genetic alterations and dna repair in human carcinogenesis

Seminars in Cancer Biology 14 (2004) 441–448

Genetic alterations and DNA repair in human carcinogenesisKathleen Dixon∗, Elizabeth Kopras

Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA

Abstract

A causal association between genetic alterations and cancer is supported by extensive experimental and epidemiological data. Mutationalinactivation of tumor suppressor genes and activation of oncogenes are associated with the development of a wide range of cancers. Thelink between mutagenesis and carcinogenesis is particularly evident for cancers induced by chemical exposures, which, in some cases,lead to characteristic patterns of mutations. These “genotoxic,” direct-acting carcinogens form covalent adducts with DNA, which causemutations during DNA replication. The link between mutagenesis and carcinogenesis is also supported by the observation that DNA repairdefects are associated with an increased cancer risk. Normally, DNA repair mechanisms serve to suppress mutagenesis by correcting DNAdamage before it can lead to heritable mutations. It has been postulated that mutagenesis plays a role in both the initiation phase and theprogression phase of carcinogenesis, and that an essential step in the carcinogenic process is the development of a mutator state in whichthe normal cellular processes that suppress mutagenesis become compromised. Given the link between mutations and cancer, attemptshave been made to use the mutational profile of cancer cells as an indicator of the causative agent. While this may be a valid approach insome cases, it is complicated by the role of endogenous processes in promoting mutagenesis. In addition, many important carcinogenicagents may enhance mutagenesis indirectly through suppression of DNA repair functions or stimulation of inappropriate cell proliferation.Epigenetic phenomena may also suppress gene expression without causing overt changes in DNA sequence.© 2004 Elsevier Ltd. All rights reserved.

Keywords: DNA repair; Mutagenesis; Tumor suppressors; Oncogenes

1. Genetic alterations in cancer

The association between genetic alterations and humancancer was first observed decades ago[1]. Cytogenetic stud-ies revealed that specific chromosomal abnormalities werelinked to the development of certain cancers. For exam-ple, a chromosomal translocation (the Philadelphia chromo-some) was frequently found in white blood cells of leukemiapatients. In addition, tumor cells often exhibited extensivegenetic instability leading to chromosome aberrations, re-arrangements, and aneuploidy. However, it was not clearwhether this widespread genetic instability was a cause ora consequence of the cancer phenotype. An understand-ing of the role of genetic alterations in cancer developmentarose out of studies of oncogenic viruses and hereditarycancers. RNA tumor viruses were found to express certain“oncogenes” (e.g., c-ras and c-myc) that contributed to thetransforming activity of the viruses and that had homologouscounterparts (proto-oncogenes) in the human genome. Later,it was shown that RAS and MYC were over-expressed incancer cells, often due to genetic translocations that placed

∗ Corresponding author. Tel.:+1 513 558 1728; fax:+1 513 558 3509.E-mail address: [email protected] (K. Dixon).

the genes under the control of strong heterologous promo-tors. The study of human retinoblastoma led to the discov-ery of theRB tumor suppressor gene; loss of function ofthis gene through inheritance of one mutant allele and thesomatic loss of the other allele lead to the formation of reti-nal tumors in children. Another important tumor suppressorprotein, p53, was first identified as a target for the SV40 tu-mor virus, and was later found to be inactivated in a varietyof tumor cells, and also in Li-Fraumeni syndrome, which isassociated with a high cancer risk. Both point mutations anddeletions are found among inherited and somatic mutationsthat inactivateRB andTP53; in addition, loss of the secondallele in the inherited cancers can often occur though lossof part or all of one of two homologous chromosomes.

A large number of tumor suppressor genes and oncogeneshave now been identified and characterized through the anal-ysis of tumor cell DNA[1–4]. It has been postulated that theminimum constellation of mutations required for oncogenictransformation in humans includes inactivation ofTP53 andRB, activation ofRAS (or other members of that pathway),and constitutive expression ofhTERT [5–7]. These genescontrol cellular functions that prevent uncontrolled prolif-eration (Fig. 1). The most prevalent mutations in humancancers occur in the tumor suppressor genes,TP53 andRB

1044-579X/$ – see front matter © 2004 Elsevier Ltd. All rights reserved.doi:10.1016/j.semcancer.2004.06.007

442 K. Dixon, E. Kopras / Seminars in Cancer Biology 14 (2004) 441–448

Fig. 1. Genetic alterations in cancer. Cancer develops over time as aconsequence of successive mutation and expansion of mutant clones. Mu-tations that inactivate tumor suppressor genes, activate proto-oncogenes,and turn on telomerase stimulate cell proliferation and inhibit cell death,providing a growth advantage.

[5]. Both base substitution mutations and gene deletions inthese genes are found in a wide variety of cancer types[8].The Rb protein is a key regulator of the cell cycle, and lossof this function can lead to increased cell proliferation anda failure in terminal differentiation, i.e., an increase in the“birth rate” of cells[7]. The p53 protein is important in cel-lular responses to stress, controlling DNA repair, cell cyclecheckpoints, and apoptosis[9]. Perhaps, the most importantof these pathways for cancer development is apoptosis; lossof p53 function can lead to decreased apoptosis, i.e., a de-crease in the “death rate” of cells. Thus, loss of these two tu-mor suppressor genes leads to a net increase in cell numbersdue to an increased birth rate and a decreased death rate.

Cancer development can also be promoted through mu-tations that activate the expression of proto-oncogenes thatregulate cell proliferation[5]. These are genes for secretedgrowth factors (e.g., PDGF), cell surface tyrosine kinase re-ceptors (e.g., EGFR, HER), signal transduction G-proteins(e.g., RAS), and nuclear transcription factors (e.g., MYC)[10]. RAS mutations are found in about 20% of tumors, in-cluding colon, lung, breast, and bladder cancer. Activatingmutations are often missense mutations that decrease theGTPase activity of the protein and prolong RAS-dependent

signaling. TheMYC gene is often activated by DNA rear-rangements that place the proto-oncogene under the controlof a strong promoter, or gene amplification events that in-crease expression through an increase in gene copy number.The net effect of activation of these proto-oncogenes is thestimulation of cell proliferation, leading to the expansion ofthe transformed cell population and augmenting the effectsof loss of tumor suppressor function. A related set of genesthat operate in signal transduction are responsible for cer-tain inherited conditions characterized by the developmentof scattered benign lesions that occasionally become ma-lignant [3]. For example, the neurofibromatosis (NF1) geneproduct regulates the RAS pathway, and the familial ade-nomatous polyposis (APC) gene regulates the WNT path-way. Affected individuals inherit mutations on one allele,and mutation of the second allele appears to be necessaryfor development of the benign lesions; further progressionrequires additional genetic “hits”.

An additional requirement for cancer development is cell“immortalization.” Normal cells are able to undergo onlya finite number of cell divisions before they reach “crisis”and die. This phenomenon has recently been attributed to agradual shortening of the small repeat telomere sequencesat the ends of chromosomes that protect them from bothdegradation and end-to-end fusions. The absence of telom-eres leads to genetic instability and ultimately apoptotic celldeath. Tumor cells overcome this process by switching onthe gene (hTERT) telomerase, an enzyme that maintainstelomere length[6].

2. Mutation spectra

Extensive analysis of mutations in theTP53 gene hasrevealed that inactivating mutations are widely distributedthroughout the gene, but certain types of mutations are moreprevalent in some cancers than in others[8]. For example,in the case of sunlight-induced carcinoma, tandem doublemutations at adjacent pyrimidines are observed at high fre-quency[11,12]; such mutations are rarely observed in othercancers. This observation is consistent with the fact that theUV portion of the sun’s spectrum dimerizes adjacent pyrim-idines in skin, and such lesions have been shown to prefer-entially lead to tandem double mutations in in vitro mutage-nesis assay systems[13,14]. Another example is the analy-sis of TP53 mutations in primary liver cancer derived frompatients exposed to aflatoxins, carcinogenic metabolites ofcertain spoilage molds[15]. In this case, a high frequency ofG:C-to-T:A mutations at the third base in codon 249 wereobserved. A similar pattern of aflatoxin-induced mutationswas observed in mutagenesis test systems[16], and this cor-relation was used to strengthen the causal link between ex-posure to aflatoxins and liver carcinogenesis in epidemiolog-ical studies[15]. An extensive database of tumor-associatedTP53 mutations has been compiled (www.iarc.fr/p53) [17]and certain additional associations between environmental

http://www.iarc.fr/p53

K. Dixon, E. Kopras / Seminars in Cancer Biology 14 (2004) 441–448 443

Fig. 2. TP53 mutations in lung cancer. Diagram from the IARC TP53 mutation database (R8, June 2003)[17]. Analysis of mutations in TP53 from avariety of lung tumors reveals characteristic hotspots for mutagenesis.

exposures and mutational spectra have emerged. An exam-ple of one such association is shown inFig. 2; there ap-pears to be an association between G:C-to-T:A mutationsat codons 157, 158, 245, 248, 249, and 273 inTP53 andcigarette smoking-associated lung cancer[18]. While theseassociations cannot confirm the link between a particular ex-posure and cancer development in a single individual, theyare suggestive of a link on a population basis.

In an attempt to determine whether general rules for themutagenic specificity of carcinogens could be derived fromthe analysis of mutational patterns (mutation spectra) of in-dividual carcinogens, several different mutation assay sys-tems have been used[19]. One such system, the pZ189shuttle vector system, has been used to analyze the speci-ficity of almost 40 different carcinogens[20]. Cluster analy-sis of these mutation spectra revealed patterns of mutationalspecificity that roughly corresponded to the known chemi-cal specificity of the agents. For example, chemicals that areknown to form DNA adducts preferentially on G residuesformed mutations preferentially at G:C base pairs, and thoseknown to form DNA adducts preferentially on A residuesformed mutations preferentially at A:T base pairs. In caseswhere whole classes of mutagenic agents form similar mu-tation spectra, back extrapolation from the characteristics ofmutations in tumors to the identity of the causative agent isnot possible. However, in cases where the mutational pat-tern is more unique (e.g., UV and aflatoxins), such back ex-trapolation can provide support with regard to questions ofcancer causation.

Additional mutation analysis systems have been estab-lished that allow determination of mutational specificity inexperimental animals[21]. In some of these systems, it ispossible to examine target organ specificity as well as muta-

tional patterns. Of these, the most widely used mutagenesisreporter genes are the endogenousAPRT [22,23]andHPRT[24] genes, and theEscherichia coli lacI or bacteriophagelambdacII transgenes[25]. The X-chromosomalHPRT genehas been used as a mutagenesis target for somatic mutationsin peripheral blood lymphocytes of both humans and ani-mals. Not only is this a useful reporter gene for point muta-tions, but it also reveals the activation of pathways normallyinvolved in gene rearrangements that can trigger the genera-tion of deletion mutations. The heterozygousAPRT± mousehas been particularly useful for understanding events thatlead to loss of heterozygosity (LOH), a common mechanismfor loss of the second allele in many inherited cancers. TheBig BlueTM mouse system[25] carries an integrated bac-teriophage lambda-based vector,�LIZ, which contains theE. coli lacI and lacZα genes; either thelacI or the lambdacII genes can be assayed for mutations in DNA recoveredfrom mouse tissues. This system has been used widely fortissue-specific analysis of mutagenesis[26]. Although eachof these systems has unique properties, generally they revealsimilar patterns of mutational specificity of environmentalcarcinogens.

3. Mutation avoidance: DNA repair andcheckpoint pathways

Cells have elaborate mechanisms for safeguarding the in-formational integrity of the genome and suppressing muta-tions. Mutation avoidance mechanisms include: (1) multiplechecks and balances within the DNA replication complexthat insure high fidelity DNA replication (<1 error in 106

nucleotides incorporated[27]); (2) pathways that suppress


Fig. 3. DNA damage responses. Cells respond to DNA damage by acti-vating a variety of DNA damage response pathways. If the DNA damageis excessive, cells die through induction of apoptosis. Alternatively, cellcycle checkpoints are induced that delay cell cycle progression to allowtime for DNA repair to occur. Specific DNA repair pathways recognizeand repair specific types of DNA damage. In the absence of DNA repair,the DNA damage results in mutations.

oxidative stress, which can result from endogenousmetabolic processes and lead to oxidative DNA damage[28]; (3) pathways that regulate cell cycle progression to in-sure an orderly duplication and segregation of chromosomes[29]; and (4) DNA repair pathways that correct all types of

Table 1Hereditary cancer syndromes with defects in DNA repair and checkpoint pathways

Pathway Genes Syndrome Cancer type

Mismatch repair MSH1, MSH2, MLH1,MSH6, PMS1, PMS2,

HNPCC Colon cancer

Nucleotide excision repair XPA–XPG Xeroderma pigmentosum (XP) Skin cancerReplication bypass XPV XP variant Skin cancerReplication fork integrity;

double-strand break repairNBS1 Nijmegen breakage syndrome Lymphoma

MRE11 A-T-like disorder Lymphoma/leukemiaWRN Werners syndrome VariousBLM/RECQL3 Blooms syndrome Leukemia, carcinomasBRCA1, BRCA2 Familial breast cancer Breast/ovarian cancer

DNA crosslink repair FANCA-FANCG Fanconi anemia LeukemiaDNA damage signaling; cell

cycle checkpointsATM Ataxia telangiectasia (A–T) Lymphoma/leukemia

TP53 Li-Fraumeni syndrome VariousRB1 Retinoblastoma Retinoblastoma

DNA damage caused by endogenous processes or exoge-nous agents (Fig. 3) [30–32]. More than 130 genes havebeen identified that contribute to DNA repair. The impor-tance of these mechanisms in cancer prevention is evidentfrom the increased cancer risk associated with disruption ofthese pathways (Table 1) [33]. This is particularly evidentfrom the study of a wide variety of familial cancers. One ofthe first widely studied hereditary diseases associated withincreased cancer risk was xeroderma pigmentosum[34,35].This defect in nucleotide excision repair leads to a dramaticincrease in the risk of sunlight-induced skin cancer. Indi-viduals with this condition are unable to excise and repairUV photoproducts in skin DNA, so that mutagenesis andcarcinogenesis are increased.

Nucleotide excision repair is important for the removal ofa wide variety of premutagenic DNA lesions in addition toUV photoproducts, including most bulky DNA adducts. Inhumans, the process of nucleotide excision repair requiresmore than 30 proteins[35]. These proteins are involved inDNA damage recognition, single-strand incision on eitherside of the lesion, excision of the single-stranded regioncontaining the lesion, DNA repair synthesis, and ligation.XPA–XPG are required for “global genome repair” (GGR),which serves to repair lesions throughout the genome.“Transcription-coupled repair” (TCR), which occurs mainlyin transcribed regions of the genome, requires the Cock-ayne syndrome gene products (CS-A and CS-B), as well asthe XP proteins, and is important in cell survival. Increasedcancer risk is associated primarily with defects in theXPgenes and not theCS genes.

The high fidelity of DNA replication is normally main-tained by the accuracy of DNA polymerase�; compromisingthe DNA polymerase� proofreading function can cause anincrease in mutation rate, and can lead to an increased can-cer risk in transgenic mice[36]. Furthermore, an increasein the expression of the less accurate DNA polymerase�,which normally functions in DNA repair, can also increasemutagenesis and is associated with cancer[37]. Certain less


accurate “bypass” polymerases can also cause mutations thatcontribute to carcinogenesis. In the cancer-prone human ge-netic disorder, xeroderma pigmentosum variant (XP-V), thefunction of DNA polymeraseη, which can accurately by-pass UV-induced TT dimers, is replaced by less accurateDNA polymerases, leading to higher UV-induced mutationrates and a higher risk of sunlight-induced cancer[38,39].

The importance of the mismatch repair pathway in the pre-vention of mutagenesis and carcinogenesis is illustrated bythe large increase in cancer risk in individuals with mismatchrepair defects. Defects in mismatch repair genes are associ-ated with increased cancer risk in hereditary non-polyposiscolon cancer (HNPCC)[40]. The mismatch repair system isresponsible for removal of base mismatches caused by basedeamination, oxidation, methylation, and DNA replicationerrors. The mismatch is recognized, and one of the two DNAstrands is selectively excised, which is followed by repairsynthesis and ligation of the resulting single-stranded DNAgap. Mutation of mismatch repair genes is associated withmicrosatellite instability and an increased rate of somaticmutations.

A number of genes associated with increased cancer riskare important for DNA damage signaling, cell cycle check-points, and DNA double-strand break (DSB) repair (Table 1)[30]. The conversion of premutagenic DNA lesions (e.g., UVphotoproducts, DNA adducts, etc.) to heritable mutationsoften requires active DNA replication and/or mitosis. Repli-cation of damaged templates can result in replication errorsor replication fork blockage. When progression of replica-tion forks is blocked by DNA damage, a number of recov-ery mechanisms are induced, some of which are thought toinvolve RecQ-like helicases, such as BLM[41] and WRN[42]. Blocked replication forks can also result in the induc-tion of DSBs, and the MRN complex (MRE11, RAD50, andNBS) participates in their repair[43]. BRCA1 and BRCA2are also thought to participate in DSB repair[44]. TheFANCgenes appear to be required for repair of DNA crosslinks[45]. Human cells have multiple regulatory pathways (calledcell cycle checkpoints) that are activated by DNA damageand that arrest cell cycle progression to allow time for DNArepair to occur[46]. For example, the protein kinase encodedby the ATM gene, which is mutated in the human geneticdisorder ataxia telangiectasia (A–T), has an important reg-ulatory role in DNA damage response[47]. This kinase isactivated in response to many types of DNA damage, and itin turn activates other proteins responsible for cell cycle reg-ulation and DNA repair. Individuals with A–T are sensitiveto certain DNA-damaging agents and exhibit a dramaticallyincreased cancer risk. The ATM kinase phosphorylates anumber of proteins required for cell cycle checkpoints (e.g.,p53) and DSB repair (e.g., NBS1). Loss of these functionsresults in genomic instability and increased cancer risk.

Given the importance of DNA repair pathways in cancerprevention, it is reasonable to speculate that disruption ofthese pathways by exogenous agents could contribute to car-cinogenesis as well. Such an agent would be expected to act

as a co-carcinogen, and enhance the mutagenic and carcino-genic activity of genotoxic carcinogens. A possible exampleof this type of co-carcinogen is arsenic[48]. Epidemiologi-cal studies show that arsenic exposure is strongly associatedwith the development of skin lesions, including skin cancers[49,50]. Elevated risk of other malignancies, such as blad-der, lung, kidney, and liver carcinomas, is also associatedwith arsenic exposure. Tests of the mutagenic activity of ar-senic in a variety of assay systems have generally been neg-ative (with a few exceptions)[51]. However, in cell culturesystems, arsenic has been shown to enhance the mutagenicactivity of other carcinogenic agents. This enhancement ofmutagenesis was shown to be associated with a suppressionof DNA repair [48]. Recently, arsenic was shown to act asa co-carcinogen with UV radiation in the induction of skintumors in the hairless mouse[52]. These results suggest thatthe carcinogenic activity of arsenic may be due in part toits ability to suppress DNA repair pathways. Certainly, it ispossible that other environmental agents may increase can-cer risk by similar mechanisms.

4. Mutators, cell proliferation, and cancerdevelopment – how many mutations?

Most solid tumors that have been studied cytogeneticallyappear to be genetically unstable; aneuploidy and chromo-somal rearrangements are common features of tumor cells.It has been estimated that some tumor cells may have thou-sands of mutations. However, it is not clear whether ge-netic instability is a prerequisite for cancer development orwhether it is a consequence of the cancer phenotype. Cer-tainly, as discussed above, defects in cell cycle checkpointsand DNA repair pathways that increase genetic instabilityalso increase cancer risk. Is induction of such a “mutator”phenotype an essential step in the carcinogenic process? Thearguments on both sides of this question[53] depend on as-sumptions concerning the number of mutations required forcancer development and the rate of cell division. The argu-ment in favor of this hypothesis[54] assumes that at leastfive “hits” (mutations) are required for cancer development.Given a normal somatic mutation rate of about 10−6 per celldoubling, the probability of the five independent hits occur-ring in a single cell is 10−30 per cell doubling. Even con-sidering that there are perhaps 1014 cells in the body andperhaps 50 cell divisions during the average life span, thisleads to a calculated cancer risk of 10−15. Since cancer ismuch more prevalent than that, this suggests that an essen-tial step in cancer development is an increase in mutationfrequency. This increase could be due to an inhibition of anyof the pathways that normally serve to maintain genomicstability. Whether disruption of normal mutation-avoidancepathways (e.g., DNA repair, DNA damage signaling path-ways, etc.) is also responsible for such genomic instabilityremains to be demonstrated. Although it is clear that an in-crease in mutagenesis can promote cancer development, it


has been argued that, at least in some highly proliferativetissues, induction of a mutator phenotype would not be aprerequisite for cancer development[3,7]; in these cases,enough cell divisions could occur within a stem cell popu-lation to allow for accumulation of mutations that providea selective advantage and clonal expansion[55]. Thus, thecounter argument invokes proliferation and selection of mu-tant cells. If the first “hit” provides a growth advantage tothe cell, this cell will proliferate, increasing the probabilityof a second hit within the expanded population. Either ar-gument is consistent with the observed increase in cancerincidence with age – a longer time and more cell divisionsincrease the probability of generating the mutator state orallowing for rounds of mutagenesis and clonal expansion.

It has been postulated that stimulation of cell prolifera-tion by tumor promoters, natural hormones, or as a resultof cell injury can enhance the mutagenic effects of endoge-nous or exogenous genotoxic agents[56,57]. A wide va-riety of non-mutagenic agents that stimulate cell prolifera-tion can increase cancer risk, perhaps through the enhance-ment of mutagenesis. The link between cell proliferationand mutagenesis has been demonstrated in mouse modelsystems. For example, a classical tumor promoter, phorbol12-myristate 13-acetate (TPA), increased the frequency ofbenzo[a]pyrene-induced mutations in the non-selectedlacIgene in the Big BlueTM mouse by promoting cell division inthe damaged cell population[58]. Likewise, the mutagenic-ity of N-ethyl-N-nitrosourea was dramatically enhanced inthe liver by partial hepatectomy, which stimulates cell pro-liferation [59]. It is possible that cell turnover caused bychronic infections, proliferation of target tissues induced byhormones, such as estrogen, or hyperplasia due to exposureto environmental agents, such as arsenic, may all enhancemutagenesis. In addition, such agents likely stimulate ex-pansion of mutant cell populations that may have a selectiveadvantage. Both these effects likely contribute to the link be-tween stimulation of cell proliferation and increased cancerrisk.

5. Epigenetic mechanisms of geneactivation and silencing

A discussion of genetic alterations in human cancer wouldbe incomplete without addressing the role of epigenetic phe-nomena in regulation of gene expression. While activationof proto-oncogenes and inactivation of tumor suppressorgenes by mutations (base substitutions, deletions, DNA rear-rangements, etc.) are certainly well documented, alterationsin expression of cancer genes can also occur by epigeneticmechanisms[4,60,61] [62]. The most well-understood epi-genetic mechanisms involve DNA methylation and histoneacetylation, methylation, and phosphorylation. Demethyla-tion of promoter regions at the CpG sequences can lead toover-expression of proto-oncogenes, and silencing of geneexpression can occur as a result of hypermethylation, some-

times leading to chromosome condensation. There appearsto be a relationship between DNA methylation and histonemodifications; patterns of histone deactylation and histonemethylation are associated with DNA methylation and genesilencing. Interestingly, these epigenetic changes in chro-matin can also alter the sensitivity of DNA sequences tomutation, thus rendering genes more susceptible to toxic in-sult. The relationship of chromatic structure to gene expres-sion, DNA repair, and mutagenesis is an important area forfurther study in carcinogenesis.

6. Concluding remarks

Given the importance of preserving genomic stability incancer prevention and the critical role that DNA damagesignaling and repair pathways play in mutation avoidance, itmay be important to ask whether these pathways may offera potential site for intervention in the carcinogenic process.Many of the damage response pathways have only recentlybeen identified, and aspects of these pathways remain to beelucidated. Although it is clear that protein kinases such asATM are important in DNA damage sensing and activationof downstream effectors, it is not well understood how thevarious responses (i.e., cell cycle checkpoints, replicationfork maintenance, DNA repair, etc.) are activated, and howthese are coordinated to minimize mutagenesis. Indeed, insome cases, mutagenesis may be the lesser of the two evilswhen the alternative is wholesale cell death brought aboutby excessive DNA damage. In any case, it would seem rea-sonable to postulate that by somehow enhancing the muta-tion avoidance pathways, it might be possible to mitigatethe carcinogenic effects of environmental agents. Perhaps,opportunities for intervention will be suggested as furtherresearch reveals the details of these elaborate cellular DNAdamage response pathways.

Acknowledgements

The helpful suggestions of Joseph R. Testa is grate-fully acknowledged. This work was supported by grantsR01-NS34782, P42-ES04908, and P30-ES06096 from theNational Institutes of Health.

References

[1] Balmain A. Cancer genetics: from Boveri and Mendel to microarrays.Nat Rev Cancer 2001;1:77–82.

[2] Balmain A, Gray J, Ponder B. The genetics and genomics of cancer.Nat Genet 2003;33(Suppl):238–44.

[3] Knudson AG. Cancer genetics. Am J Med Genet 2002;111:96–102.[4] Klein G. Introduction: genetic and epigenetic contributions to tumor

evolution. Semin Cancer Biol 2002;12:327–30.[5] Hahn WC, Weinberg RA. Rules for making human tumor cells. N

Engl J Med 2002;347:1593–603.


[6] Cech TR. Beginning to understand the end of the chromosome. Cell2004;116:273–9.

[7] Knudson AG. Two genetic hits (more or less) to cancer. Nat RevCancer 2001;1:157–62.

[8] Greenblatt MS, Bennett WP, Hollstein M, Harris CC. Mutations in thep53 tumor suppressor gene: clues to cancer etiology and molecularpathogenesis. Cancer Res 1994;54:4855–78.

[9] Fridman JS, Lowe SW. Control of apoptosis by p53. Oncogene2003;22:9030–40.

[10] Hesketh R. In: The oncogene and tumour suppressor gene facts book.San Diego: Academic Press.

[11] Dumaz N, Stary A, Soussi T, Daya-Grosjean L, Sarasin A. Canwe predict solar ultraviolet radiation as the causal event in humantumours by analysing the mutation spectra of the p53 gene? MutatRes 1994;307:375–86.

[12] Wikonkal NM, Brash DE. Ultraviolet radiation induced signaturemutations in photocarcinogenesis. J Invest Dermatol Symp Proc1999;4:6–10.

[13] Brash DE, Seetharam S, Kraemer KH, Seidman MM, Bredberg A.Photoproduct frequency is not the major determinant of UV basesubstitution hot spots or cold spots in human cells. Proc Natl AcadSci USA 1987;84:3782–6.

[14] Munson PJ, Hauser J, Levine AS, Dixon K. Test of models for thesequence specificity of UV-induced mutations in mammalian cells.Mutat Res 1987;179:103–14.

[15] Wogan GN. Impacts of chemicals on liver cancer risk. Semin CancerBiol 2000;10:201–10.

[16] Bailey EA, Iyer RS, Stone MP, Harris TM, Essigmann JM. Mutationalproperties of the primary aflatoxin B1-DNA adduct. Proc Natl AcadSci USA 1996;93:1535–9.

[17] Olivier M, Eeles R, Hollstein M, Khan MA, Harris CC, HainautP. The IARC TP53 database: new online mutation analysis andrecommendations to users. Hum Mutat 2002;19:607–14.

[18] Hainaut P, Pfeifer GP. Patterns of G to T transversions in lungcancers reflect the primary mutagenic signature of DNA-damage bytobacco smoke. Carcinogenesis 2001;22:367–74.

[19] Seidman M, Dixon K. Mutational analysis of genotoxic chemicals.In: Puga A, Wallace KB, editors. Molecular biology of the toxicresponse. Philadelphia: Taylor & Francis; 1998, p. 93–109.

[20] Dixon K, Medvedovic M. Mutational specificity of environmentalcarcinogens. In: Wilson SH, Wuk WA, editors. Biomarkers of envi-ronmentally associated disease, New York: Lewis Publishers; 2002,p. 183–207.

[21] Battalora MD, Tennant RW. The use of transgenic mice in mutagen-esis and carcinogenesis research and in chemical safety assessment.In: Puga A, Wallace KB, editors. Molecular biology of the toxicresponse. Philadelphia: Taylor and Francis; 1998, p. 111–26.

[22] Stambrook PJ, Shao C, Stockelman M, Boivin G, Engle SJ, TischfieldJA. APRT: a versatile in vivo resident reporter of local mutation andloss of heterozygosity. Environ Mol Mutagen 1996;28:471–82.

[23] Vrieling H, Wijnhoven S, van Sloun P, Kool H, Giphart-Gassler M,van Zeeland A. Heterozygous Aprt mouse model: detection and studyof a broad range of autosomal somatic mutations in vivo. EnvironMol Mutagen 1999;34:84–9.

[24] Albertini RJ. HPRT mutations in humans: biomarkers for mechanisticstudies. Mutat Res 2001;489:1–16.

[25] Thybaud V, Dean S, Nohmi T, de Boer J, Douglas GR, Glickman BW,et al. In vivo transgenic mutation assays. Mutat Res 2003;540:141–51.

[26] de Boer JG. Polymorphisms in DNA repair and environmental in-teractions. Mutat Res 2002;509:201–10.

[27] Burgers PM. Eukaryotic DNA polymerases in DNA replication andDNA repair. Chromosoma 1998;107:218–27.

[28] Hussain SP, Hofseth LJ, Harris CC. Radical causes of cancer. NatRev Cancer 2003;3:276–85.

[29] Jallepalli PV, Lengauer C. Chromosome segregation and cancer:cutting through the mystery. Nat Rev Cancer 2001;1:109–17.

[30] Christmann M, Tomicic MT, Roos WP, Kaina B. Mechanisms ofhuman DNA repair: an update. Toxicology 2003;193:3–34.

[31] Ronen A, Glickman BW. Human DNA repair genes. Environ MolMutagen 2001;37:241–83.

[32] Wood RD, Mitchell M, Sgouros J, Lindahl T. Human DNA repairgenes. Science 2001;291:1284–9.

[33] Digweed M. Response to environmental carcinogens in DNA-repair-deficient disorders. Toxicology 2003;193:111–24.

[34] Bootsma D, Kraemer KH, Cleaver J, Hoeijmakers JHJ. Nucleotideexcision repair syndromes: xeroderma pigmentosum, Cockayne syn-drome and trichothiodystrophy. In: Vogelstein B, Kinzler KW, edi-tors. The genetic basis of human cancer. New York: McGraw-Hill;1998, p. 245–74.

[35] van Hoffen A, Balajee AS, van Zeeland AA, Mullenders LH. Nu-cleotide excision repair and its interplay with transcription. Toxicol-ogy 2003;193:79–90.

[36] Goldsby RE, Lawrence NA, Hays LE, Olmsted EA, Chen X, SinghM, et al. Defective DNA polymerase-delta proofreading causes cancersusceptibility in mice. Nat Med 2001;7:638–9.

[37] Srivastava DK, Husain I, Arteaga CL, Wilson SH. DNA polymerasebeta expression differences in selected human tumors and cell lines.Carcinogenesis 1999;20:1049–54.

[38] Sarasin A. An overview of the mechanisms of mutagenesis andcarcinogenesis. Mutat Res 2003;544:99–106.

[39] Friedberg EC, Wagner R, Radman M. Specialized DNA poly-merases, cellular survival, and the genesis of mutations. Science2002;296:1627–30.

[40] Lynch HT, Smyrk TC, Watson P, Lanspa SJ, Lynch JF, Lynch PM,et al. Genetics, natural history, tumor spectrum, and pathology ofhereditary nonpolyposis colorectal cancer: an updated review. Gas-troenterology 1993;104:1535–49.

[41] Ellis NA, Groden J, Ye TZ, Straughen J, Lennon DJ, Ciocci S, etal. The Bloom’s syndrome gene product is homologous to RecQhelicases. Cell 1995;83:655–66.

[42] Huang S, Li B, Gray MD, Oshima J, Mian IS, Campisi J. Thepremature ageing syndrome protein WRN is a 3′→5′ exonuclease.Nat Genet 1998;20:114–6.

[43] Varon R, Vissinga C, Platzer M, Cerosaletti KM, Chrzanowska KH,Saar K, et al. Nibrin, a novel DNA double-strand break repair protein,is mutated in Nijmegen breakage syndrome. Cell 1998;93:467–76.

[44] Moynahan ME, Pierce AJ, Jasin M. BRCA2 is required forhomology-directed repair of chromosomal breaks. Mol Cell2001;7:263–72.

[45] D’Andrea AD. The Fanconi road to cancer. Genes Dev2003;17:1933–6.

[46] Nyberg KA, Michelson RJ, Putnam CW, Weinert TA. Toward main-taining the genome: DNA damage and replication checkpoints. AnnuRev Genet 2002;36:617–56 (Epub@2002 Jun 11).

[47] Goodarzi AA, Block WD, Lees-Miller SP. The role of ATM andATR in DNA damage-induced cell cycle control. Prog Cell CycleRes 2003;5:393–411.

[48] Rossman TG. Mechanism of arsenic carcinogenesis: an integratedapproach. Mutat Res 2003;533:37–65.

[49] Tseng WP, Chu HM, How SW, Fong JM, Lin CS, Yeh S. Prevalenceof skin cancer in an endemic area of chronic arsenicism in Taiwan.J Natl Cancer Inst 1968;40:453–63.

[50] Tseng WP. Effects and dose–response relationships of skin cancer andblackfoot disease with arsenic. Environ Health Perspect 1977;19:109–19.

[51] Basu A, Mahata J, Gupta S, Giri AK. Genetic toxicology of a para-doxical human carcinogen, arsenic: a review. Mutat Res 2001;488:171–94.

[52] Rossman TG, Uddin AN, Burns FJ, Bosland MC. Arsenite is acocarcinogen with solar ultraviolet radiation for mouse skin: ananimal model for arsenic carcinogenesis. Toxicol Appl Pharmacol2001;176:64–71.


[53] Marx J. Debate surges over the origins of genomic defects in cancer.Science 2002;297:544–6.

[54] Loeb LA, Loeb KR, Anderson JP. Multiple mutations and cancer.Proc Natl Acad Sci USA 2003;100:776–81.

[55] Fearon ER, Vogelstein B. A genetic model for colorectal tumorige-nesis. Cell 1990;61:759–67.

[56] Cohen SM, Ellwein LB. Cell proliferation in carcinogenesis. Science1990;249:1007–11.

[57] Blount BC, Ames BN. DNA damage in folate deficiency. BaillieresClin Haematol 1995;8:461–78.

[58] Miller ML, Vasunia K, Talaska G, Andringa A, de Boer J,Dixon K. The tumor promoter TPA enhances benzo[a]pyrene and

benzo[a]pyrene diolepoxide mutagenesis in Big Blue mouse skin.Environ Mol Mutagen 2000;35:319–27.

[59] Hara T, Sui H, Kawakami K, Shimada Y, Shibuya T. Partial hepate-ctomy strongly increased the mutagenicity ofN-ethyl-N-nitrosoureain MutaMouse liver. Environ Mol Mutagen 1999;34:121–3.

[60] Kopelovich L, Crowell JA, Fay JR. The epigenome as a targetfor cancer chemoprevention. J Natl Cancer Inst 2003;95:1747–57.

[61] Jones PA, Baylin SB. The fundamental role of epigenetic events incancer. Nat Rev Genet 2002;3:415–28.

[62] Feinberg AP, Tycko B. The history of cancer epigenetics. Nat RevCancer 2004;4:143–53.

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