MLH1 and MSH2 Expression in Pterygia

PURPOSE

Pterygia have been reported to share some of the genetic defects seen in cancers, including microsatellite instability (MSI). We examined pterygia for the presence of proteins typically missing or defective in adenocarcinomas with MSI. We also performed microsatellite analysis on DNA from pterygia to test for instability in the size of the microsatellites, using markers conventionally used to characterize MSI in tumors (Bethesda convention markers).

METHODS

We examined 13 pterygia by immunohistochemistry for MLH1 and MSH2, 2 proteins involved in DNA mismatch repair. In addition, we amplified the pterygial DNA with primers specific for 5 Bethesda markers (BAT25, BAT26, D2S123, D5S346, and D17S250).

RESULTS

MLH1 staining was present at low levels in the basal cells of the cornea and migrating limbal cells of the pterygia. MSH2 staining was present in basal and in maturing epithelial cells of the cornea and migrating limbal cells of pterygia. We observed no reproducible examples of MSI or loss of heterozygosity (LOH).

CONCLUSIONS

We were unable to confirm the presence of MSI and LOH by using the markers we examined. MSH2 staining appeared to be normal in pterygia. MLH1 staining was present but in reduced amounts compared with that seen in the conjunctiva.

Novel insights into RNAi off-target effects using C. elegans paralogs

Background

In the few years since its discovery, RNAi has turned into a very powerful tool for the study of gene function by allowing post-transcriptional gene silencing. The RNAi mechanism, which is based on the introduction of a double-stranded RNA (dsRNA) trigger whose sequence is similar to that of the targeted messenger RNA (mRNA), is subject to off-target cross-reaction.

Results

We use a novel strategy based on phenotypic analysis of paralogs and predict that, in Caenorhabditis elegans, off-target effects occur when an mRNA sequence shares more than 95% identity over 40 nucleotides with the dsRNA. Interestingly, our results suggest that the minimum length necessary of a high-similarity stretch between a dsRNA and its target in order to observe an efficient RNAi effect varies from 30 to 50 nucleotides rather than 22 nucleotides, which is the length of siRNAs in C. elegans.

Conclusion

Our predictive methods would improve the design of dsRNA and ultimately the use of RNAi as a therapeutic tool upon experimental verification.

Impact of the loss of AtMSH2 on double-strand break-induced recombination between highly diverged homeologous sequences in Arabidopsis thaliana germinal tissues

We experimented a novel reporter system to analyze intrachromosomal recombination between homeologous sequences in Arabidopsis germ cell lineages. The recombination substrates used are the BAR and PAT genes which diverge by about 13% at the nucleotide level and confer resistance to the herbicide glufosinate. DNA double-strand breaks (DSBs) were generated by the I-Sce1 endonuclease to induce recombination. Loss of AtMSH2 induces a 3-fold increase of the frequency of recombination events indicating that AtMSH2 is involved in the anti-recombination activity that prevents exchange between highly diverged sequences in Arabidopsis. Molecular analysis of recombined alleles indicates that in wild type plants the single strand annealing (SSA) pathway can process more efficiently homologous 3' ends than 3' ends generated by resection of non-homologous overhangs. The loss of AtMSH2 disturbs this process, leading to a modification of the distribution of the BAR/PAT junctions and therefore showing that the MSH2 function is also involved in determining the structure of the recombined alleles. In addition, conversion tracts were observed in some alleles. They are shorter in MSH2 deficient plants than in wild-type, suggesting that a short-patch mismatch repair, not controlled by MSH2, could exist in Arabidopsis.

Chip-based microelectrodes for detection of single-nucleotide mismatch

Microelectrode arrays having eight 10-microm-diameter gold microelectrodes arranged on a gold-covered Si chip were designed and characterized. The chips prove useful for the detection of single-nucleotide mismatches in unlabeled and prehybridized DNA by electrochemical impedance spectroscopy.

Rapid SNP diagnostics using asymmetric isothermal amplification and a new mismatch-suppression technology

We developed a rapid single nucleotide polymorphism (SNP) detection system named smart amplification process version 2 (SMAP 2). Because DNA amplification only occurred with a perfect primer match, amplification alone was sufficient to identify the target allele. To achieve the requisite fidelity to support this claim, we used two new and complementary approaches to suppress exponential background DNA amplification that resulted from mispriming events. SMAP 2 is isothermal and achieved SNP detection from whole human blood in 30 min when performed with a new DNA polymerase that was cloned and isolated from Alicyclobacillus acidocaldarius (Aac pol). Furthermore, to assist the scientific community in configuring SMAP 2 assays, we developed software specific for SMAP 2 primer design. With these new tools, a high-precision and rapid DNA amplification technology becomes available to aid in pharmacogenomic research and molecular-diagnostics applications.

Enhanced electrochemical detection of DNA hybridization with carbon nanotube modified paste electrode

A novel electrochemical genesensor using twice hybridization enhancement of gold nanoparticles based on carbon paste modified electrode is described. The carbon nanotube modified carbon paste electrode (CNTPE) and mesoporous molecular sieve SBA-15 modified carbon paste electrode (MSCPE) were investigated. The assay relies on the immobilization of streptavidin-biotin labeled target oligonucleotides onto the electrode surface and its hybridization to the gold nanoparticle-labeled DNA probe. After twice hybridization enhanced connection of gold nanoparticles to the hybridized system, the differential pulse voltammetry (DPV) signal of total gold nanoparticles was monitored. It was found that the adsorption of oligonucleotide and hybridized DPV signal on CNTPE were both enhanced in comparison with that of pure carbon paste electrode (CPE). But this trend was reverse on MSCPE. The DPV detection of twice hybridized gold nanoparticles indicated that the sensitivity of the genesensor enhanced about one order of magnitude compared with one-layer hybridization. One-base mismatched DNA and complementary DNA could be distinguished clearly. However, no distinct advantage of MSCPE over CPE was found.

Molecular testing for microsatellite instability and its value in tumor characterization

Molecular analysis of tumor tissue has become a rapidly expanding field in medical research, exploiting the advantages of new technologies adapted to high-throughput examination of genetic alterations, gene and protein expression patterns. Only exceptionally, these approaches have found their way into routine clinical diagnosis and therapy. Microsatellite instability testing has been established as a very powerful tool to identify patients with hereditary nonpolyposis colorectal cancer, one of the most common familial cancer syndromes. In addition, there is emerging evidence that microsatellite instability analysis may become increasingly important for the clinician, having considerable impact on patients' prognosis as well as therapeutic decisions, at least in colorectal cancer patients. A better understanding of the microsatellite instability phenotype, its pathogenesis and implications for the course of the disease will pave the way for novel diagnostic and therapeutic strategies specifically tailored to microsatellite-unstable tumors. This review summarizes the current significance of molecular testing for microsatellite instability in several tumor entities and provides prospects of future developments.

Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates

Distance-based methods for phylogeny reconstruction are the fastest and easiest to use, and their popularity is accordingly high. They are also the only known methods that can cope with huge datasets of thousands of sequences. These methods rely on evolutionary distance estimation and are sensitive to errors in such estimations. In this study, a novel Bayesian method for estimation of evolutionary distances is developed. The proposed method enables the use of a sophisticated evolutionary model that better accounts for among-site rate variation (ASRV), thereby improving the accuracy of distance estimation. Rate variations are estimated within a Bayesian framework by extracting information from the entire dataset of sequences, unlike standard methods that can only use one pair of sequences at a time. We compare the accuracy of a cascade of distance estimation methods, starting from commonly used methods and moving towards the more sophisticated novel method. Simulation studies show significant improvements in the accuracy of distance estimation by the novel method over the commonly used ones. We demonstrate the effect of the improved accuracy on tree reconstruction using both real and simulated protein sequence alignments. An implementation of this method is available as part of the SEMPHY package.

Nanodiagnostics: fast colorimetric method for single nucleotide polymorphism/mutation detection

Advances in nanosciences are having a significant impact in many areas of research. The impact of new nanotechnologies has been particularly large in biodiagnostics, where a number of nanoparticle-based assays have been introduced for biomolecules detection. To date, applications of nanoparticles have largely focused on DNA-functionalised gold nanoparticles used as the target-specific probes. These gold nanoparticle-based systems can be used for the detection of specific sequences of DNA (pathogen detection, characterisation of mutation and/or single nucleotide polymorphisms) or RNA (without prior retro-transcription and amplification). Here a rapid and inexpensive nanoparticle-based method for single-base mismatch detection (single nucleotide polymorphism/mutation) in DNA samples is reported. Gold nanoparticles derivatised with thiol modified oligonucleotides complementary to DNA targets -- Au-nanoprobes -- are used to distinguish fully complementary from mismatched sequences, with a single-base mismatch. The authors have successfully applied this strategy to detect common mutations within the beta-globin gene.

Reactivity of Ferrocenylcarbodiimide with DNA Duplex Containing Single-mismatched Base Pairs

Ferrocenylcarbodiimide (1), which is known to react with a guanine (G) or thymine (T) base of single stranded DNA, was allowed to react with DNA duplex having a single mismatched base pair of G-T, T-T, or T-cytosine (C). Electrophoreograms of the reaction mixture showed that 1 could react with G or T base of the mismatched sites on the DNA duplex. However, 1 also reacted with the G base of the terminal site on the DNA duplex. This showed that 1 can react with an unpaired base or unstable base pair such as a terminal or mismatched base on the DNA duplex. Electrochemical mismatch detection could be achieved after hybridization of the ferrocenylated mismatched DNA duplex with a selected DNA probe-immobilized electrode. These results revealed that 1 has a potentiality of serving as a labeling reagent of mismatched bases on the DNA duplex, which is important in the search for heterozygous single nucleotide polymorphisms (SNPs).

Low worldwide genetic diversity in the basking shark (Cetorhinus maximus)

The basking shark (Cetorhinus maximus) is found in temperate waters throughout the world's oceans, and has been subjected to extensive exploitation in some regions. However, little is known about its current abundance and genetic status. Here, we investigate the diversity of the mitochondrial DNA control region among samples from the western North Atlantic, eastern North Atlantic, Mediterranean Sea, Indian Ocean and western Pacific. We find just six haplotypes defined by five variable sites, a comparatively low genetic diversity of pi=0.0013 and no significant differentiation between ocean basins. We provide evidence for a bottleneck event within the Holocene, estimate an effective population size (Ne) that is low for a globally distributed species, and discuss the implications.

Robust prediction of consensus secondary structures using averaged base pairing probability matrices

MOTIVATION

Recent transcriptomic studies have revealed the existence of a considerable number of non-protein-coding RNA transcripts in higher eukaryotic cells. To investigate the functional roles of these transcripts, it is of great interest to find conserved secondary structures from multiple alignments on a genomic scale. Since multiple alignments are often created using alignment programs that neglect the special conservation patterns of RNA secondary structures for computational efficiency, alignment failures can cause potential risks of overlooking conserved stem structures.

RESULTS

We investigated the dependence of the accuracy of secondary structure prediction on the quality of alignments. We compared three algorithms that maximize the expected accuracy of secondary structures as well as other frequently used algorithms. We found that one of our algorithms, called McCaskill-MEA, was more robust against alignment failures than others. The McCaskill-MEA method first computes the base pairing probability matrices for all the sequences in the alignment and then obtains the base pairing probability matrix of the alignment by averaging over these matrices. The consensus secondary structure is predicted from this matrix such that the expected accuracy of the prediction is maximized. We show that the McCaskill-MEA method performs better than other methods, particularly when the alignment quality is low and when the alignment consists of many sequences. Our model has a parameter that controls the sensitivity and specificity of predictions. We discussed the uses of that parameter for multi-step screening procedures to search for conserved secondary structures and for assigning confidence values to the predicted base pairs.

AVAILABILITY

The C++ source code that implements the McCaskill-MEA algorithm and the test dataset used in this paper are available at http://www.ncrna.org/papers/McCaskillMEA/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Voltammetric detection of single base-pair mismatches and quantification of label-free target ssDNA using a competitive binding assay

The application of electrochemical techniques for DNA detection is motivated by their potential to detect hybridisation events in a more rapid, simplistic and cost-effective manner compared to conventional optical assays. Here, we present an electrochemical DNA sensor for the specific and quantitative detection of single-stranded DNA (ssDNA). Probe oligonucleotides were immobilised onto thin gold film electrodes by a 5'-thiol-linker. Hybridisation was detected by means of the electroactive redox-marker methylene blue (MB) covalently attached to the 5'-end of the target ssDNA and voltammetric techniques. MB-labeled target ssDNA was recognised down to 30 pmol. By application of a competitive binding assay, non-labeled ssDNA was detected down to 3 pmol. In addition, the DNA-modified electrodes were capable of sensing single base-pair mismatches at different positions within the sequence of the hybridised double-stranded DNA (dsDNA).

Chemotherapeutic agents for colorectal cancer with a defective mismatch repair system: The state of the art

Mismatch repair (MMR) proteins are capable of recognizing and processing not only single base-pair mismatches and insertion-deletion loops that occur during DNA replication, but also adducts in DNA resulting from treatment with cancer chemotherapy agents. MMR deficiency leads to microsatellite instability (MSI) and results in resistance to antimetabolites, alkylating and platinating agents, DNA minor groove binders, and inhibitors of topoisomerases. Therefore, anticancer agents that can be recommended for use in MMR deficient colorectal cancers are those that exert their cytotoxicity regardless of the MMR status. These include some alkylating drugs, brostacillin, gemcytabine, photodynamic therapy, taxanes. An approach that is currently receiving much attention is the use of agents such as 5-azacytidine, an inhibitor of the DNA methyltransferases, in combination with inhibitors of histone de-acetylation, to restore the MMR function. A strong anti-proliferative efficacy with a relatively low direct cytotoxicity, obtainable with oloumicine and roscovitine (selective cyclin-dependent kinases inhibitors) can represent a new expedient for the therapeutic treatment of MMR deficient colorectal cancers. The question of how MMR defects modulate the response to chemotherapeutics deserves further investigation, to enable a more aware choice of cancer treatment.

Electrochemiluminescent hybridization chip with electric field aided mismatch discrimination

This paper describes a heterogeneous DNA-hybridization assay based on electrochemiluminescence (ECL) detection on gold electrodes. Short, 15-mer oligonucleotides were conjugated with a synthesized electrochemiluminescent label, bis(2,2'-bipyridine)-5-isothiocyanato-1,10-phenanthroline ruthenium(II) at the amino-modified 5'-end. Gold electrodes were derivatized with 15-mer oligonucleotide probes via 1-(3-(dimethylamino)propyl)-3-ethylcarbodiimide hydrochloride (EDC)/N-hydroxysuccinimide (NHS) cross-linking reaction and hybridized with Ru-labeled strands. Two types of self-assembled-monolayers have been utilized for the immobilization reaction, 3-mercaptopropanoic acid (3-MHA) and 16-mercaptohexadecanoic acid (16-MHA). Longer thiols were more stable at high electrode potentials needed for the ECL generation. The system was sensitive down to 1 fmol of labeled complementary strand, detected in 30 microL of buffer. Mismatch discrimination was achieved both passively by washing and actively by application of negative electrode potential on electrodes prior to detection, but active denaturing lead to better results. Two base-pair mismatches were discriminated at room temperature.

Identification of mismatch repair gene mutations in young patients with colorectal cancer and in patients with multiple tumours associated with hereditary non-polyposis colorectal cancer

BACKGROUND

Patients with early-onset colorectal cancer (CRC) or those with multiple tumours associated with hereditary non-polyposis colorectal cancer (HNPCC) raise suspicion of the presence of germline DNA mismatch repair (MMR) gene mutations.

AIM

To analyse the value of family history, microsatellite instability (MSI) analysis and MMR protein staining in the tumour to predict the presence of an MMR gene mutation in such patients.

METHODS

In 281 patients diagnosed with CRC before the age of 50 years or with CRC and at least one additional HNPCC-associated cancer, germline mutation analysis in MLH1, MSH2 and MSH6 was carried out with denaturing gradient gel electrophoresis and multiplex ligation-dependent probe amplification. MSI analysis with five consensus markers and MMR protein staining for MLH1, MSH2 and MSH6 were carried out in the tumours.

RESULTS

25 pathogenic mutations (8 in MLH1, 9 in MSH2 and 8 in MSH6) were found. MSI analysis missed three and immunohistochemistry (IHC) missed two mutation carriers. Sensitivities of family history, MSI analysis and IHC for the presence of a mutation were 76%, 82% and 88%, specificities were 64%, 70% and 84%, and positive predictive values were 19%, 23% and 38%, respectively. Multivariate analysis showed the highest odds ratio for IHC (38.3, 95% confidence interval 9.0 to 184). Prevalence of pathogenic germline MMR gene mutations in patients with CRC before the age of 50 years was 6% and in those with > or =2 HNPCC-associated tumours was 22%. In the second group, no mutation carriers were found among the 29 patients who were diagnosed with their first tumour after the age of 60 years.

CONCLUSION

Family history, MSI analysis and IHC are indicative parameters to select patients with CRC for MMR gene mutation analysis. The data show that IHC is the best single selection criterion.

Mismatch induced speciation in Salmonella: model and data

In bacteria, DNA sequence mismatches act as a barrier to recombination between distantly related organisms and can potentially promote the cohesion of species. We have performed computer simulations which show that the homology dependence of recombination can cause de novo speciation in a neutrally evolving population once a critical population size has been exceeded. Our model can explain the patterns of divergence and genetic exchange observed in the genus Salmonella, without invoking either natural selection or geographical population subdivision. If this model was validated, based on extensive sequence data, it would imply that the named subspecies of Salmonella enterica correspond to good biological species, making species boundaries objective. However, multilocus sequence typing data, analysed using several conventional tools, provide a misleading impression of relationships within S. enterica subspecies enterica and do not provide the resolution to establish whether new species are presently being formed.

Cyclooxygenase 2 expression in colorectal cancer with DNA mismatch repair deficiency

BACKGROUND

Cyclooxygenase 2 (COX-2) overexpression is a frequent but not universal event in colorectal cancer. It has been suggested that COX-2 protein expression is reduced in colorectal cancer with a defective mismatch repair (MMR) system, a phenomenon commonly associated with hereditary nonpolyposis colorectal cancer (HNPCC) but also present in up to 15% of sporadic tumors.

AIM

To assess COX-2 expression in a large series of fully characterized colorectal cancer patients with respect to the MMR system and to dissect the mechanisms responsible for altered COX-2 expression in this setting.

PATIENTS AND METHODS

MMR-deficient colorectal cancer were identified in a nationwide, prospective, multicenter study (EPICOLON project). Control MMR-proficient colorectal cancer patients were randomly selected. COX-2 expression was evaluated by immunohistochemistry. Personal and familial characteristics, as well as MSH2/MLH1 expression and germ line mutations, were evaluated.

RESULTS

One hundred fifty-three patients, 46 with MMR deficiency and 107 with MMR proficiency, were included in the analysis. Overall, tumor COX-2 overexpression was observed in 107 patients (70%). COX-2 overexpression was observed in 85 patients (79%) with a MMR-proficient system, but only in 22 patients (48%) with a MMR-deficient colorectal cancer (P < 0.001). The lack of COX-2 overexpression was independently associated with a MMR-deficient system (odds ratio, 3.89; 95% confidence interval, 1.78-8.51; P = 0.001) and a poor degree of differentiation (OR, 3.83; 95% CI, 1.30-11.31; P = 0.015). In the subset of patients with a MMR-deficient colorectal cancer, lack of COX-2 overexpression correlated with a poor degree of differentiation, no fulfillment of Amsterdam II criteria, absence of MSH2/MLH1 germ line mutations, presence of tumor MSH2 expression, and lack of tumor MLH1 expression. CpG island promoter hypermethylation of COX2 was observed in 6 of 18 (33%) tumors lacking COX-2 expression in comparison with 2 of 28 (7%) tumors expressing this protein (P = 0.04).

CONCLUSIONS

Up to half of MMR-deficient colorectal cancer do not show COX-2 overexpression, a fact observed almost exclusively in patients with sporadic forms. COX2 hypermethylation seems to be responsible for gene silencing in one third of them. These results suggest the potential utility of nonsteroidal anti-inflammatory drugs in HNPCC chemoprevention and may explain the lack of response of this approach in some sporadic tumors.

Pan-genome isolation of low abundance transcripts using SAGE tag

The SAGE (serial analysis of gene expression) method is sensitive at detecting the lower abundance transcripts. More than a third of human SAGE tags identified are novel representing the low abundance unknown transcripts. Using the GLGI method (generation of longer 3' EST from SAGE tag for gene identification), we converted 1009 low-copy, human X chromosome-specific SAGE tags into 10210 3' ESTs. We identified 3418 unique 3' ESTs, 46% of which are novel and originated from the lower abundance transcripts. However, nearly all 3' ESTs were mapped to various regions across the genome but not X chromosome. Detailed analysis indicates that those 3' ESTs were isolated by SAGE tag mis-priming to the non-parent transcripts. Replacing SAGE tags with non-transcribed genomic DNA tags resulted in poor amplification, indicating that the sequence similarity between different transcripts contributed to the amplification. Our study shows the prevalence of novel low abundance transcripts that can be isolated efficiently through SAGE tags mis-priming.

The mismatch repair gene hPMS2 is mutated in primary breast cancer

Mismatch repair (MMR) genes play a fundamental role in the correction of replication errors and their mutation leads to cancer development. In the present study we have analyzed the hPMS2 MMR gene for mutation using 20 primary breast cancers and seven breast tissues obtained from areas adjacent to breast cancer. For this purpose we have used cDNA sequence analysis and Western blotting using the specific antibody against the amino-terminal domain E-19. In primary breast cancers we found that the hPMS2 gene had 9 missense mutations [codons: 513 (by change of Ser x Asp) in 14 tumors, 520 (Ala x Val) in 8 tumors, 573 (by change of Thr x Ser in 19 tumors), 578 (by change of Arg x Leu in 9 tumors), 587 (by change of Ser x Asp in 7 tumors), 590 (by change of Ile x Leu in 12 tumors), 598 (by change of Gln x His in 5 tumors), 601 (by change of Ser x Leu in 13 tumors), 608 (by change of Ala x Ser in 9 tumors. Nine out of 20 breast cancers had a non-sense mutation in nucleotide 1862 by changing Adenine by Thymine (AAG x TAG), which corresponded with a change in codon 613 by a change of Lys by stop codon. This non-sense mutation is responsible for the premature truncation of the protein hPMS2, which is reflected in the Western blotting by two bands, one corresponding with the wild-type form (100 kDa) and a lower one (75 kDa) corresponding with the truncated form of the hPMS2 MMR protein. This truncated protein and the mutations in the hPMS2 gene were also detected in two samples of normal-appearing tissue adjacent to their corresponding cancerous lesion. Altogether the present report demonstrates that primary breast cancers harbor mutations in this MMR gene and that normal-appearing breast tissue adjacent to the primary lesion also harbors the same mutations before the neoplastic process is manifested.

Reagentless Ultrasensitive Specific DNA Array Detection Based on Responsive Polymeric Biochips

Self-assembled molecular structures immobilized on solid substrates and composed of fluorophore-tagged oligonucleotide probes and an optical polymeric transducer were investigated for the trace level detection of DNA target molecules. Rapid and efficient energy transfer between the polymeric transducer and fluorophores within the molecular aggregates leads to a massive intrinsic amplification of the fluorescence signal and to the label-free detection of as little as 300 DNA molecules, with the specificity required for the detection of single-nucleotide mismatches. This capacity for attomolar detection levels while the sensing structures are attached onto solid supports could lead to the development of biochip platforms for fast and simple PCR-free multitarget DNA detection.

Human DNA polymerase kappa forms nonproductive complexes with matched primer termini but not with mismatched primer termini

Human DNA polymerase kappa (pol kappa) is a member of the Y family of DNA polymerases that function in translesion synthesis. It synthesizes DNA with moderate fidelity and does not efficiently incorporate nucleotides opposite DNA lesions. Pol kappa has the unusual ability to efficiently extend from mismatched primer termini, and it extends readily from nucleotides inserted by other DNA polymerases opposite a variety of DNA lesions. All of this has suggested that pol kappa functions during the extension step of translesion synthesis. Here, we have carried out pre-steady-state kinetic studies of pol kappa using DNA with matched and mismatched primer termini. Interestingly, we find that mismatches present only a modest kinetic barrier to nucleotide incorporation by pol kappa. Moreover, and quite surprisingly, active-site titrations revealed that the concentration of active pol kappa is very low with matched DNA, and from DNA trapping experiments we determined that this was due to the formation of nonproductive protein.DNA complexes. In marked contrast, we found that the concentration of active pol kappa was six-fold greater with mismatched DNA than with matched DNA. Thus, pol kappa forms nonproductive complexes with matched but not with mismatched DNA. From these observations, we conclude that pol kappa has evolved to specifically function on DNA substrates with aberrant primer-terminal base pairs, such as the ones it would encounter during the extension step of translesion synthesis.

The natural history of a combined defect in MSH6 and MUTYH in a HNPCC family

In the inherited syndromes, MUTYH-associated polyposis (MAP) and hereditary nonpolyposis colorectal cancer (HNPCC), somatic mutations occur due to loss of the caretaker function that base-repair (BER) and mismatch repair (MMR) genes have, respectively. Recently, we identified a large branch from a MSH6 HNPCC family in which 19 family members are heterozygous or compound heterozygous for MUTYH germ line mutations. MSH6/MUTYH heterozygote mutation carriers display a predominant HNPCC molecular tumour phenotype, with microsatellite instability and underrepresentation of G>T transversions. A single unique patient is carrier of the MSH6 germline mutation and is compound heterozygote for MUTYH. Unexpectedly, this patient has an extremely mild clinical phenotype with sofar only few adenomas at age 56. Four out of five adenomas show characteristic G>T transversions in APC and/or KRAS2, as seen in MUTYH associated polyposis. No second hit of MSH6 is apparent in any of the adenomas, due to retained MSH6 nuclear expression and a lack of microsatellite instability. Although this concerns only one case, we argue that the chance to find an additional one is extremely small and currently a mouse model with this genotype combination is not available. Moreover, the patients brother who is also compound heterozygous for MUTYH but lacks the MSH6 germline mutation presented with a full blown polyposis coli. In conclusion, these data would support the notion that abrogation of both MSH6 DNA mismatch repair and base repair might be mutually exclusive in humans.

Complex formation with Rev1 enhances the proficiency of Saccharomyces cerevisiae DNA polymerase zeta for mismatch extension and for extension opposite from DNA lesions

Rev1, a Y family DNA polymerase (Pol) functions together with Polzeta, a B family Pol comprised of the Rev3 catalytic subunit and Rev7 accessory subunit, in promoting translesion DNA synthesis (TLS). Extensive genetic studies with Saccharomyces cerevisiae have indicated a requirement of both Polzeta and Rev1 for damage-induced mutagenesis, implicating their involvement in mutagenic TLS. Polzeta is specifically adapted to promote the extension step of lesion bypass, as it proficiently extends primer termini opposite DNA lesions, and it is also a proficient extender of mismatched primer termini on undamaged DNAs. Since TLS through UV-induced lesions and various other DNA lesions does not depend upon the DNA-synthetic activity of Rev1, Rev1 must contribute to Polzeta-dependent TLS in a nonenzymatic way. Here, we provide evidence for the physical association of Rev1 with Polzeta and show that this binding is mediated through the C terminus of Rev1 and the polymerase domain of Rev3. Importantly, a rev1 mutant that lacks the C-terminal 72 residues which inactivate interaction with Rev3 exhibits the same high degree of UV sensitivity and defectiveness in UV-induced mutagenesis as that conferred by the rev1Delta mutation. We propose that Rev1 binding to Polzeta is indispensable for the targeting of Polzeta to the replication fork stalled at a DNA lesion. In addition to this structural role, Rev1 binding enhances the proficiency of Polzeta for the extension of mismatched primer termini on undamaged DNAs and for the extension of primer termini opposite DNA lesions.