Hypermutability in carcinogenesis

Polyamine as a signaling molecule for controlling an adaptive mutation

In the absence of exogenous polyamines, the polyamine-deficient Escherichia coli mutant shows not only a characteristic dual-phase growth with abnormal growth, growth arrest, and normal growth after mutation, but also a higher expression of the SOS genes than the polyamine-proficient wild type. The interval of the growth arrest is inversely regulated in a polyamine concentration-dependent manner. These results indicate that the polyamines can act as a signal not only for provoking an adaptive mutation, but also for hastening generation of an adaptive mutation.

Somatic mutations and germline sequence variants in the expressed tyrosine kinase genes of patients with de novo acute myeloid leukemia

Activating mutations in tyrosine kinase (TK) genes (eg, FLT3 and KIT) are found in more than 30% of patients with de novo acute myeloid leukemia (AML); many groups have speculated that mutations in other TK genes may be present in the remaining 70%. We performed high-throughput resequencing of the kinase domains of 26 TK genes (11 receptor TK; 15 cytoplasmic TK) expressed in most AML patients using genomic DNA from the bone marrow (tumor) and matched skin biopsy samples ("germline") from 94 patients with de novo AML; sequence variants were validated in an additional 94 AML tumor samples (14.3 million base pairs of sequence were obtained and analyzed). We identified known somatic mutations in FLT3, KIT, and JAK2 TK genes at the expected frequencies and found 4 novel somatic mutations, JAK1(V623A), JAK1(T478S), DDR1(A803V), and NTRK1(S677N), once each in 4 respective patients of 188 tested. We also identified novel germline sequence changes encoding amino acid substitutions (ie, nonsynonymous changes) in 14 TK genes, including TYK2, which had the largest number of nonsynonymous sequence variants (11 total detected). Additional studies will be required to define the roles that these somatic and germline TK gene variants play in AML pathogenesis.

Silent mutations in the gene encoding the p53 protein are preferentially located in conserved amino acid positions and splicing enhancers

The last release of p53 somatic mutation database contains more than 20,000 of mutation among which 951 are silent (synonymous). This striking amount of silent mutations is much more than what would be expected if synonymous mutations were effectively neutral. The prevalent explanation to reconcile this vast amount of silent mutations with the neutral expectation is that they are just the subproduct of the hypermutability process that affect cancer cells. Some evidences have been presented in this direction, and the explanation has been taken as granted. Assuming that silent mutations are effectively neutral has major implication in the investigation of mutational processes that affect the gene encoding the p53 protein, since on the basis of this assumption they are considered the Null hypothesis, for instance for measuring and comparing among tissues the endogenous mutability. From this it follows that determining whether silent mutations in the p53 gene, and in all disease genes in general, are or not basically mutational noise, is of paramount importance. In this paper we readdress this topic by testing whether there is a relationship between the spatial distribution of silent mutations inside the p53 gene and functional significant features of the gene. For this purpose we divided the population of silent mutations in three groups: those that are found accompanied by other mutations (doublets and multiplest), those that were isolated as singlets, but the same mutation was also isolated as being part of a doublet (or multiplet) in another individual. And the last group is composed by those that were always found as singlets and never as being part of a doublet or a multiplet. This last group was expected to be enriched in functionally significant silent mutations. We found that all silent mutations, but particularly those of the last group, are preferentially located in conserved amino acid positions (i.e. functionally important amino acids) and also tend to be located inside suspected splicing enhancers. Noteworthy, this association remains even after eliminating the possible contribution of mutation hotspots. Besides, we present additional evidence in the direction that these putative splicing enhancers are real functional enhancers.

Dynamics of metastasis suppressor gene inactivation

For most cancer cell types, the acquisition of metastatic ability leads to clinically incurable disease. Twelve metastasis suppressor genes (MSGs) have been identified that reduce the metastatic propensity of cancer cells. If these genes are inactivated in both alleles, metastatic ability is promoted. Here, we develop a mathematical model of the dynamics of MSG inactivation and calculate the expected number of metastases formed by a tumor. We analyse the effects of increased mutation rates and different fitness values of cells with one or two inactivated alleles on the ability of a tumor to form metastases. We find that mutations that are negatively selected in the main tumor are unlikely to be responsible for the majority of metastases produced by a tumor. Most metastases-causing mutations will be present in all (or most) cells in the main tumor.

Molecular mechanisms of human carcinogenesis

Intensive research efforts during the last several decades have increased our understanding of carcinogenesis, and have identified a genetic basis for the multi-step process of cancer development. Tumors grow through a process of clonal expansion driven by mutation. Several forms of molecular alteration have been described in human cancers, and these can be generally classified as chromosomal abnormalities and nucleotide sequence abnormalities. Most cancer cells display a phenotype characterized by genomic hypermutability, suggesting that genomic instability may precede the acquisition of transforming mutations in critical target genes. Reduced to its essence, cancer is a disease of abnormal gene expression, and these genetic abnormalities contribute to cancer pathogenesis through inactivation of negative mediators of cell proliferation (including tumor suppressor genes) and activation of positive mediators of cell proliferation (including proto-oncogenes). In several human tumor systems, specific genetic alterations have been shown to correlate with well-defined histopathological stages of tumor development and progression. Although the significance of mutations to the etiological mechanisms of tumor development has been debated, a causal role for such genetic lesions is now commonly accepted for most human cancers. Thus, genetic lesions represent an integral part of the processes of neoplastic transformation, tumorigenesis, and tumor progression, and as such represent potentially valuable markers for cancer detection and staging.

Possible role of adaptive mutation in resistance to antiandrogen in prostate cancer cells

BACKGROUND

Some mutations of androgen receptor (AR) confer resistance to antiandrogen to prostate cancer (PC) cells. Previously we reported that LNCaP-cxD2 cells established from androgen-dependent LNCaP-FGC PC cells as an antiandrogen bicalutamide-resistant subline harbor W741C/L mutation in the AR gene. In this report, we examined one possible mechanism of the resistance.

METHODS

Change in the gene expression and the protein levels relevant to mutagenesis in LNCaP-FGC cells during bicalutamide-treatment was assessed. The AR sequence of bicalutamide-resistant LNCaP-cxD2 cells was compared with that of parental LNCaP-FGC cells.

RESULTS

The expression of DNA polymerases (Pol) switched from high-fidelity subset to error-prone subset, and DNA mismatch repair proteins (MMR) were down-regulated. The rate of multiple mutations in the AR gene was higher in LNCaP-cxD2 cells than LNCaP-FGC cells.

CONCLUSIONS

These results suggest the hypermutational state might occur in LNCaP-FGC cells during bicalutamide-treatment, which might create the W741C/L mutant AR leading to bicalutamide-resistance.

Clusters of mutations from transient hypermutability

Collections of mutants usually contain more mutants bearing multiple mutations than expected from the mutant frequency and a random distribution of mutations. This excess is seen in a variety of organisms and also after DNA synthesis in vitro. The excess is unlikely to originate in mutator mutants but rather from transient hypermutability resulting from a perturbation of one of the many transactions that maintain genetic fidelity. The multiple mutations are sometimes clustered and sometimes randomly distributed. We model some spectra as populations comprising a majority with a low mutation frequency and a minority with a high mutation frequency. In the case of mutants produced in vitro by a bacteriophage RB69 mutator DNA polymerase, mutants with two mutations are in approximately 10-fold excess and mutants with three mutations are in even greater excess. However, phenotypically undetectable mutations seen only as hitchhikers with detectable mutations are approximately 5-fold more frequent than mutants bearing detectable mutations, indicating that they arose in a subpopulation with a higher mutation frequency. Excess multiple mutations may contribute critically to carcinogenesis and to adaptive mutation, including the adaptations of pathogens as they move from host to host. In the case of the rapidly mutating riboviruses, the viral population appears to be composed of a majority with a mutation frequency substantially lower than the average and a minority with a huge mutational load.

Population genetics of tumor suppressor genes

Cancer emerges when a single cell receives multiple mutations. For example, the inactivation of both alleles of a tumor suppressor gene (TSG) can imply a net reproductive advantage of the cell and might lead to clonal expansion. In this paper, we calculate the probability as a function of time that a population of cells has generated at least one cell with two inactivated alleles of a TSG. Different kinetic laws hold for small and large populations. The inactivation of the first allele can either be neutral or lead to a selective advantage or disadvantage. The inactivation of the first and of the second allele can occur at equal or different rates. Our calculations provide insights into basic aspects of population genetics determining cancer initiation and progression.

Use of cytological specimens for p53 gene alteration detection in oral squamous cell carcinoma risk patients

AIMS

Recurrence and multifocal nature are two important characteristics of oral squamous cell carcinoma. Leukoplakia is the most frequent pre-cancerous oral lesion and, in most cases, it is not possible to predict malignant capacity. The objective of this study is to identify p53 alterations in cells taken from the oral cavity of at-risk patients.

MATERIALS AND METHODS

The following samples were collected from 34 patients with oral leukoplakia with and without previous carcinoma: oral rinse, a brush swabbed over the lesions and hair roots. Mutational analysis of the p53 gene was performed by single-strand conformation polymorphisms and confirmed by DNA sequencing.

RESULTS

We detected 11 mutations in p53 gene in oral cytological specimens. These alterations were observed only in brush cytology samples in patients without previous carcinoma, and in both samples (rinse and brush) in patients with previous carcinoma. Three of these patients had disease recurrence.

CONCLUSION

This non-invasive technique may be useful in the follow-up of at-risk patients, and introduces new possibilities to analyse molecular markers before malignant lesions are clinically apparent.

Analysis of p53 mutations in cells taken from paraffin-embedded tissue sections of ductal carcinoma in situ and atypical ductal hyperplasia of the breast

Mutations in the p53 tumor suppressor gene are frequent in breast tumors but the implication of p53 mutations in breast cancer development remains poorly understood. In this study, we applied laser capture microdissection (LCM) microscope to histologically review and sample cells from paraffin-embedded breast tissue sections obtained from six cases of ductal carcinoma in situ (DCIS) and ten cases of atypical ductal hyperplasia (ADH). p53 mutations were detected, using single stranded conformational polymorphism (SSCP) and sequencing, in cell samples of three cases with DCIS and five cases with ADH. p53 mutations are therefore present in DCIS and ADH of the breast, considered as pre-malignant precursors to breast cancer, and some of them may represent early events in breast cancer development.

Problems of somatic mutation and cancer

Somatic mutation plays a key role in transforming normal cells into cancerous cells. The analysis of cancer progression therefore requires the study of how point mutations and chromosomal mutations accumulate in cellular lineages. The spread of somatic mutations depends on the mutation rate, the number of cell divisions in the history of a cellular lineage, and the nature of competition between different cellular lineages. We consider how various aspects of tissue architecture and cellular competition affect the pace of mutation accumulation. We also discuss the rise and fall of somatic mutation rates during cancer progression.

Stationary phase mutagenesis: mechanisms that accelerate adaptation of microbial populations under environmental stress

Microorganisms are exposed to constantly changing environmental conditions. In a growth-restricting environment (e.g. during starvation), mutants arise that are able to take over the population by a process known as stationary phase mutation. Genetic adaptation of a microbial population under environmental stress involves mechanisms that lead to an elevated mutation rate. Under stressful conditions, DNA synthesis may become more erroneous because of the induction of error-prone DNA polymerases, resulting in a situation in which DNA repair systems are unable to cope with increasing amounts of DNA lesions. Transposition may also increase genetic variation. One may ask whether the rate of mutation under stressful conditions is elevated as a result of malfunctioning of systems responsible for accuracy or are there specific mechanisms that regulate the rate of mutations under stress. Evidence for the presence of mutagenic pathways that have probably been evolved to control the mutation rate in a cell will be discussed.

Moderate Hypermutability of a TransgeniclacZReporter Gene inMyc-Dependent Inflammation-Induced Plasma Cell Tumors in Mice

Mutator phenotypes, a common and largely unexplained attribute of human cancer, might be better understood in mouse tumors containing reporter genes for accurate mutation enumeration and analysis. Previous work on peritoneal plasmacytomas (PCTs) in mice suggested that PCTs have a mutator phenotype caused by Myc-deregulating chromosomal translocations and/or phagocyte-induced mutagenesis due to chronic inflammation. To investigate this hypothesis, we generated PCTs that harbored the transgenic shuttle vector, pUR288, with a lacZ reporter gene for the assessment of mutations in vivo. PCTs exhibited a 5.5 times higher mutant frequency in lacZ (40.3 +/- 5.1 x 10(-5)) than in normal B cells (7.36 +/- 0.77 x 10(-5)), demonstrating that the tumors exhibit the phenotype of increased mutability. Studies on lacZ mutant frequency in serially transplanted PCTs and phagocyte-induced lacZ mutations in B cells in vitro indicated that mutant levels in tumors are not determined by exogenous damage inflicted by inflammatory cells. In vitro studies with a newly developed transgenic model of inducible Myc expression (Tet-off/MYC) showed that deregulated Myc sensitizes B cells to chemically induced mutations, but does not cause, on its own, mutations in lacZ. These findings suggested that the hypermutability of PCT is governed mainly by intrinsic features of tumor cells, not by deregulated Myc or chronic inflammation.

Mutation-selection networks of cancer initiation: tumor suppressor genes and chromosomal instability

In this paper, we derive analytic solutions of stochastic mutation-selection networks that describe early events of cancer formation. A main assumption is that cancer is initiated in tissue compartments, where only a relatively small number of cells are at risk of mutating into cells that escape from homeostatic regulation. In this case, the evolutionary dynamics can be approximated by a low-dimensional stochastic process with a linear Kolmogorov forward equation that can be solved analytically. Most of the time, the cell population is homogeneous with respect to relevant mutations. Occasionally, such homogeneous states are connected by 'stochastic tunnels'. We give a precise analysis of the existence of tunnels and calculate the rate of tunneling. Finally, we calculate the conditions for chromosomal instability (CIN) to precede inactivation of the first tumor suppressor gene. In this case, CIN is an early event and a driving force of cancer progression. The techniques developed in this paper can be used to study arbitrarily complex mutation-selection networks of the somatic evolution of cancer.

Cancerous hyper-mutagenesis in p53 genes is possibly associated with transcriptional bypass of DNA lesions

The database of tumor-associated p53 base substitutions includes about 5% of tumors with two or more base substitutions. These multiplet base substitutions in one tumor are evidence for hyper-mutagenesis. Our retrospective analysis of this database indicates that most multiplets arise from a single transient hyper-mutagenic event in one cell that subsequently proliferated into a clonal tumor. The hyper-mutagenesis, 1.8 x 10(-4) substitutions per base pair, is detected as multiple mutations in p53 genes of tumors. It requires one strongly tumorigenic p53 substitution, usually missense, called the driver mutation. The occurrence frequencies of ancillary base substitutions, those that hitch-hike along with the driver mutation, are independent of their amino acid coding properties. In this respect, they act like neutral mutations. In support of this neutrality, we find that the frequency distribution of hitch-hiking CpG transitions along the p53 exons, their mutational spectrum, approximates the spontaneous pre-selection mutational spectrum of most human tissues and is correlated with the mutational spectrum of p53 pseudogenes in mammalian germ cells. The driver substitutions of multiplets predominantly originate along the transcribed strand while the ancillary substitutions tend to originate along the non-transcribed strand. This data is consistent with a model of time-dependent mutagenesis in non-dividing stem cells for generating multiple strand-asymmetric p53 mutations in tumors. By transcriptional bypass of DNA lesions with concomitant misincorporation, transcriptional mutagenesis generates a transient mutant p53 mRNA. The associated mutant p53 protein could allow the host cell a growth advantage, release from G1-arrest. Then, during subsequent DNA replication and misreading of the same lesion, the damaged base along the transcribed DNA strand would serve as the origin of the p53 base substitution that drives the hyper-mutagenic event leading to tumors with multiple p53 mutations.

Mutations in the TP53 gene in human malignant melanomas derived from sun-exposed skin and unexposed mucosal membranes

Mutations in the p53 tumour suppressor gene ( ) have been linked to several types of cancer. We therefore investigated whether such mutations occur in malignant melanomas and, if so, whether they are linked to ultraviolet (sun) light exposure. For the first time, mutations in mucosal membranes and adjacent tissues shielded from sunlight were compared with those in cutaneous melanomas from sun-exposed skin. Archival tissues were obtained from 35 patients with a primary melanoma taken from unexposed mucosal areas and from 34 patients with a primary melanoma located in chronically sun-exposed head and neck skin. was characterized by means of polymerase chain reaction amplification and single-strand conformation polymorphism assay followed by nucleotide sequencing. The results showed that 17.6% of the primary cutaneous and 28.6% of the primary mucosal melanomas had point mutations in. Among the cutaneous melanomas, one showed three mutations in exon 7, and one had two mutations in exon 5; the mutation was in the same allele in both cases. One mucosal melanoma had two mutations in exon 7, both in the same allele, and another had two mutations, one in exon 7 and one in intron 6, both in the same allele. C<--T mutations at dipyrimidine sites, considered fingerprints for ultraviolet light-induced mutations, were about equally distributed among patients with melanomas from chronically sun-exposed areas (six out of nine; 67%) and those with melanomas from unexposed mucosal areas and adjacent skin (eight out of 14; 57%). Our data, demonstrating the presence of such mutations even in melanomas from mucosal membranes, clearly suggest that factors other than, or additional to, ultraviolet radiation are operational in the induction of mutations in melanomas.

Detecting rare mutations associated with cancer risk

For more than a decade, investigators have been searching for a means of determining the risk of individuals developing cancer by detecting rare oncogenic mutations. The accumulation of mutations and the clonal evolvement of tumors provide opportunities for monitoring disease development and intervening prior to the presentation of clinical symptoms, or determining the risk of disease relapse during remission. A number of techniques, mostly polymerase chain reaction (PCR)-based, have been developed that enable the detection of rare oncogenic mutations within the range of 10(-2) to 10(-4) wild-type cells. Only a handful of procedures enable the detection of intragenic single base mutations at one mutant in 10-6 or better. These ultra-sensitive mutation detection techniques have produced some interesting results regarding single base mutation spectra and frequencies in p53, Harvey-ras, N-ras, and other reporter genes and DNA sequences in human tissues. Although there is evidence that some individuals may harbor cells or clones expressing genomic instability, the connection with the processes of carcinogenesis is still tenuous. There remains a need for rigorous epidemiological studies employing these ultra-sensitive mutation detection procedures. Since genomic instability is considered key to tumor development, the relevance of the detection of hypermutable clones in individuals is discussed in the context of cancer risk.

Multiple mutations are common at mouse Aprt in genotoxin-exposed mismatch repair deficient cells

Mismatch repair deficiency is known to contribute to elevated rates of mutations, particularly at mono- and dinucleotide repeat sequences. However, such repeats are often missing from the coding regions of endogenous genes. To determine the types of mutations that can occur within an endogenous gene lacking highly susceptible repeat sequences, we examined mutagenic events at the 2.3 kb mouse Aprt gene in kidney cell lines derived from mice deficient for the PMS2 and MLH1 mismatch repair proteins. The Aprt mutation rate was increased 33-fold and 3.6-20-fold for Mlh1 and Pms2 null cell lines, respectively, when compared with a wild-type kidney cell line. For the Pms2 null cells this increase resulted from both intragenic events, which were predominantly base-pairs substitutions, and loss of heterozygosity events. Almost all mutations in the Mlh1 null cells were due to base-pair substitutions. A:T-->G:C transitions (54% of small events) were predominant in the Pms2 null cells whereas G:C-->A:T transitions (36%) were the most common base-pair change in the Mlh1 null cells. Interestingly, 4-9% of the spontaneous mutant alleles in the mismatch repair deficient cells exhibited two well-separated base-pair substitution events. The percentage of mutant alleles with two and occasionally three base-pair substitutions increased when the Pms2 and Mlh1 null cells were treated with ultraviolet radiation (15-21%) and when the Mlh1 null cells were treated with hydrogen peroxide (35%). In most cases the distance separating the multiple base-pair substitutions on a given allele was in excess of 100 base-pairs, suggesting that the two mutational events were not linked directly to a single DNA lesion. The significance of these results is discussed with regards to the roles for the PMS2 and MLH1 proteins in preventing spontaneous and genotoxin-related mutations.

Msh2 deficiency increases the mutation frequency in all parts of the mouse colon

The Msh2 DNA mismatch repair gene is one of five genes implicated in the pathogenesis of hereditary nonpolyposis colorectal cancer (HNPCC). To address the possible mechanisms of the site-specific occurrence of HNPCC, the effect of Msh2 deficiency on mutations in different parts of the colon was investigated using the BC-1(lacI)/Msh2 double transgenic mouse. Compared to the Msh2(+/+) mice, Msh2(-/-) mice had an 8-9-fold increase of mutation frequency (MF) in the lacI gene from the cecum and the proximal and distal colon. The mutational spectra were also significantly different between Msh2(+/+) and Msh2(-/-) mice, with a significant increase in the frequency of -1 frameshifts and G:C-->A:T base substitutions in the repair-deficient mice. However, in spite of the site-specific predisposition of HNPCC in humans, we found no significant difference in the MF or mutation spectrum between the three parts of the colon in Msh2(+/+), Msh2(+/-), or Msh2(-/-) mice. In addition, 11 independent mutants harboring complex mutations within the lacI gene were recovered in the Msh2(-/-) mice. Interestingly, while the Msh2(+/-) mice displayed an overall MF similar to that observed in the wild-type mice, sequencing revealed a significantly different mutational spectrum between Msh2(+/+) and Msh2(+/-) mice, mainly characterized by an increase in -1 frameshifts. Due to the prevalence of frameshift mutations in HNPCC patients, this haploinsufficiency effect of the Msh2 gene in safeguarding genomic integrity may have important implications for human carrier status.

Role in tumorigenesis of silent mutations in the TP53 gene

Over 10,000 mutations in the TP53 suppressor gene have been recorded in the International Agency for Research on Cancer (IARC) tumor data base. About 4% of these mutations are silent. It is a question whether these mutations play a role in tumor development. In order to approach this question, we asked whether the reported silent mutations are randomly distributed throughout the TP53 gene. The p53 data base was searched exon by exon. From the frequency of codons with no silent mutations, the average number of silent mutations per codon for each exon was calculated using the Poisson distribution. The results indicate the distribution to be non-random. About one-third of all silent mutations occur in "hot-spots" and after subtraction of these hot-spots, the remaining silent mutations are randomly distributed. In addition, the percentage of silent mutations among the total in the silent mutation hot-spots is close to that expected for random mutation. We conclude that most of the silent mutations recorded in tumors play no role in tumor development and that the percentage of silent mutation is an indication of the amount of random mutation during tumorigenesis. Silent mutations occur to a significantly different extent in different tumor types. Tumors of the esophagus and colon have a low frequency of silent mutations, tumors of the prostate have a high frequency.

DNA polymerase zeta introduces multiple mutations when bypassing spontaneous DNA damage in Saccharomyces cerevisiae

Spontaneous DNA damage can be dealt with by multiple repair/bypass pathways that have overlapping specificities. We have used a frameshift reversion assay to examine spontaneous mutations that accumulate in yeast strains defective for the high-fidelity nucleotide excision repair or recombination pathways. In contrast to the simple frameshift mutations that occur in wild-type strains, the reversion events in mutant strains are often complex in nature, with the selected frameshift mutation being accompanied by one or more base substitutions. Genetic analyses demonstrate that the complex events are dependent on the Pol zeta translesion polymerase, thus implicating the DNA damage bypass activity of low-fidelity translesion polymerases in hypermutation phenomena.

Human lung cancer and p53: the interplay between mutagenesis and selection

It is an almost consensus opinion that the major carcinogenic risk of tobacco smoke is in its direct mutagenic action on DNA of cancer-related genes. The key data supposedly linking smoke-induced mutations to lung cancer were obtained from the adduct spectrum of the p53 tumor suppressor gene. Results of our analysis of p53 mutations compiled from the International Agency for Research on Cancer p53 database (April 1999 update) and from the literature point to a different causative link. Our new analytical tests focused on complementary base substitutions and showed that it is strand-specific repair of primary lesions and site-specific selection of the resultant mutations that determine the lung cancer-specific hot spots of G:C to T:A transversions along the p53 gene and also their increased abundance in lung tissues as compared with smoke-inaccessible tissues. However, on each of the two strands of p53 DNA, our tests revealed no significant difference between smokers and nonsmokers, either in the frequency of different types of mutations or in the frequency of their occurrence along the p53 gene. Moreover, in both smokers and nonsmokers, there was the same frequency of lung tumors with silent p53 mutations. Accordingly, we offer here a selection-based explanation of why lung cancers with nonsilent p53 mutations are more common in smokers than in nonsmokers. We conclude that physiological stresses (not necessarily genotoxic) aggravated by smoking are the leading risk factor in the p53-associated etiology of lung cancer.

The SOS response regulates adaptive mutation

Upon starvation some Escherichia coli cells undergo a transient, genome-wide hypermutation (called adaptive mutation) that is recombination-dependent and appears to be a response to a stressful environment. Adaptive mutation may reflect an inducible mechanism that generates genetic variability in times of stress. Previously, however, the regulatory components and signal transduction pathways controlling adaptive mutation were unknown. Here we show that adaptive mutation is regulated by the SOS response, a complex, graded response to DNA damage that includes induction of gene products blocking cell division and promoting mutation, recombination, and DNA repair. We find that SOS-induced levels of proteins other than RecA are needed for adaptive mutation. We report a requirement of RecF for efficient adaptive mutation and provide evidence that the role of RecF in mutation is to allow SOS induction. We also report the discovery of an SOS-controlled inhibitor of adaptive mutation, PsiB. These results indicate that adaptive mutation is a tightly regulated response, controlled both positively and negatively by the SOS system.

DNA repair and recombination factor Rad51 is over-expressed in human pancreatic adenocarcinoma

Molecular processes that could contribute to differences in chemo- and radioresistance include variations in DNA repair mechanisms. In mammalian cells, the product of the rad51 gene mediates DNA repair via homologous recombination. We describe that in contrast to conventional monolayer cell systems Rad51 protein accumulates to high-levels in three-dimensional cell culture models as well as in orthotopic xeno-transplants of human pancreatic cancer cells. Strikingly, over-expression of wild-type Rad51 was also found in 66% of human pancreatic adenocarcinoma tissue specimens. Functional analysis revealed that Rad51 over-expression enhances survival of cells after induction of DNA double strand breaks. These data suggest that perturbations of Rad51 expression contribute to the malignant phenotype of pancreatic cancer. Oncogene (2000).

Genetic pathways in colorectal and other cancers

Cells from cancers show aberrant behaviour such as unrestrained growth, invasion into adjacent tissue and metastasis. All these features of cancer cell behaviour can be explained in terms of genetic changes and the functional impact of these changes. In this review, colorectal cancer (CRC) is examined as a classical example of multistep carcinogenesis. First there is an overview which shows that cancers develop by a process of somatic evolution. This gives rise to preferred genetic pathways of tumorigenesis. The factors which may influence the development and ultimate choice of genetic pathways are then examined. Next, CRC is studied as a specific disease and the putative genetic pathways are described. The mutations that comprise these pathways and the possible functional sequelae of these are explored. The review concludes with a look at those avenues which may further elucidate the natural history of CRC and lead to improved therapy.

Multiple mutations in a shuttle vector modified by ultraviolet irradiation, (+/-)-7 beta,8 alpha-dihydroxy-9 alpha,10 alpha-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene, and aflatoxin B(1) have different properties than single mutations and may be generated during translesion synthesis

Shuttle vector-based systems are extensively employed to study the mutational properties of various mutagens in mammalian cells. Such vectors are designed for the detection of point mutations, that is small deletions and single base and tandem substitutions. However, mutant target genes carrying two or more point mutations, referred to as multiple mutations, can also be found in various proportions depending on the mutagen and the cells used. To evaluate the frequency and characteristics of multiple mutations, we used a system where the plasmid, pYZ289, was treated by ultraviolet irradiation, aflatoxin B(1) or (+/-)-7 beta,8 alpha-dihydroxy-9 alpha, 10 alpha-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene before transfection into mouse fibroblast cells. The kinds of mutations and the mutational spectra were different for single and multiple mutations. In addition, in at least 75% of the cases, mutations of multiples appeared to arise in the same strand. Furthermore, mutational spectra for multiple mutations were different for 5' and 3' members of multiple sets. These observations suggest that multiple mutations arise via a different mechanism than single mutations. Moreover, these findings suggest that multiples arise during translesion DNA synthesis and involve an error-prone polymerase able to introduce a base opposite misinstructive or noninstructional DNA lesions and subject to subsequent misincorporation errors.

Frameshift mutation, microsatellites and mismatch repair

The structure of eukaryotic DNA, with its repeated sequences, makes base addition and loss a major obstacle to the maintenance of genetic stability. As compared to the bacteria, much of the mismatch repair capacity of the eukaryotic cell must be devoted to the surveillance of frameshift changes. Any alteration in the activity of proteins which recognize frameshifts or which hold the DNA in place during replication is likely to result in genomic instability.

Novel somatic mutations in the VHL gene in Swedish archived sporadic renal cell carcinomas

Frequent loss-of-function somatic mutations of the VHL gene have been detected in sporadic renal cell carcinoma (RCC), indicating that inactivation of the VHL gene plays a critical role in RCC. In this study, we collected 35 archived Swedish sporadic RCCs identified from an epidemiological study on occupational exposure and kidney cancer to test how well stored pathological specimens could be retrieved and analyzed for VHL mutations. Thirty specimens were successfully analyzed with PCR-SSCP and sequencing. Aberrant SSCP bands were detected in 16 out of the 30 samples (53%). Sequencing analysis of the aberrant bands revealed seven deletions, one insertion, one base substitution on a splicing site, six missense mutations, one silent mutation and several base substitutions in the 5' non-coding region and intron 1. Most were novel somatic mutations that have not been reported in sporadic RCC. The mutations were found in three types of non-papillary RCC cases, i.e. 14 clear cells, one granular chromophilic and one sarcomatoid RCC. Interesting multiple mutations were found in three cases (5, 3, 2 mutations, respectively).

Loss of transcription factor IRF-1 affects tumor susceptibility in mice carrying the Ha-ras transgene or nullizygosity for p53

The transcription factor IRF-1 has been implicated in tumor suppression: IRF-1 suppresses cell transformation and mediates apoptosis in vitro. Here we show that the loss of IRF-1 alleles per se has no effect on spontaneous tumor development in the mouse but dramatically exacerbates previous tumor predispositions caused by the c-Ha-ras transgene or by nullizygosity for p53. Grossly altered tumor spectrum, as compared to p53-null mice, was also observed in mice lacking both IRF-1 and p53, and cells from these mice show significantly higher mutation rate. Our results suggest that IRF-1 is a new member of the tumor susceptibility genes.

Lineage selection and the evolution of multistage carcinogenesis

A wide array of proto-oncogenes and tumour suppressor genes are involved in the prevention of cancer. Each form of cancer requires mutations in a characteristic group of genes, but no single group controls all cancers. This lack of generality shows that the control of cancer is not an ancient, fixed property of cells. By contrast, it supports a dynamic evolutionary model, whereby genetic controls over unregulated cell growth are recruited independently through evolutionary time in different tissues within different taxa. The complexity of this genetic control can be predicted from a population genetic model of lineage selection driven by the detrimental fitness effects of cancer. Cancer occurs because the genetic control of cell growth is vulnerable to somatic mutations (or 'hits'), particularly in large, continuously dividing tissues. Thus, compared to small rodents, humans must have evolved more complex genetic controls over cell growth in at least some of their tissues because of their greater size and longevity; an expectation relevant to the application of mouse data to humans. Similarly, the 'two-hit' model so successfully applied to retinoblastoma, which originates in a small embryonic tissue, is unlikely to be generally applicable to other human cancers; instead, more complex scenarios are expected to dominate, with complexity depending upon a tissue's size and its pattern of proliferation.

Genetic pathways in colorectal and other cancers

Cells from cancers show aberrant behaviour such as unrestrained growth, invasion into adjacent tissue and metastasis. All these features of cancer cell behaviour can be explained in terms of genetic changes and the functional impact of these changes. In this review, colorectal cancer (CRC) is examined as a classical example of multistep carcinogenesis. First there is an overview which shows that cancers develop by a process of somatic evolution. This gives rise to preferred genetic pathways of tumorigenesis. The factors which may influence the development and ultimate choice of genetic pathways are then examined. Next, CRC is studied as a specific disease and the putative genetic pathways are described. The mutations that comprise these pathways and the possible functional sequelae of these are explored. The review concludes with a look at those avenues which may further elucidate the natural history of CRC and lead to improved therapy.

Strand asymmetry of CpG transitions as indicator of G1 phase-dependent origin of multiple tumorigenic p53 mutations in stem cells

In dividing cells, expression of mutations is DNA strand symmetric. Of all mutations originating de novo in nondividing cells, only those in the transcribed (noncoding) strand are immediately expressed in mRNA and protein. In contrast, any new mutation in the nontranscribed (coding) strand remains unexpressed until the cells enter S phase and begin proliferation. This previously unrecognized difference enables us to examine the cell cycle-dependent origin of multiple tumorigenic mutations in stem cells. The human p53 gene, which acts as a gatekeeper in the control of G1 to S phase transition, was chosen for the analysis. Of all multiple mutations contained in p53 databases, we have tested in detail CpG transitions. Three features of CpG sites dictate this choice: C --> T transitions at methylated mCpG are the direct product of mC deamination and are replication-independent; it is easy to identify the strand bearing a primary mC --> T event because C --> T on the transcribed strand appears as G --> A on the nontranscribed strand; and CpG transitions are the most frequent (as both singular and multiple occurrences) tumor-related p53 mutations. The origin of double nonsilent CpG transitions in nondividing cells predicts a significant excess of the heterostrand (C --> T, G --> A) doublets over the homostrand (C --> T, C --> T and G --> A, G --> A) doublets. For p53, we found such an excess. Based on this result, along with the results of three other tests reported here, we conclude that the majority of multiple p53 mutations from human tumors occurred in quiescent stem cells.