Despite years of intensive study and substantial progress inunderstanding susceptibility to breast and ovarian cancer, thesediseases remain important causes of death in women. However,several recent critical advances sequencing of the humangenome and the development of high-throughput techniques foridentifying DNA-sequence variants, changes in copy numbers,and global expression profiles have dramatically acceleratedthe pace of research aimed at preventing and curing these diseases.We review some of the important discoveries in the geneticsof breast and ovarian cancer, ongoing studies to isolate additionalsusceptibility genes, and early work on molecular profilinginvolving microarrays.
BRCA1 and BRCA2 mutations occur in approximately 20 percent of families with evidence of inherited susceptibility to breast cancer. Germ-line mutations in TP53 cause the LiFraumeni syndrome and account for no more than 1 percent of cases of familial breast cancer, but women who survive the childhood cancers associated with the LiFraumeni syndrome have as much as a 90 percent risk of breast cancer.8 Mutations in the cell-cyclecheckpoint kinase gene (CHEK2) account for about 5 percent of all cases of familial breast cancer (defined by the diagnosis of breast cancer in two or more family members before the age of 60 years), but the risk for individual mutation carriers is probably less than 20 percent.9 All other cases of breast cancer are presumed to be due to an undefined number of additional susceptibility genes with various degrees of penetrance, exposure to hormonal and environmental factors, and stochastic genetic events.
The prediction that there are common DNA-sequence variants thatconfer a small but appreciable enhanced risk of cancer has beenvalidated with the recent discovery of the 1100delC mutationin the cell-cyclecheckpoint kinase gene (CHEK2).9 Thismutation was found in 1.1 percent of women without breast cancer,1.4 percent of women with a personal but no family history ofbreast cancer, and 4.2 percent of index patients from 718 familiesin which two or more members had been given a diagnosis of breastcancer before the age of 60 years but in which there was nodetectable BRCA1 or BRCA2 mutation. This mutation doubles therisk of breast cancer among women and increases the risk amongmen by a factor of 10. CHEK2, an important component of thecellular machinery that recognizes and repairs damaged DNA,is activated after phosphorylation by the checkpoint gene ATMand in turn activates BRCA1. The role of ATM mutations in thepredisposition to the early onset of breast cancer remains controversial,but some missense mutations do appear to increase susceptibilityto breast cancer in humans10 and mice.11
There is convincing evidence that additional high-penetrancegenes that increase susceptibility to breast cancer exist. Incontrast, it has been suggested that, other than BRCA1 and BRCA2,high-penetrance genes that confer susceptibility to ovariancancer do not exist.12 An ovarian-cancersusceptibilitylocus on chromosome 3p2225 has putatively been identified,but this finding has yet to be confirmed by an independent group.13
Many additional genetic variants in low-penetrance susceptibilityalleles may moderately increase the risk of breast cancer, ovariancancer, or both. These genetic variants are much more commonin the population than are high-penetrance gene mutations and,thus, in aggregate may make a substantially greater contributionto breast and ovarian cancer in the population than mutationsin high-risk genes.14 However, genetic heterogeneity and therarity of high-penetrance genes make both high- and low-penetrancegenes difficult to identify.
Identification of Genes That Increase Susceptibility to Breast and Ovarian Cancer
Identification of High-Penetrance Genes
Genetic linkage was used to identify the BRCA1 and BRCA2 locion chromosomes 17q and 13q, respectively.15,16 In both cases,no information was initially available on the location, structure,or function of the genes, and they were identified through positionalcloning. Loss-of-heterozygosity mapping was of little assistancein either search; however, a homozygous deletion on chromosome13 in a pancreatic adenocarcinoma helped identify the locationof BRCA2.17 Finally, critical data in the search for BRCA2 camefrom studies of breast cancer in Iceland, whose population derivesfrom a small group of settlers from Norway and Ireland.18,19Such populations share more genetic information than large,admixed populations and have been used successfully many timesin gene mapping.20 After the BRCA1 locus was identified, ittook almost four years to isolate the gene and involved severallabor-intensive strategies.2 By contrast, the BRCA2 locus wasone of the first genomic intervals to be systematically sequencedas part of the Human Genome Project. These data, together withother information about the genes in the region, reduced thetime it took to isolate BRCA2 to two years.3 Thus, informationfrom the human genome sequence greatly enhances the utilityof linkage analysis for gene identification (Figure 2).
Figure 2. Effect of Sequencing the Human Genome on Gene-Discovery Strategies.
The annotated DNA sequence of the human genome can be used to locate genes, repeat sequences, and other features and has revolutionized the identification of cancer genes. A sequence without annotation is of limited utility (Panel A). As shown in Panel B, an annotated sequence shows genetic markers such as CA and GT repeats along with other data, such as CpG islands, known genes, genes predicted to exist on the basis of computational models, and Basic Local Alignment Search Tool (BLAST) matches. Using publicly available data (http://www.ensembl.org, http://www.ncbi.nlm.nih.gov, and http://www.genome.ucsc.edu), it is possible to jump from a genetic region of interest to the identification of candidate genes in a matter of seconds and download the relevant data (Panel C). With these data in hand, experiments, such as those involving the polymerase chain reaction (PCR), can be designed to analyze the genes for mutations (Panel D). The final step in the identification of genes is to compare the sequence from patients with the disease of interest with the normal reference sequence to discover the mutations (Panel E).
BRCA3 and beyond
Several candidate regions for BRCA3 have been proposed, includingchromosome 13q2121 and chromosome 8p1222,22 but bothhave been strongly refuted by analysis of data from independentfamilies.23,24 The search for BRCA3 has been difficult for severalreasons. First, ovarian cancer and male breast cancer were recognizedas components of syndromes of breast-cancer susceptibility beforeeither BRCA1 or BRCA2 was isolated, allowing targeted identificationof affected families. Since no such phenotype has been associatedwith the putative BRCA3 gene or genes, families in current studiesare selected only on the basis of a young age at the diagnosisof breast cancer and the absence of ovarian and male breastcancer. Ideally, these families should have multiple memberswith early-onset breast cancer and strong evidence against theinvolvement of either BRCA1 or BRCA2. However, the breast cancersin most such families are in fact due to germ-line mutationsin BRCA1 or BRCA2,25 and those that are not may represent theeffects of multiple susceptibility alleles (genetic heterogeneity),reducing the power of linkage analysis. What is needed to furtherthis effort are larger families to increase the statisticalpower of such studies, as well as novel means of clusteringfamilies into subgroups most likely to represent single-genedisorders.
One approach is to classify families with breast cancer accordingto the molecular profile of the associated tumors. These analysescould be based either on expression profiling or on array-basedcomparative genomic hybridization, both of which provide uniquemolecular signatures (Figure 3). Nonetheless, hundreds of smallpedigrees may be needed to identify the BRCA3 locus.
In Panel A, bacterial artificial chromosome clones or complementary DNAs are placed on glass slides at high density; tumor and normal DNA are labeled with CY3 and CY5, respectively; and the combined probe is hybridized to the array. The array is analyzed with use of a laser scanner that reads each color channel individually and then calculates an intensity ratio for each spot. In Panel B, spots with intensity ratios greater than 1.25 (green spots) represent increases in copy number (amplification), and those with intensity ratios of less than 0.75 (red spots) represent decreases in copy number (deletion). Each spot is a DNA segment that can be linked directly to the human genome sequence (Panel C), thus defining changes in the number of copies of a specific gene. In Panel D, the plotting of intensity ratios for the chromosome 9 bacterial artificial chromosome clones on the array in linear order identifies a homozygous loss of CDKN2A in a melanoma cell line.
Use of the Human Genome Sequence to Identify Low-Penetrance Genes
As noted, the susceptibility genes identified to date are notresponsible for most breast and ovarian cancers, leaving a considerablepotential contribution from less penetrant genes. One of theimplicit problems in isolating low-penetrance genes is thatsuch genes will rarely produce striking familial patterns involvingmultiple cases that can be used in traditional linkage studies.An additional concern is that very large studies, with statisticalpower to evaluate multiple interactions between genes, may beneeded before genetic profiles involving this class of genescan be used for risk prediction.14 As the computational methodsfor finding coding sequences embedded in a sequence of genomicDNA become increasingly powerful, the value of the human genomesequence as a tool for identifying unknown genes also increases.These algorithms for finding genes have largely replaced laboriousexperimental techniques to identify potential coding sequencesof unknown genes for mutation analysis within linkage regions.These methods are another illustration of the fact that it isthe annotation of the genomic sequence (i.e., the identificationof genes and their function) that brings the sequence to life.Annotation parses the sequence into genes and noncoding regions.By including genomic features such as CpG islands, which markthe promoter regions of many genes, annotations produce a completerendering of each sequence. Annotated sequences are publiclyavailable in several data bases (http://www.ensembl.org, http://www.ncbi.nlm.nih.gov,and http://www.genome.ucsc.edu) with associated genome browsers.
The depth and value of annotation have also grown through theaddition of millions of single-nucleotide polymorphisms, whichare invaluable in the search for susceptibility genes.26 Onesuch example is the recent demonstration that a silent single-nucleotidepolymorphism in LIG4, a gene encoding a DNA ligase importantin the repair of breaks in double-stranded DNA, is associatedwith survival among patients with breast cancer.27 This effectwas demonstrated in a British population-based study that included2430 cases of breast cancer. DNA from these patients was genotypedfor polymorphisms in 22 DNA-repair, hormone-metabolism, carcinogen-metabolism,and other genes, and the effect of each single-nucleotide polymorphismon the outcome was assessed by Cox regression analysis. Thesilent polymorphism D501D (t>c) in LIG4 had the largest effect.The estimated hazard ratio for death among patients homozygousfor the polymorphism, as compared with those homozygous forthe wild-type sequence, was 4.0 (95 percent confidence interval,2.1 to 7.7; P=0.002), and this effect remained significant afterstratification according to tumor stage, grade, and type (hazardratio, 4.2; 95 percent confidence interval, 1.8 to 9.4; P=0.01).The inclusion of these single-nucleotide polymorphisms in theannotation of the human genome sequence greatly facilitatedthis analysis, which would otherwise have had to have been precededby an extensive sequence-based effort to identify single-nucleotidepolymorphisms.
Whole-Genome Approaches to the Analysis of Breast and Ovarian Cancer
Many genomic approaches to the identification of cancer genesare based on microarray techniques. For gene-expression profiling,each element usually represents one gene and is created withthe use of a complementary DNA (cDNA) or oligonucleotide forthe gene in question. Similar arrays have been produced withlarge genomic clones for array-based comparative genomic hybridizationto identify changes in the number of copies of DNA. This approachreplaced lower-resolution comparative genomic hybridizationof cells in metaphase and provides a direct link to genes inthe altered region (Figure 3).
A comparative genomic hybridization can be used to identifythe loss of one or both copies of a given gene as well as regionsof amplification. Arrays made with cDNAs can be used for expressionprofiling and comparative genomic hybridization simultaneously.28This approach allows a direct comparison between the numberof copies of a gene and the level of expression of that gene,but the results of comparative genomic hybridization may bevariable, presumably because the cDNA sequence and the genomicsequence are not collinear. However, the alternative approachof using large cloned segments of genomic DNA in the bacterialartificial chromosomes consistently provides excellent data.29The genomic clones can be spaced evenly across the genome, andthe array set can be enriched with selected clones that containcandidate cancer genes to enhance resolution. The use of DNAmicroarrays has been suggested for other applications; however,epigenetic changes such as changes in DNA methylation, whichare likely to be a critical component in the development ofcancer, have been notoriously difficult to assay regardlessof the format.
The power of a comparative genomic hybridization was recentlydemonstrated by Albertson and colleagues, who used this approachto map the recurrent breast-cancer amplicon at chromosome 20q12.3.30This approach clearly demonstrated that what had previouslybeen described as a single amplicon was, in fact, two distinctamplicons, one containing the putative oncogene ZNF21731 andthe other containing CYP24, which encodes vitamin D24-hydroxylase.32The overexpression of this enzyme alters the control of growthmediated by vitamin D. There were two distinct peaks of highcopy numbers within this 2-Mb region, with a gene at the peakof each amplicon. The ability of comparative genomic hybridizationto show peaks in increases in copy numbers across regions ofrecurrent abnormality at high resolution is very useful forlocating oncogenes in many human cancers.
Much less advanced, but critically important, are techniquesinvolving proteomics, which examine the entire complement ofproteins expressed in a specific tissue or cell. The informationsupplied complements that provided by a comparative genomichybridization, expression profiling, and screening for mutationsin cancer research,33 since the genetic code does not indicatewhich proteins are expressed, in what quantity, and in whatform. For example, post-translational modifications, such asphosphorylation or glycosylation, may determine the functionor stability of a protein and are not detected by transcriptionalanalyses. Many differences between normal tissue and malignanttumors are due to post-translational modifications, and a completeanalysis of the cancer phenotype will require a whole-proteomeapproach.
Diffuse large -cell lymphoma was the first human cancer to undergogene-expression profiling, and a microarray containing 17,800cDNAs was used.34 Breast and ovarian cancer have now been subjectedto molecular profiling as well. In the first such study, Perouand colleagues used a cDNA microarray containing 8000 genesto assay 65 breast-biopsy specimens, primarily invasive breastcancers.35 Perhaps not surprisingly, estrogen-receptor statuswas a key predictor of the outcome and treatment response, withestrogen-receptor and coregulated genes being the primary elementsneeded for these tumors to cluster. In addition, a profile oftumors that overexpress ERBB2 was easily identifiable. Thus,the primary clusters recognized were tumors that expressed estrogenreceptor and had a luminal-cell pattern of gene expression,tumors that did not express estrogen receptor and had a myoepithelial-cellpattern of expression, tumors that overexpressed ERBB2, anda fourth group of tumors that clustered with normal breast tissue.More recently, Hedenfalk and colleagues suggested that transcriptionalprofiling can also accurately differentiate breast cancers withunderlying germ-line mutations in BRCA1 or BRCA2 from thosewithout such mutations, an advance that could facilitate theidentification of high-risk families on the basis of molecularphenotyping, as well as identify characteristic molecular differencesthat may be useful clinical targets for directed therapy.36
Ovarian cancers have been subjected to transcriptional profilingwith similar results. In one series, 27 serous papillary ovariancancers and 3 samples of normal ovarian tissue underwent gene-expressionprofiling with oligonucleotide-based arrays representing morethan 6000 human genes.37 Normal ovarian tissue was clearly distinguishablefrom malignant tissues, and three types of tumors were identified.The first subtype clustered with normal tissue and was welldifferentiated on conventional histologic analyses. The secondgroup was characterized by the expression of genes from admixedstromal cells and infiltrating lymphocytes. Although this profilecould represent a random admixture of cell types, it could alsorepresent an immune response to the tumor, as suggested recentlyby Zhang and colleagues.38 The third group of tumors had a highlevel of expression of cell-cycleassociated genes, mostlikely reflecting a high proliferative rate. More than halfthe tumors in this cluster were poorly differentiated on histologicanalysis. Which of the differentially expressed genes in thisand other series represent the root causes of malignant transformationrather than markers of progression is not known but must bedetermined in order to distinguish diagnostic markers from therapeutictargets.
Microarrays have also been used to show how an expression profilecan change as cancer cells develop resistance to doxorubicin-basedtherapy.39 In these experiments, a set of genes that were transientlyoverexpressed after initial exposure to doxorubicin includeda subgroup of genes that became constitutively overexpressedas resistance to doxorubicin developed. These experiments, althoughjust the beginning of what will be a fundamental change in molecularoncology owing to the deciphering of the human genome sequence,demonstrate the power of this approach.
In perhaps the most extensive and informative study to date,the expression profiles of 117 primary breast cancers were comparedwith known prognostic markers and the clinical outcome at leastfive years after diagnosis.40 Expression profiling with theuse of 25,000 genes separated the tumors into two groups, onein which distant metastases developed in 34 percent at fiveyears and one in which metastases developed in 70 percent atfive years. From the original 25,000 genes in the array, 70were identified as having the greatest accuracy in predictingrecurrent disease. When the tumors were sorted on the basisof this smaller set of genes, fewer than 10 percent of the tumorsin the poor-prognosis group were misclassified. A comparativemultivariate analysis using clinical prognostic factors thatincluded tumor grade, tumor size, the presence or absence ofangiolymphatic invasion, patients' age, and tumor estrogen-receptorstatus demonstrated that as compared with the good-prognosisgene-expression signature, the poor-prognosis microarray profilewas an independent predictor of recurrence, with an odds ratioof 18 (95 percent confidence interval, 3 to 94). This approachhas now been tested in 295 consecutive patients with stage Ior II breast cancer.41 Of these, 180 had the poor-prognosisprofile and 115 had the good-prognosis profile. Ten years afterthe diagnosis of breast cancer, the probability of remainingfree of metastases was 51 percent among women with a poor-prognosisprofile and 85 percent among those with a good-prognosis profile.These data provide compelling evidence that the genetic programof a cancer cell at diagnosis defines its biologic behaviormany years later, refuting a competing hypothesis that the geneticchanges driving the development of metastatic disease are acquiredin residual cells after adjuvant treatment.
Clinical Management of Inherited Susceptibility to Breast and Ovarian Cancer
Several computational models have been developed to predictan individual woman's risk of breast cancer, including one inwhich family history is the predominant risk factor. This model,developed by Claus and colleagues and published as a seriesof tables clinicians can use,42 is based on the number and degreeof relatedness of family members with breast cancer and theirage at diagnosis. However, this model does not provide estimatesof the likelihood that an individual woman will have a germ-linemutation in BRCA1 or BRCA2. Several studies have identifiedfactors that are associated with an increased likelihood thata BRCA1 or BRCA2 mutation will be identified, including early-onsetbreast cancer, the occurrence of breast and ovarian cancer inthe same woman, a history of male family members with breastcancer, and Ashkenazi Jewish ancestry. These characteristicshave also been included in predictive models designed for useby clinicians.43,44,45
The use of tamoxifen to prevent breast cancer in carriers of BRCA1 and BRCA2 mutations remains controversial.One retrospectivestudy suggested that adjuvant tamoxifen therapy in carriersof BRCA1 and BRCA2 mutations with estrogen-receptorpositivebreast cancer reduced the risk of contralateral breast cancersby the same amount as that in unselected patients with breastcancer.53 However, data showing that most BRCA1-associated breastcancers are negative for estrogen receptors54 and recent datafrom the Breast Cancer Prevention Trial (BCPT) of the NationalSurgical Adjuvant Breast and Bowel Project have led to widespreadspeculation that tamoxifen will not prevent breast cancer inwomen with germ-line BRCA1 mutations.55 It is important to considerthat all available data suggest that endogenous exposure tohormones has a central role in defining the risk of cancer amongcarriers of BRCA1 mutations, that breast cancer developed inonly eight carriers of BRCA1 mutations in the BCPT, and thatthe lack of a preventive effect of tamoxifen was statisticallyinsignificant (odds ratio, 1.67; 95 percent confidence interval,0.41 to 8.00). The length of treatment in the BCPT is also consistentwith an early treatment effect, rather than true prevention,which, given the preponderance of estrogen-receptornegativetumors among carriers of BRCA1 mutations, would produce thedata seen in this study. Thus, we recommend that carriers ofBRCA1 mutations consider taking tamoxifen once they discontinuehormone-replacement therapy at about the age of 50 years.
Summary
The past decade has been a period of unparalleled discoveryin the field of the genetics and genomics of breast and ovariancancer. Two major susceptibility genes have been isolated, andsubsequent work provided sufficient management information toallow genetic testing for BRCA1 and BRCA2 mutations to becomea part of routine practice in many clinical centers. In addition,work has begun on the characterization of genetic variants that,although associated with a lower risk of cancer than germ-lineBRCA1 and BRCA2 mutations, are far more common in the populationand thus may have a substantial role in defining the risk ofcancer. Finally, gene-expression profiling, coupled with thesequencing of most or all of the genes in the human genome,is revolutionizing the study of the biology and the molecularclassification of breast and ovarian cancer. Combined with datafrom projects conducting a genome-wide mutation analysis ofall genes implicated in the development of cancer, the importanceof which has just been illustrated with the discovery that morethan 60 percent of melanomas have mutations in BRAF (v-raf murinesarcoma viral oncogene homologue B1),56 and progress in developingeffective preventive measures, a marked reduction in mortalityfrom breast and ovarian cancer is a realistic goal for the nextdecade.
Source Information
From the Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom (R.W.); and the University of Pennsylvania, Philadelphia (B.L.W.).
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