High-frequency MSI (MSI-H) was found in 21 tumors (16.8%). hMLH1 mRNA was absent in 10 of these 21 tumors (47.6%). In each case, coordinated hypermethylation of both regions A and C of the promoter was identified. Microsatellite stable and low-frequency MSI tumors all were found to express not only hMLH1 but the other MMR genes as well (P < 0.001). Absence of expression of hMSH2 and the four other MMRs occurred in tumors with absent hMLH1 mRNA expression because of CpG island hypermethylation. No absence of expression of hMSH2, hMSH3, hMSH6, PMS1, or PMS2 was found to occur in tumors expressing hMLH1. None of the 11 MSI-H tumors without promoter hypermethylation demonstrated a null mutation in hMLH1 or hMSH2.

CONCLUSIONS

A molecular mechanism to explain > 50% of the MSI-H phenotype in ovarian carcinoma cases was demonstrated. MSI-H may occur because of MMR defects, especially hMLH1 promoter hypermethylation. Additional mechanisms are required to explain the balance between the cases of MSI-H as well as the phenomenon of MSI-L tumors.

A role for DNA mismatch repair in sensing and responding to fluoropyrimidine damage

The phenomenon of damage tolerance, whereby cells incur DNA lesions that are nonlethal, largely ignored, but highly mutagenic, appears to play a key role in carcinogenesis. Typically, these lesions are generated by alkylation of DNA or incorporation of base analogues. This tolerance is usually a result of the loss of specific DNA repair processes, most often DNA mismatch repair (MMR). The availability of genetically matched MMR-deficient and -corrected cell systems allows dissection of the consequences of this unrepaired damage in carcinogenesis as well as the elucidation of cell cycle checkpoint responses and cell death consequences. Recent data indicate that MMR plays an important role in detecting damage caused by fluorinated pyrimidines (FPs) and represents a repair system that is probably not the primary system for detecting damage caused by these agents, but may be an important system for correcting key mutagenic lesions that could initiate carcinogenesis. In fact, clinical studies have shown that there is no benefit of FP-based adjuvant chemotherapy in colon cancer patients exhibiting microsatellite instability, a hallmark of MMR deficiency. MMR-mediated damage tolerance and futile cycle repair processes are discussed, as well as possible strategies using FPs to exploit these systems for improved anticancer therapy.

Reduction of Htt inclusion formation in strains of Saccharomyces cerevisiae deficient in certain DNA repair functions: a statistical analysis of phenotype

Saccharomyces cerevisiae has been used as a model system to examine the aggregation of the huntingtin protein (Htt), a well-established marker in the pathology of the triplet expansion disorder Huntington's disease (HD). Several genetic backgrounds, such as Deltahsp104, have proven to be refractory to inclusion formation through a process yet to be fully elucidated. These results have prompted a wide-ranging search for other mutant strains that exhibit a lower level of Htt aggregation. A novel assay system in which Htt is expressed as a fusion protein containing eGFP enables an analysis of aggregation and the factors that suppress it. We have examined several strains that are devoid of certain mismatch repair genes and find that some of these support a reduced level of inclusion body formation. We apply a detailed and stringent statistical analysis to the results obtained for all yeast strains that exhibit a definable phenotype. Such analyses should be useful and applicable to other in vivo analyses of related phenomena.

Therapy-related leukemia cutis: case study of an aggressive disorder

Therapy-related leukemia cutis has not yet been described. We report a 55-year-old male who developed aleukemic leukemia cutis 15 months after chemotherapy and radiotherapy for non-Hodgkin's lymphoma. Despite intensive therapy including allogeneic hematopoietic stem cell transplantation, the patient died of progressive disease. Sequence analysis of the TP53 gene and screening for defective DNA mismatch repair revealed no abnormalities. This case demonstrates that therapy-related aleukemic leukemia cutis is an aggressive disorder resistant to conventional antineoplastic treatment approaches. As the number of patients developing therapy-related myelodysplasia or leukemia is increasing, clinicians might be confronted more frequently with atypical, extramedullary presentations of these disorders.

Lack of microsatellite instability in neoplasms of ampulla of Vater

To clarify the genetic background of ampullary neoplasm, we investigated the occurrence of microsatellite instability (MSI) in 64 samples of neoplasm of the ampulla of Vater. Eight out of 22 adenomas (34.6%), nine out of 32 carcinomas (28.1%) and one metastatic lesion (10.0%) showed MSI in 1-3 of the nine dinucleotide markers; those cases are categorized into microsatellite instability-low (MSI-L). The remaining samples were stable with respect to all of the tested markers. None of the samples showed a frameshift mutation in the poly A-tract of BAT-26 or transforming growth factor-beta type II receptor, which are frequently mutated in gastric or colorectal cancers showing microsatellite instability. To confirm our finding, we stained 93 ampullary neoplasms with antibodies against the mismatch repair proteins: hMLH1 and hMSH2. All tumors were found to express mismatch repair proteins. In contrast to gastric or colorectal cancers, MSI does not play an important role in the carcinogenesis of ampullary carcinoma.

Electrocatalytic Detection of Pathogenic DNA Sequences and Antibiotic Resistance Markers

The detection of specific DNA sequences using electrochemical readout would permit the rapid and inexpensive detection and identification of bacterial pathogens. A new assay developed for this purpose is described that harnesses a sensitive electrocatalytic process to monitor DNA hybridization. Two sequences belonging to the pathogenic microbe Helicobacter pylori are used to demonstrate the versatility and specificity of the assay: one that codes for an unique H. pylori protein and one that represents a small portion of the 23S rRNA from this organism. Both sequences can be monitored into the nanomolar concentration range. Target sequences introduced to the electrode surface as synthetic oligonucleotides, PCR products, and RNA transcripts are all detected with high specificity. In addition to reporting the presence of pathogen-related sequences, this assay can accurately resolve single-base changes in target sequences. An A2143C substitution within the H. pylori rRNA that confers antibiotic resistance significantly attenuates hybridization to an immobilized probe corresponding to the WT sequence. The single-base mismatch introduced by this mutation slows the kinetics of hybridization and permits discrimination of the two sequences when short hybridization times are employed. The remarkable sensitivity of this label-free assay to small sequence changes may provide the basis of a new method for the detection and genotyping of infectious bacteria using electrochemical methods.

Assessment of microsatellite instability in bladder and thyroid malignancies

Microsatellite instability (MSI) is an indicator of a defective DNA mismatch repair system (MMR) that results from somatic mutations. The present work has been planned to investigate MSI and its clinical significance in human urinary bladder and thyroid cancers in Indian patients. Tumor tissues of histologically confirmed cases of urinary bladder and thyroid cancers, respectively, were obtained. Clinical data on tumor stage and histopathological grades were recorded. Corresponding matched peripheral blood was taken as a control. Genomic DNA was isolated from the tumor tissues and blood using a standard phenol-chloroform extraction method. Polymerase chain reaction was done to amplify mononucleotide microsatellite markers, BAT-26, BAT-40, TGFbetaRII, IGFIIR, hMSH3, and Bax by using specific primer sequences. For analysis of allelic patterns, the PCR products were run on 8% denaturing Polyacrylamide gel and sizing was done using a pUC18 sequencing ladder. The instability with BAT-26 and BAT-40 was found to be 20% and 45% in urinary bladder and 33% and 19% in thyroid cancers, respectively. However, no instability was observed with the other four-mononucleotide markers in either of the cancers studied. Eighty-three percent of the unstable urinary bladder cancers were found to have a high grade in a superficial group, whereas only 27% MSI+ve were muscle invasive cancers. Forty percent of unstable thyroid lesions were found to be at high risk of developing metastasis. Association of BAT-26 and BAT-40 instabilities with high grade tumors as well as risk tumors may help in choosing a more definite therapy at the outset.

Artificial intelligence in predicting bladder cancer outcome: a comparison of neuro-fuzzy modeling and artificial neural networks

PURPOSE

New techniques for the prediction of tumor behavior are needed, because statistical analysis has a poor accuracy and is not applicable to the individual. Artificial intelligence (AI) may provide these suitable methods. Whereas artificial neural networks (ANN), the best-studied form of AI, have been used successfully, its hidden networks remain an obstacle to its acceptance. Neuro-fuzzy modeling (NFM), another AI method, has a transparent functional layer and is without many of the drawbacks of ANN. We have compared the predictive accuracies of NFM, ANN, and traditional statistical methods, for the behavior of bladder cancer.

EXPERIMENTAL DESIGN

Experimental molecular biomarkers, including p53 and the mismatch repair proteins, and conventional clinicopathological data were studied in a cohort of 109 patients with bladder cancer. For all three of the methods, models were produced to predict the presence and timing of a tumor relapse.

RESULTS

Both methods of AI predicted relapse with an accuracy ranging from 88% to 95%. This was superior to statistical methods (71-77%; P < 0.0006). NFM appeared better than ANN at predicting the timing of relapse (P = 0.073).

CONCLUSIONS

The use of AI can accurately predict cancer behavior. NFM has a similar or superior predictive accuracy to ANN. However, unlike the impenetrable "black-box" of a neural network, the rules of NFM are transparent, enabling validation from clinical knowledge and the manipulation of input variables to allow exploratory predictions. This technique could be used widely in a variety of areas of medicine.

Microsatellite instability is a predictive factor of the tumor response to irinotecan in patients with advanced colorectal cancer

The aim of our study was to assess the relationship between colorectal tumor responsiveness to irinotecan and microsatellite instability (MSI), a feature of colorectal tumors with DNA mismatch repair defect. Seventy-two patients with metastatic colorectal cancer were included in our retrospective study. A complete response to irinotecan was observed in 1 patient and a partial response in 10 patients, whereas 61 patients did not respond to this treatment. We analyzed the protein expression of hMLH1, hMSH2, and BAX by immunohistochemistry, determined the MSI phenotype, and looked for mutations in the coding repeats located in the transforming growth factor beta-RII, BAX, hMSH3, and hMSH6 genes. All 44 tumors analyzed expressed detectable levels of hMLH1; 1 tumor lacked hMSH2 staining, whereas 4 tumors showed a marked decrease in BAX expression. A better response to irinotecan was observed in the patients whose tumors have lost BAX expression (P < 0.001). Among the 7 tumors that displayed a MSI-H phenotype, 4 responded to irinotecan, whereas only 7 of the 65 MSI-L/ microsatellite stable tumors did (P = 0.009). Seven of the 72 tumors had inactivating mutations in the coding repeats of the target genes. Three tumors displayed a mutation in the poly-A10 tract of the transforming growth factor beta-RII gene, associated with a 1-bp deletion in the poly-A8 tract of hMSH3 in one tumor and with a 1-bp deletion in the poly-G8 tract of BAX in another. Four tumors displayed mutations in the poly-G8 repeat of BAX, whereas 2 mutations in hMSH6 and hMSH3 were characterized. Among the 7 tumors with mutations in these target genes, 5 responded to irinotecan, whereas only 6 of the other 65 tumors did (P < 0.001), indicating that MSI-driven inactivation of target genes modifies tumor chemosensitivity. Our observations allowed us to define the first useful predictive criteria for irinotecan response in patients with colorectal cancer.

Reduction of stability of arabidopsis genomic and transgenic DNA-repeat sequences (microsatellites) by inactivation of AtMSH2 mismatch-repair function

Highly conserved mismatch repair (MMR) systems promote genomic stability by correcting DNA replication errors, antagonizing homeologous recombination, and responding to various DNA lesions. Arabidopsis and other plants encode a suite of MMR protein orthologs, including MSH2, the constant component of various specialized eukaryotic mismatch recognition heterodimers. To study MMR roles in plant genomic stability, we used Arabidopsis AtMSH2::TDNA mutant SALK_002708 and AtMSH2 RNA-interference (RNAi) lines. AtMSH2::TDNA and RNAi lines show normal growth, development, and fertility. To analyze AtMSH2 effects on germ line DNA fidelity, we measured insertion-deletion mutation of dinucleotide-repeat sequences (microsatellite instability) at nine loci in 16 or more progeny of two to four different wild-type or AtMSH2-deficient plants. Scoring 992 total alleles revealed 23 (2.3%) unique and 51 (5.1%) total repeat length shifts ([+2], [-2], [+4], or [-4] bp). For the six longest repeat loci, the corresponding frequencies were 22/608 and 50/608. Two of four AtMSH2-RNAi plants showed similar microsatellite instability. In wild-type progeny, only one unique repeat length allele was found in 576 alleles tested. This endogenous microsatellite instability, shown for the first time in MMR-defective plants, is similar to that seen in MMR-defective yeast and mice, indicating that plants also use MMR to promote germ line fidelity. We used a frameshifted reporter transgene, (G)(7)GUS, to measure insertion-deletion reversion as blue-staining beta-glucuronidase-positive leaf spots. Reversion rates increased only 5-fold in AtMSH2::TDNA plants, considerably less than increases in MSH2-deficient yeast or mammalian cells for similar mononucleotide repeats. Thus, MMR-dependent error correction may be less stringent in differentiated leaf cells than in plant equivalents of germ line tissue.

Enzymatic repair of an expanded genetic information system

The excision repair machinery of a thermophilic bacterium has been shown to recognize and repair an expanded genetic base pair. Native Thermus aquaticus DNA polymerase will remove a mispaired natural base and replace it with a non-natural base to form an expanded base pair. In addition, DNA ligase will recognize a nick formed by polymerase between two non-natural base pairs and covalently attach the two strands, thus demonstrating complete repair of a bifurcated base-paired model duplex. These results add evidence to the idea that the cellular replication and repair machinery of an organism containing an expanded genetic alphabet could recognize and properly repair a site containing consecutive unnatural bases.

Expression of the DNA mismatch repair proteins (hMLH1 and hMSH2) in infiltrating pancreatic cancer and its relation to some phenotypic features

DNA mismatch repair system defects cause microsatellite instability (MSI) and form an alternative pathway in cancer development. Germline mutations of DNA mismatch repair genes account for hereditary nonpolyposis colorectal cancer, which has a different morphology and biology than sporadic cancers. MSI has also been found in sporadic neoplasms and some inflammatory conditions (chronic pancreatitis, ulcerative colitis). The purpose of the present study was to evaluate the expression of hMLH1 and hMLH2 proteins in infiltrating pancreatic cancer and to find out whether there is a relationship between some phenotypic manifestations and expression of MMR genes. We studied 30 cases of infiltrating pancreatic cancer and apart from hMLH1 and hMLH2 expression cytokeratin 7 and chromogranin were measured as markers of ductal and endocrine differentiation, respectively. All ductal pancreatic cancers expressed cytokeratin 7. In most cases the expression was strong, present in 50-100% of cells in moderately differentiated cancers and in 80-100% of cells in poorly differentiated cancers. Chromogranin expression was seen in 5 moderately differentiated cancers and in 6 poorly differentiated cancers (up to 20% of positive cells). In all cases DNA mismatch repair genes expression was present.

CONCLUSION

Ductal pancreatic carcinomas express hMLH1 and hMLH2 proteins irrespective of their differentiation. The expression of cytokeratin 7 is typical of ductal pancreatic carcinoma and its level is related to cancer differentiation. Some ductal pancreatic carcinomas irrespective of their differentiation show the expression of chromogranin, which is associated with the expression of hMSH2 gene.

Msh2 separation of function mutations confer defects in the initiation steps of mismatch repair

In eukaryotes the MSH2-MSH3 and MSH2-MSH6 heterodimers initiate mismatch repair (MMR) by recognizing and binding to DNA mismatches. The MLH1-PMS1 heterodimer then interacts with the MSH proteins at or near the mismatch site and is thought to act as a mediator to recruit downstream repair proteins. Here we analyzed five msh2 mutants that are functional in removing 3' non-homologous tails during double-strand break repair but are completely defective in MMR. Because non-homologous tail removal does not require MSH6, MLH1, or PMS1 functions, a characterization of the msh2 separation of function alleles should provide insights into early steps in MMR. Using the Taq MutS crystal structure as a model, three of the msh2 mutations, msh2-S561P, msh2-K564E, msh2-G566D, were found to map to a domain in MutS involved in stabilizing mismatch binding. Gel mobility shift and DNase I footprinting assays showed that two of these mutations conferred strong defects on MSH2-MSH6 mismatch binding. The other two mutations, msh2-S656P and msh2-R730W, mapped to the ATPase domain. DNase I footprinting, ATP hydrolysis, ATP binding, and MLH1-PMS1 interaction assays indicated that the msh2-S656P mutation caused defects in ATP-dependent dissociation of MSH2-MSH6 from mismatch DNA and in interactions between MSH2-MSH6 and MLH1-PMS1. In contrast, the msh2-R730W mutation disrupted MSH2-MSH6 ATPase activity but did not strongly affect ATP binding or interactions with MLH1-PMS1. These results support a model in which MMR can be dissected into discrete steps: stable mismatch binding and sensing, MLH1-PMS1 recruitment, and recycling of MMR components.

Mismatch repair in human nuclear extracts: effects of internal DNA-hairpin structures between mismatches and excision-initiation nicks on mismatch correction and mismatch-provoked excision

DNA mismatch repair (MMR) couples recognition of base mispairs by MSH2.MSH6 heterodimers to initiation, hundreds of nucleotides away, of nascent strand 3'-5' or 5'-3' excision through the mispair. Mismatch-recognition complexes have been hypothesized to move along DNA to excision-initiation signals, in eukaryotes, perhaps ends of nascent DNA, or to remain at mismatches and search through space for initiation signals. Subsequent MMR excision, whether simple processive digestion of the targeted strand or tracking of an excision complex, remains poorly understood. In human cell-free extracts, we analyzed correction of a mismatch in a 2.2-kilobase pair (kbp) circular plasmid containing a pre-existing excision-initiation nick for initiation, and measured MMR excision (in the absence of exogenous dNTPs) at specific locations. Excision specificities were approximately 100:1 for nicked versus continuous strands, 80:1 for mismatched versus homoduplex DNA, and 30:1 for shorter (0.3-kbp) versus longer (1.9-kbp) nick-mispair paths. To test models for recognition-excision coupling and excision progress, we inserted potential blockades, 20-bp hairpins, into nick-mispair paths, using a novel technique to first generate gapped plasmid. Continuous strand longer-path hairpins did not affect mismatch correction, but shorter-path hairpins reduced correction 4-fold, and both together eliminated it. Shorter-path hairpins had little effect on initiation of (3'-5') excision, measured 30-60 nucleotides 5' to the nick, but blocked subsequent progress of excision to the mismatch; longer-path hairpins blocked the (lower level) 5'-3' excision to the mismatch. Thus, (a) MMR excision protein(s) cannot move past DNA hairpins. Hairpins at both ends of substrate-derived 0.5-kbp DNA fragments did not prevent ATP-induced dissociation of mismatch-bound human MSH2.MSH6, so recognition complexes at mismatches might provoke excision at nicks beyond hairpins, or loosely sliding MSH2.MSH6 dimers might move to the nicks.

[Mismatch repair gene promoter methylation and expression in hydatidiform moles and the malignant transformation]

OBJECTIVE

In this study, we assayed promoter hypermethylation and protein expression of the mismatch repair gene (MMR) hMLH1 and hMSH2 in gestational trophoblastic diseases to understand the significance of MMR promoter methylation and expression in the pathogenesis and malignant transformation of hydatidiform mole.

METHODS

DNA was extracted from chorion of early pregnancies, partial hydatidiform moles, complete hydatidiform moles, and invasive moles were over digested by methylation sensitive endonuclease Hpa II. Then the promoters were amplificated by polymerase chain reaction. The protein was detected by immunohistochemistry.

RESULTS

In the normal placenta, neither hMLH1 nor hMSH2 promoter methylation was detected. Expression of hMLH1 and hMSH2 in cytotrophoblasts was strongly positive, and that was negative or weakly positive in syncytiotrophobasts. In all normal chorion, expression of hMLH1 and hMSH2 in cytotrophoblasts was strongly positive. In partial hydatidiform mole and complete hydatidiform mole, the methylation of hMLH1 and hMSH2 promoters was significantly higher than that of early placenta (P < 0.05), and the protein expression in cytotrophoblasts was significantly lower (P < 0.05). In the invasive mole, hMLH1 and hMSH2 promoter methylation were not significantly different as compared with the partial hydatidiform mole and complete hydatidiform mole (P > 0.05). Expression of hMLH1 in the invasive mole (54.5%, 6/11) was not significantly different as compared with the partial hydatidiform mole and complete hydatidiform mole (P > 0.05). But expression of hMSH2 in the invasive mole (36.4%, 4/11) was weaker than that in complete hydatidiform mole (P = 0.044). Promoter methylation and less expression of hMSH2 had correlations in complete hydatidiform mole or invasive mole.

CONCLUSIONS

Strong expressions of hMLH1 and hMSH2 in the cytotrophoblasts of normal placenta may keep the genome stability. Promoter methylation and down-regulation of hMLH1 and hMSH2 are probably involved in the pathogenesis of hydatidiform mole.

Analyzing tumor suppressor activities in the murine small intestine

We have used mice deficient in a series of genes with either known or potential tumor suppressive activity to determine the phenotype of loss of function of these genes in the mouse. We have tested a series of endpoints that derive from the hypothesis that loss of an apoptotic program would be predicted to fail to delete cells carrying DNA damage, that this would lead to increased clonogenic survival and thereby to an increased mutation burden and tumor predisposition. For p53 deficiency, we show that loss of the apoptotic program does not translate into an increase in spontaneous mutation rate. However, p53 deficiency can lead to increased clonogenic survival, although this is highly damage-type dependent. Furthermore, p53 deficiency weakly accelerates tumorigenesis associated with inactivation of the adenomatous polyposis coli gene, Apc. We have also analyzed mice mutant for the mismatch repair genes Msh2, Mlh1, and Pms2, describing circumstances in which all of these strains show defective apoptosis, increased clonogenic survival, and increased mutation rate. However, these effects are highly drug-type dependent and the pattern of dependency argues strongly that mutation rate increases as a direct result from loss of the apoptotic program. We have also identified a new role for p53 by intercrossing the p53 and Msh2 mutants, so demonstrating that heterozygosity for p53 accelerates microsatellite instability. Finally, we have analyzed mice mutant for Mbd4 and show that this gene functions in vivo as a tumor suppressor.

Alignment of BLAST high-scoring segment pairs based on the longest increasing subsequence algorithm

MOTIVATION

The popular BLAST algorithm is based on a local similarity search strategy, so its high-scoring segment pairs (HSPs) do not have global alignment information. When scientists use BLAST to search for a target protein or DNA sequence in a huge database like the human genome map, the existence of repeated fragments, homologues or pseudogenes in the genome often makes the BLAST result filled with redundant HSPs. Therefore, we need a computational strategy to alleviate this problem.

RESULTS

In the gene discovery group of Celera Genomics, I developed a two-step method, i.e. a BLAST step plus an LIS step, to align thousands of cDNA and protein sequences into the human genome map. The LIS step is based on a mature computational algorithm, Longest Increasing Subsequence (LIS) algorithm. The idea is to use the LIS algorithm to find the longest series of consecutive HSPs in the BLAST output. Such a BLAST+LIS strategy can be used as an independent alignment tool or as a complementary tool for other alignment programs like Sim4 and GenWise. It can also work as a general purpose BLAST result processor in all sorts of BLAST searches. Two examples from Celera were shown in this paper.

Germline mutations at microsatellite loci in homozygous and heterozygous mutants for mismatch repair and PCNA genes in Drosophila

Microsatellite instability (MSI) is a phenotype associated with the deficient repair of replication errors. Replication errors persist in defective mismatch repair (MMR) conditions, although alterations in components of the replication machinery, such as the proliferating cell nuclear antigen (PCNA) factor, could also increase the replication errors; therefore, MSI is expected in both situations. It also seems that heterozygous individuals for MMR genes have a high risk of cancer, as in the case of human non-polyposis colon carcinoma (HNPCC), characterised by MSI. Thus, here we investigate the effect of heterozygosity for a Msh2-null allele or for altered PCNA alleles, on the stability of microsatellite sequences. The study was carried out in Drosophila germ cells analysing the progeny of individual crosses. We found that one Msh2 disrupted allele is sufficient to produce MSI in germ cells. Although the MSI in Msh2(-/+) individuals was in the same order of magnitude as in Msh2(-/-) individuals, the former manifested a MSI that was four-fold lower. To a lesser extent, PCNA homozygous and heterozygous mutants also show MSI in the germline, which reveals the importance of DNA replication factors to maintain genomic stability in vivo. Furthermore, the high MSI found both in heterozygous Msh2 and PCNA mutants suggests a high degree of genomic instability in individuals bearing a mutant allele of these genes, which could have important implications in cancer susceptibility.

Allele-specific Holliday junction formation: a new mechanism of allelic discrimination for SNP scoring

We report here a new mechanism for allelic discrimination--allele-specific Holliday Junction formation. The Holliday Junction (HJ) is a unique DNA structure that can be formed in a sequence-nonspecific manner by routine PCR. To cause the PCR-based HJ formation to occur in an allele-specific manner, the PCR primers are manipulated such that an extra mismatch next to a SNP of interest is introduced between a target and a reference amplicon and a GC-clamp is added. Based on this new mechanism, novel SNP genotyping methods were developed, including a homogeneous fluorescence polarization (FP) competition assay that requires neither labeled primers/probes nor expensive enzymes/substrates. Using this novel genotyping technology, we were able to convert >95% of SNP sequences into genotyping assays that work well under a universal set of assay conditions and achieved 100% accuracy in clinical samples.

Rapid single-base mismatch detection in genotyping for phenylketonuria

Phenylketonuria (PKU) is a metabolic disorder that results from a deficiency of hepatic phenylalanine hydroxylase (PAH). Identification of the PKU genotype is useful for predicting clinical PKU phenotype. More than 400 mutations resulting in PAH deficiency have been reported worldwide. We used a genedetecting instrument to identify the nine prevalent Japanese mutations in the PAH gene among 31 PKU patients as a preliminary study. This instrument can automatically detect mutations through the use of allelespecific oligonucleotide (ASO) capture probes, and gave results comparable to those of sequencing studies. Each country has uniquely prevalent and specific mutations causing PKU, and less than 50 types of such mutations are generally present in each country. Early genotyping of PKU makes it possible to identify the phenotype and select the optimal therapy for the disease. For early genotyping, the instrumental method described here shortens the time required for genotyping based on mRNA and/or genomic DNA of PKU parents.