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>http://content.nejm.org/cgi/content/full/359/7/722

Volume 359:722-734
August 14, 2008
Number 7
Chromosomal Abnormalities in Cancer

Cytogenetic abnormalities are a characteristic attribute ofcancer cells. To date, clonal chromosome aberrations have beenfound in all major tumor types from more than 54,000 patients(http://cgap.nci.nih.gov/Chromosomes/Mitelman), and their identificationcontinues as a result of technical improvements in conventionaland molecular cytogenetics. The World Health Organization Classificationof Tumours recognizes a growing number of such genetic changesand uses them to define specific disease entities. Many of theseaberrations have emerged as prognostic and predictive markersin hematologic cancers and certain types of solid tumors. Furthermore,the molecular characterization of cytogenetic abnormalitieshas provided insights into the mechanisms of tumorigenesis andhas, in a few instances, led to treatment that targets a specificgenetic abnormality. This article discusses examples of twomain classes of chromosomal abnormalities â ” balanced
chromosomalrearrangements and chromosomal imbalances (Figure 1 and Figure 2)â ” with particular focus on their functional consequencesand their implications (actual or potential) for the developmentof effective anticancer therapies.

Structure of a Human Chromosome.
Each human chromosome, shown here at a resolution of 400 bands per haploid genome, contains two specialized structures, a centromere and two telomeres. The centromere divides the chromosome into short (p) and long (q) arms and is essential for the segregation of chromosomes during cell division. The telomeres "cap" the p and q arms and are important for the structural integrity of the chromosome, for complete DNA replication at the ends of the chromosome, and for the establishment of the three-dimensional architecture of the nucleus. Chromosomes are isolated at the metaphase or prometaphase stage of the cell cycle and are treated chemically (e.g., by enzymatic digestion and staining with a DNA-binding dye) to reveal specific patterns of light and dark bands that are microscopically visible. Analysis of the distribution of bands on individual chromosomes allows the identification of structural chromosomal abnormalities. Â

Chromosomal Abnormalities in Human Cancer.
The two main classes of chromosomal abnormalities found in human cancer are shown. Balanced chromosomal rearrangements can be categorized into those that lead to the formation of a chimeric fusion gene and those that lead to the aberrant juxtaposition of gene regulatory elements to the coding sequence of a structurally intact gene. The formation of a chimeric fusion gene results in the expression of a chimeric protein with new or altered activity. In the majority of cases, only one of the two fusion genes generated and not the reciprocal counterpart (indicated by the dashed arrows) contributes to cancer pathogenesis. The deregulated expression of a structurally normal gene results in deregulated expression of a normal protein. Chromosomal imbalances can be categorized into genomic gains and genomic losses. Genomic gains include complete or partial trisomies and intrachromosomal or extrachromosomal amplifications, which can be identified cytogenetically
as homogeneously staining regions (HSR) and double-minute chromosomes (dmin), respectively. HSR are chromosomal regions that display no typical banding pattern; dmin are circular, acentric, autonomously replicating DNA strands of varying size; mRNA denotes messenger RNA. Genomic losses include monosomies and large-scale or submicroscopical deletions. Â
Causes of Chromosomal Abnormalities
The cause of chromosomal abnormalities remains poorly understood.Studies of various types of leukemia have shown that certainenvironmental and occupational exposures and therapy with cytotoxicdrugs can induce chromosomal aberrations. For example, casesof the myelodysplastic syndrome or acute myeloid leukemia thatarise after treatment with alkylating agents are frequentlyassociated with unbalanced abnormalities, primarily deletionor loss of chromosome 5 or 7 (or both), whereas therapy withtopoisomerase II inhibitors is typically associated with balancedabnormalities, most commonly translocations involving the MLLgene on chromosome band 11q23.1 For most cancer-associated chromosomalabnormalities, however, no specific initiating factor has beenidentified.
Insights into molecular mechanisms underlying the formationof chromosomal aberrations have been gained from studies ofrare cancer-predisposing chromosomal instability syndromes,such as the inherited bone marrow failure syndromes,2 in whichgenetic changes that are associated with the development ofleukemia can be followed over time. Cases of the myelodysplasticsyndrome or acute myeloid leukemia arising in patients withFanconi's anemia, for example, typically have complex, unbalancedchromosomal abnormalities, which are thought to result frominactivation of components of the Fanconi's anemia pathway thatregulates the recognition and repair of damaged DNA.3 The complexgenetic changes in Fanconi's anemia appear to be preceded byisolated focal gains or cryptic rearrangements of chromosomeband 3q26 that cause overexpression of the EVI1 gene.4 Thisearly genetic event may have a role in the development of cancersthat result from a constitutional imbalance between
genotoxicstress and DNA repair. Whether similar mechanisms are relevantto the pathogenesis of chromosomal abnormalities that are associatedwith sporadic cancers remains to be determined. (The full namesof all genes that are mentioned in this review are listed inthe Supplementary Appendix, available with the full text ofthis article at Chromosomal>www.nejm.org.)
Chromosomal Rearrangements
Reciprocal translocations, inversions, and insertions are typicalchromosomal rearrangements. There is substantial evidence thatthese alterations are early or even initiating events in tumorigenesis.For instance, certain translocations that are associated withchildhood leukemia arise in utero, years before the appearanceof overt disease.5 Furthermore, most chromosomal rearrangementsare closely associated with specific tumor types, even thoughindividual genes â ” such as MLL, ETV6, and NUP98 â ”can participate in multiple different translocations, sometimeswith distinct clinicopathological associations.6 Notably, certainchromosomal rearrangements, such as the BCR-ABL1 fusion gene,serve as sensitive indicators in the assessment of the responseto cancer treatment.7
With regard to their functional consequences, recurrent chromosomalrearrangements are of two general types: aberrations that resultin the formation of a chimeric fusion gene with new or alteredactivity and chromosomal changes that lead to deregulated expressionof a structurally normal gene (Figure 2 and Figure 3). Table 1lists examples in these two functional categories.

Functional Consequences of Balanced Chromosomal Rearrangements.
Panels A through C illustrate the functional consequences of different chromosomal rearrangements that result in the formation of a chimeric fusion gene. Rearrangements leading to the expression of a chimeric protein with constitutive tyrosine kinase activity in the absence of physiologic activating signals are represented by the translocation t(9;22)(q34.1;q11.23) associated with chronic myeloid leukemia (CML) and acute lymphoblastic leukemia (ALL) (Panel A). Rearrangements leading to the expression of a chimeric protein with aberrantly increased transcriptional activity are represented by the translocation t(11;22)(q24.1-q24.3;q12.2) associated with Ewing's sarcoma (Panel B). Rearrangements leading to the expression of a chimeric protein that mediates aberrant transcriptional repression through interaction with chromatin-modifying proteins are represented by the translocation t(15;17)(q22;q21) associated with acute promyelocytic leukemia (APL) (Panel
C). Panels D and E show different chromosomal rearrangements that result in deregulated expression of a structurally normal gene. In Burkitt's lymphoma, the translocation t(8;14)(q24.21;q32.33) leads to the aberrant juxtaposition of the enhancer (E) of the IGHG1 gene on band 14q32.33 with the coding sequence of the MYC gene on band 8q24.21, resulting in overexpression of the MYC transcription factor in lymphoid tissues (Panel D). In prostate cancer, a small interstitial deletion or cryptic insertion involving chromosome band 21q22.3 fuses androgen-regulated sequences in the promoter (P) of the prostate-specific TMPRSS2 gene to the coding region of the ERG gene, resulting in aberrant expression of the ERG transcription factor in prostate tissue (Panel E). The term mRNA denotes messenger RNA. Â

Until recently, chromosomal rearrangements have been linkedmainly to hematologic cancers and tumors of mesenchymal origin.8,9However, a number of recent studies have shown that genomicrearrangements that juxtapose two genes also play major rolesin the pathogenesis of epithelial cancers, such as prostatecancer and nonâ “small-cell lung cancer.10,11 It is possiblethat similar rearrangements in other solid tumors exist buthave escaped notice because of technical problems, such as thedifficulty in growing tumor cells for chromosomal analysis,or because they are cytogenetically invisible or masked by multiplecomplex and often nonspecific karyotypic changes, which arethought to reflect secondary genetic events acquired duringtumor progression.
Chimeric Fusion Genes
The majority of chromosomal rearrangements result in the formationof a chimeric gene through the fusion of parts of two genes.The two main groups of genes that participate in such fusionsare those encoding tyrosine kinases and those encoding transcriptionfactors.
Â Â Â Â Â Â Â Â Â Â Â Â Tyrosine Kinase Genes
The classic example of a cytogenetic abnormality leading tothe formation of a chimeric fusion gene is the Philadelphiachromosome,12 a truncated chromosome 22 that is present in virtuallyall patients with chronic myeloid leukemia, in approximately20% of patients with acute lymphoblastic leukemia, and in rarecases of acute myeloid leukemia. The Philadelphia chromosomeis the result of a reciprocal translocation, t(9;22)(q34.1;q11.23),13in which sequences of the BCR gene on band 22q11.23 are joinedto portions of the gene encoding the cytoplasmic ABL1 tyrosinekinase on band 9q34.1 (Figure 3A; for an explanation of thenomenclature used for translocations, inversions, monosomies,trisomies, deletions, derivative chromosomes, and additionalmaterial of unknown origin, see the Supplementary Appendix).14,15,16The resulting chimeric protein, BCR-ABL1, contains the catalyticdomain of ABL1 fused to a domain of BCR that mediates constitutiveoligomerization of the fusion
protein in the absence of physiologicactivating signals, thereby promoting aberrant tyrosine kinaseactivity.17
The discovery of the Philadelphia chromosome and the understandingof its molecular basis have had far-reaching implications. First,these findings provided evidence that human cancer can arisefrom acquired genetic alterations in somatic cells. Second,the aberrant tyrosine kinase signaling in chronic myeloid leukemialed to the use of a selective tyrosine kinase inhibitor, imatinibmesylate, to treat the disease.18,19 Third, imatinib-resistantkinase domain mutations have been identified as a major causeof relapse during imatinib therapy,20 and this finding, in turn,has led to the development of second-generation BCR-ABL1 inhibitors,such as dasatinib and nilotinib.21,22,23,24
In addition to t(9;22)(q34.1;q11.23), several other translocationsform tyrosine kinase fusion proteins with constitutive enzymaticactivity,25 and some of these fusions also confer sensitivityto tyrosine kinase inhibitors (Table 1).26,27 These observationshighlight the usefulness of conventional chromosomal analysisfor guiding the development of new anticancer agents, but theadvent of molecular cytogenetic techniques, such as fluorescencein situ hybridization,28 has further improved the detectionof genomic rearrangements that could serve as the basis fornew treatments.29,30,31 Molecular cytogenetic analyses haverevealed, for example, that approximately 5% of adults withT-cell acute lymphoblastic leukemia harbor an imatinib-sensitivefusion of ABL1 to the NUP214 gene on band 9q34.1. This fusionoccurs on episomes â ” extrachromosomal elements that areinvisible by standard cytogenetic analysis.31
Constitutively activated tyrosine kinases also drive many typesof epithelial cancers.25 Point mutation or genomic amplificationof tyrosine kinase genes have been well documented as mechanismsunderlying aberrant tyrosine kinase activity in epithelial tumors.25Nevertheless, the rarity of cytogenetically visible rearrangementshas led to the commonly held belief that tyrosine kinase fusionproteins have no major role in the pathogenesis of carcinomas.This view has recently been challenged by the discovery of acryptic inversion â ” inv(2)(p22-p21p23) â ” in 6.7%of Japanese patients with nonâ “small-cell lung cancer,which results in the formation of a fusion gene comprising portionsof EML4 and the gene encoding the ALK receptor tyrosine kinase.32
Â Â Â Â Â Â Â Â Â Â Â Â Transcription Factor Genes
Chromosomal rearrangements that disrupt transcription factorgenes can result in fusion proteins with enhanced or aberranttranscriptional activity or fusion proteins that mediate transcriptionalrepression. A fusion protein with enhanced or aberrant transcriptionalactivity is present in virtually all cases of Ewing's sarcoma,in which unique translocations â ” t(11;22)(q24.1-q24.3;q12.2)and t(21;22)(q22.3;q12.2) â ” fuse the EWSR1 gene on band22q12.2 to a gene encoding a member of the ETS family of transcriptionfactors, most frequently FLI1 on band 11q24.1-q24.3 (in approximately85% of patients) and ERG on band 21q22.3 (in approximately 10%of patients) (Figure 3B).33,34 The resulting chimeric transcriptionfactors retain the DNA-binding domain of the respective ETSfamily member and possess, in the EWSR1 portion of the fusionprotein, a potent transactivation domain that induces the transcriptionof various genes whose aberrant expression appears to be
requiredfor EWSR1-ETSâ “mediated tumor growth.35,36
The functional role of many oncogenic transcription factorshas been well characterized. Even so, selective inhibition ofthe abnormal transcriptional activity has proved to be a lesstractable pharmacologic goal than inhibition of constitutivetyrosine kinase activity.37 As a consequence, approaches tospecific targeting of overactive transcription factors havenot yet reached clinical development.
Chromosomal rearrangements that entail aberrant transcriptionalrepression occur in a substantial proportion of patients withacute myeloid leukemia.38 For example, the chimeric proteinsresulting from fusion genes such as PML-RARA (Figure 3C), RUNX1-RUNX1T1,and CBFB-MYH11 all contain a transcription factor that retainsits DNA-binding motif and an unrelated protein that interactswith inhibitors of gene transcription. As a result, bindingof the chimeric transcription factors to their target genes,which include genes required for normal myeloid differentiation,causes aberrant transcriptional repression, thereby contributingto the accumulation of immature myeloid cells in acute myeloidleukemia.39
One of the fusion proteins associated with transcriptional repressionhas been targeted with success in the clinic. In acute promyelocyticleukemia, all-trans retinoic acid and arsenic trioxide reversethe transcriptional repression caused by the PML-RARA fusionprotein by forcing the release of transcription inhibitors fromthe fusion protein or stimulating degradation of PML-RARA orboth. These two drugs are remarkably effective in acute promyelocyticleukemia.40,41,42
Deregulation of Expression of Normal Genes
Chromosomal rearrangements that juxtapose tissue-specific regulatoryelements, such as gene promoters or enhancer sequences, to thecoding sequence of a proto-oncogene deregulate expression ofthe proto-oncogene. This abnormality is exemplified by the reciprocaltranslocations associated with Burkitt's lymphoma, in whichthe enhancer of an immunoglobulin gene (IGHG1, band 14q32.33;IGKC, 2p12; and IGLC1, 22q11.2) drives the constitutive expressionof the gene encoding the MYC transcription factor on band 8q24.21(Figure 3D).43
Chromosomal changes that cause overexpression of structurallynormal genes occur in other cancers of B-cell or T-cell origin44but were believed to be very rare in nonlymphoid cancers. Thisview has changed since the recent discovery that prostate canceris associated with chromosomal rearrangements that bring aboutoverexpression of members of the ETS family of transcriptionfactors.11 The most common of these rearrangements fuses allcoding exons of the ERG gene to androgen-regulated sequencesin the promoter of the prostate-specific TMPRSS2 gene; thesesequences mediate the aberrant expression of ERG in prostatetissue (Figure 3E).45,46 Both genes are located on band 21q22.3,approximately 3 Mb apart, and multiple genomic alterations,such as heterozygous and homozygous deletions or insertions,contribute to the formation of various TMPRSS2-ERG fusion transcripts.45,47In addition, fusions between other ETS family members and TMPRSS2and ETS rearrangements involving
alternative fusion partners(including androgen-repressed and androgen-insensitive genes)occur.46,48,49,50 It will be of prime importance to evaluatethe use of these new genetic biomarkers for early detectionand outcome prediction in prostate cancer.51,52,53,54
Chromosomal Imbalances
Chromosomal imbalances â ” gains or losses of genetic materialâ ” can range from alterations spanning entire chromosomesto intragenic duplications or deletions. Unlike rearrangements,in which the genes that become deregulated and the functionalconsequences of the rearrangements can be readily identifiedthrough analysis of the breakpoint regions, most chromosomalimbalances have functional consequences that are unknown. Determiningthe implications of some chromosomal gains or losses involvingsingle genes has been relatively straightforward, but most imbalancesaffect large genomic regions containing multiple genes, andmany tumors have numerous unbalanced chromosomal abnormalities.Although this degree of genetic complexity has hampered thedelineation of the roles of individual chromosomal gains orlosses in cancer, recent studies suggest that integration ofgenomewide analysis of gene dosage, global gene-expression profiling,and functional genomic techniques
could identify functionallyrelevant genes within genomic regions that are affected by chromosomalimbalances.55 Selective examples of chromosomal imbalances arelisted in Table 2.

Genomic Gains
Most recurrent genomic gains probably contribute to tumorigenesisby enhancing the activity of specific genes in the affectedchromosomal regions. Some of these genes encode proteins thatcan be specifically targeted by new anticancer agents. One example,which occurs in approximately 30% of women with breast cancer,is amplification of the gene on band 17q21.1 that encodes theERBB2 receptor tyrosine kinase. The resulting overexpressionof ERBB2 represents a target for the monoclonal antibody trastuzumab;the combination of trastuzumab with chemotherapy reduces therate of death from breast cancer in both the adjuvant and metastaticsettings.56,57
Â Â Â Â Â Â Â Â Â Â Â Â Large-Scale Genomic Gains
Genomic gains commonly arise from chromosomal nondisjunctionor unbalanced translocations, which cause complete or partialchromosomal trisomies, or from amplification events affectingDNA segments of different size (Figure 2). Numerous examplesof large-scale genomic gains are associated with specific typesof cancer (Table 2). Since such aberrations involve multiplegenes, the identification of their functionally relevant targetshas proved to be difficult. One way to "filter" the genes withinregions of DNA copy-number gain is to identify those that arealso altered at the RNA or protein level, assuming that geneswhose increased dosage translates into increased expressionare most likely to be involved in malignant transformation.This strategy has uncovered new oncogenes in malignant melanoma(MITF and NEDD9 on bands 3p14.2-p14.1 and 6p25-p24, respectively)58,59and hepatocellular carcinoma (YAP1 and BIRC2 on bands 11q13and 11q22, respectively)60 and has
identified candidate breast-cancergenes.61,62
Â Â Â Â Â Â Â Â Â Â Â Â Focal Genomic Gains
Gains affecting small genomic regions or even single genes havebeen described less frequently than large gains. However, itis now possible to identify focal gains by scanning cancer genomesfor variations in DNA copy numbers with new high-resolutionmethods, such as comparative genomic hybridization (CGH) andsingle-nucleotide polymorphism (SNP) genotyping.63,64 Array-basedCGH and SNP genotyping analyses, for example, have shown amplificationof a small segment of band 6q25.1 containing the gene encodingestrogen receptor 1 (ESR1) in a subgroup of women with breastcancer, although additional studies will be required to determinethe exact frequency of these amplifications as well as theirclinical ramifications.65,66 These amplifications correlatewith increased ESR1 protein levels, and preliminary clinicaldata suggest that ESR1 amplification is associated with increasedsensitivity to tamoxifen.65
The power of high-resolution SNP arrays to identify focal genomicgains is also illustrated by a recent study that revealed amplificationof a 480-kb interval on band 14q13, comprising two known genes,in approximately 12% of patients with nonâ “small-cell lungcancer.67 Subsequent functional studies identified the NKX2-1gene, which encodes a lung-specific transcription factor, asan oncogene that may be involved in this focal event.
The analysis of genes that are recurrently amplified in tumorscan also reveal alternative pathogenetic mechanisms that canbe exploited therapeutically, as exemplified by the identificationof point mutations in the catalytic domain of the EGFR receptortyrosine kinase in patients with nonâ “small-cell lung cancerthat are associated with responsiveness to the kinase inhibitorsgefitinib and erlotinib.68 By contrast, genomic gains can alsounderlie acquired resistance to targeted cancer therapy, asexemplified by the recent discovery that amplification and overexpressionof the gene encoding the MET receptor tyrosine kinase on band7q31 can restore aberrant signal transduction downstream ofmutant EGFR in nonâ “small-cell lung cancer cells treatedwith an EGFR inhibitor.69
Genomic Losses
The spectrum of genomic losses ranges from cytogenetically visiblealterations, such as complete or partial chromosomal monosomies,to single-gene or intragenic deletions that are detectable onlyby techniques that provide high spatial resolution. Most recurrentgenomic losses probably contribute to malignant transformationby reducing the function of specific genes in the affected chromosomalregions. Since restoration of gene function is more challengingthan, for example, inhibition of increased kinase activity,it is unclear whether direct pharmacologic targeting of genomiclosses will ever be possible. Nevertheless, an improved understandingof the functional consequences of these aberrations may leadto the identification of indirect targets for therapeutic intervention.For example, inactivation of the PTEN tumor-suppressor geneon band 10q23.3, which occurs with high frequency in glioblastoma,prostate cancer, and endometrial cancer,70 increases
signalingthrough the phosphoinositide-3-kinaseâ “AKTâ “mammaliantarget of rapamycin (PI3Kâ “AKTâ “mTOR) pathway andpromotes tumor-cell proliferation and survival. Experimentalmodels and early clinical trials indicate that PTEN-deficienttumors are sensitized to the growth-suppressive activity ofmTOR inhibitors, such as sirolimus (also called rapamycin).71,72,73
The dissection of the mechanisms through which genomic lossespromote tumorigenesis is challenging. Recent developments includethe application of modern genomic techniques to the study oflarge-scale genomic losses, the identification of new tumor-suppressorgenes that act through allelic insufficiency, and the discoveryof noncoding genes as functionally relevant targets of recurrentgenomic losses.
Â Â Â Â Â Â Â Â Â Â Â Â Large-Scale Genomic Losses
Extensive genomic deletions affecting multiple genes are frequentin tumors, making it difficult to identify which lost gene contributesto the development of the cancer. The classic approach to identifyinga tumor-suppressor gene compares multiple tumors with a specificchromosomal deletion to determine the minimal genomic regionthat is lost in all cases. Candidate genes from this regionare then screened for deletions, mutations, or epigenetic modificationsthat inactivate the remaining allele.74,75 This strategy hasidentified important tumor-suppressor genes such as RB1 (band13q14.2), TP53 (17p13.1), APC (5q21-q22), NF1 (17q11.2), PTEN(10q23.3), and ATM (11q22-q23).
For many recurrent genomic losses, however, such as 1p deletionsin neuroblastoma,76 3p deletions in lung cancer,77 and 7q deletionsin myeloid cancers,78,79 the critical genes are unknown. Regardlessof whether the respective disease genes have been identified,some deletions have proved to be of great value for determiningthe prognosis and guiding treatment decisions, as exemplifiedby the deletion of chromosome 5q in acute myeloid leukemia38;deletions of chromosomes 11q, 13q, and 17p in chronic lymphocyticleukemia80; and the concurrent deletion of chromosomes 1p and19q in anaplastic oligodendroglioma.81
New genomic techniques have considerably improved the identificationof functionally relevant genes within regions of recurrent chromosomaldeletions. For example, RNA interference screening in combinationwith high-resolution DNA copy-number analysis identified theREST gene as a suppressor of epithelial-cell transformationthat maps to a segment of band 4q12 that is frequently deletedin colon cancer.82 The power of array-based SNP genotyping asa tool for gene discovery in cancers associated with genomiclosses is demonstrated by recent studies that revealed deletionsof PAX5 (band 9p13) and IKZF1 (7p13-p11.1) in approximately30% of children with B-progenitor acute lymphoblastic leukemiaand in more than 80% of patients with BCR-ABL1â “positiveacute lymphoblastic leukemia, respectively.83,84
Â Â Â Â Â Â Â Â Â Â Â Â Genomic Losses Resulting in Allelic Insufficiency
Another difficulty in the analysis of chromosomal deletionsoccurs in the identification of genes that contribute to tumorigenesisby inactivation of a single allele.85 Since such haplo-insufficienttumor-suppressor genes cannot be identified through analysisof the remaining allele, alternative approaches are requiredto assess the consequences of monoallelic deletion. An exampleis a recent study in which graded down-regulation of multiplecandidate genes by RNA interference was used to identify RPS14as a causal gene for the 5q minus syndrome,86 a subtype of themyelodysplastic syndrome characterized by a 1.5-Mb commonlydeleted region on chromosome band 5q32.87 Notably, patientswith the 5q minus syndrome are highly responsive to the thalidomidederivative lenalidomide,88 although the mechanisms through whichlenalidomide restores normal erythropoiesis remain unknown.
Monoallelic deletions can completely inactivate tumor-suppressorgenes that are located on the X chromosome because humans carryonly one functional copy of all X-linked genes. This mechanismwas documented in a recent study that identified small deletionsof band Xq11.1, targeting the FAM123B tumor-suppressor gene,in 21.6% of patients with sporadic Wilms' tumors.89 DNA sequenceanalysis subsequently identified additional patients with inactivatingFAM123B mutations,89 again highlighting the potential of chromosomalimbalances for guiding the discovery of alternative geneticchanges with similar functional consequences.
Â Â Â Â Â Â Â Â Â Â Â Â Genomic Losses Affecting Noncoding Genes
Cancer-associated chromosomal losses may act through inactivationof genes that do not encode proteins. For example, several genomicregions that are recurrently deleted in a variety of tumorscontain microRNA genes.90,91 These genes encode small RNAs involvedin post-transcriptional regulation of gene expression, and thereis growing evidence that the loss of specific microRNAs withtumor-suppressive activity may contribute to tumorigenesis.This pathogenetic mechanism was shown by the observation thatMIRN15A and MIRN16-1 are located within a segment of band 13q14.3that is deleted in approximately 50% of patients with chroniclymphocytic leukemia92 and the subsequent discovery that MIRN15Aand MIRN16-1 negatively regulate the expression of the antiapoptoticprotein BCL2.93 Given that many chromosomal regions that arerecurrently deleted in cancer appear to lack protein-codinggenes that normally act to limit cell proliferation, it seemsplausible that the analysis
of cancer-associated genomic losseswill reveal additional tumor-suppressor microRNAs.
Summary
Cancer is caused by genetic alterations that disrupt the normalbalance among cell proliferation, survival, and differentiation.The examples described here illustrate that many of these alterationsare mediated by genetic changes associated with chromosomalabnormalities. Of particular importance for the treatment ofcancer, many of the most specific drug targets, such as ABL1,ERBB2, and EGFR, undergo genetic changes that conventional cytogeneticmethods or modern genomic techniques can detect. Therefore,the analysis of chromosomal abnormalities can be used to identifythe subpopulation of patients who are most likely to benefitfrom a particular drug treatment.
However, the strategy of gene-targeted therapy has thus farhad limited application, because only a fraction of the geneticlesions that are responsible for cancer development have beenidentified. The hope is that continued improvements in genomictechniques, providing ever-increasing resolution, will leadto the identification of additional genetic changes that canbe exploited to design better therapeutic strategies.
No potential conflict of interest relevant to this article wasreported.
Source Information
We thank Dr. Peter Lichter for his critical reading of the manuscriptand Dr. Claudia Scholl for her assistance in the initial preparationof the figures.
From the Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston (S.F.); and the Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany (H.D.).
Address reprint requests to Dr. DÃ¶hner at the Department of Internal Medicine III, University Hospital of Ulm, Robert Koch Str. 8, 89081 Ulm, Germany, or at hartmut.doehner@uniklinik-ulm.de .
References
1. Pedersen-Bjergaard J, Andersen MT, Andersen MK. Genetic pathways in the pathogenesis of therapy-related myelodysplasia and acute myeloid leukemia. Hematology Am Soc Hematol Educ Program 2007;2007:392-397.Â [Medline]
2. Alter BP. Diagnosis, genetics, and management of inherited bone marrow failure syndromes. Hematology Am Soc Hematol Educ Program 2007;2007:29-39.Â [Medline]
3. Taniguchi T, D'Andrea AD. Molecular pathogenesis of Fanconi anemia: recent progress. Blood 2006;107:4223-4233.Â [CrossRef][ISI][Medline]
4. Meyer S, Fergusson WD, Whetton AD, et al. Amplification and translocation of 3q26 with overexpression of EVI1 in Fanconi anemia-derived childhood acute myeloid leukemia with biallelic FANCD1/BRCA2 disruption. Genes Chromosomes Cancer 2007;46:359-372.Â [CrossRef][ISI][Medline]
5. Greaves MF, Wiemels J. Origins of chromosome translocations in childhood leukaemia. Nat Rev Cancer 2003;3:639-649.Â [CrossRef][ISI][Medline]
6. Mitelman F, Johansson B, Mertens F. The impact of translocations and gene fusions on cancer causation. Nat Rev Cancer 2007;7:233-245.Â [CrossRef][ISI][Medline]
7. Hughes T, Deininger M, Hochhaus A, et al. Monitoring CML patients responding to treatment with tyrosine kinase inhibitors: review and recommendations for harmonizing current methodology for detecting BCR-ABL transcripts and kinase domain mutations and for expressing results. Blood 2006;108:28-37.Â [CrossRef][ISI][Medline]
8. Rabbitts TH. Chromosomal translocations in human cancer. Nature 1994;372:143-149.Â [CrossRef][ISI][Medline]
9. Rowley JD. The critical role of chromosome translocations in human leukemias. Annu Rev Genet 1998;32:495-519.Â [CrossRef][ISI][Medline]
10. Meyerson M. Cancer: broken genes in solid tumours. Nature 2007;448:545-546.Â [CrossRef][ISI][Medline]
11. Shaffer DR, Pandolfi PP. Breaking the rules of cancer. Nat Med 2006;12:14-15.Â [CrossRef][ISI][Medline]
12. Nowell PC, Hungerford DA. Chromosome studies on normal and leukemic human leukocytes. J Natl Cancer Inst 1960;25:85-109.Â [ISI][Medline]
13. Rowley JD. A new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and Giemsa staining. Nature 1973;243:290-293.Â [CrossRef][ISI][Medline]
14. de Klein A, van Kessel AG, Grosveld G, et al. A cellular oncogene is translocated to the Philadelphia chromosome in chronic myelocytic leukaemia. Nature 1982;300:765-767.Â [CrossRef][ISI][Medline]
15. Groffen J, Stephenson JR, Heisterkamp N, de Klein A, Bartram CR, Grosveld G. Philadelphia chromosomal breakpoints are clustered within a limited region, bcr, on chromosome 22. Cell 1984;36:93-99.Â [CrossRef][ISI][Medline]
16. Heisterkamp N, Stephenson JR, Groffen J, et al. Localization of the c-ab1 oncogene adjacent to a translocation break point in chronic myelocytic leukaemia. Nature 1983;306:239-242.Â [CrossRef][ISI][Medline]
17. Goldman JM, Melo JV. Chronic myeloid leukemia -- advances in biology and new approaches to treatment. N Engl J Med 2003;349:1451-1464.Â [FreeÂ FullÂ Text]
18. Deininger M, Buchdunger E, Druker BJ. The development of imatinib as a therapeutic agent for chronic myeloid leukemia. Blood 2005;105:2640-2653.Â [CrossRef][ISI][Medline]
19. Druker BJ, Guilhot F, O'Brien SG, et al. Five-year follow-up of patients receiving imatinib for chronic myeloid leukemia. N Engl J Med 2006;355:2408-2417.Â [FreeÂ FullÂ Text]
20. Gorre ME, Mohammed M, Ellwood K, et al. Clinical resistance to STI-571 cancer therapy caused by BCR-ABL gene mutation or amplification. Science 2001;293:876-880.Â [FreeÂ FullÂ Text]
21. Kantarjian H, Giles F, Wunderle L, et al. Nilotinib in imatinib-resistant CML and Philadelphia chromosome-positive ALL. N Engl J Med 2006;354:2542-2551.Â [FreeÂ FullÂ Text]
22. Shah NP, Tran C, Lee FY, Chen P, Norris D, Sawyers CL. Overriding imatinib resistance with a novel ABL kinase inhibitor. Science 2004;305:399-401.Â [FreeÂ FullÂ Text]
23. Talpaz M, Shah NP, Kantarjian H, et al. Dasatinib in imatinib-resistant Philadelphia chromosome-positive leukemias. N Engl J Med 2006;354:2531-2541.Â [FreeÂ FullÂ Text]
24. Weisberg E, Manley PW, Breitenstein W, et al. Characterization of AMN107, a selective inhibitor of native and mutant Bcr-Abl. Cancer Cell 2005;7:129-141. [Erratum, Cancer Cell 2005;7:399.]Â [CrossRef][ISI][Medline]
25. Krause DS, Van Etten RA. Tyrosine kinases as targets for cancer therapy. N Engl J Med 2005;353:172-187.Â [FreeÂ FullÂ Text]
26. Apperley JF, Gardembas M, Melo JV, et al. Response to imatinib mesylate in patients with chronic myeloproliferative diseases with rearrangements of the platelet-derived growth factor receptor beta. N Engl J Med 2002;347:481-487.Â [FreeÂ FullÂ Text]
27. David M, Cross NC, Burgstaller S, et al. Durable responses to imatinib in patients with PDGFRB fusion gene-positive and BCR-ABL-negative chronic myeloproliferative disorders. Blood 2007;109:61-64.Â [CrossRef][ISI][Medline]
28. Lichter P, Ward DC. Is non-isotopic in situ hybridization finally coming of age? Nature 1990;345:93-94.Â [CrossRef][ISI][Medline]
29. Baccarani M, Cilloni D, Rondoni M, et al. The efficacy of imatinib mesylate in patients with FIP1L1-PDGFRalpha-positive hypereosinophilic syndrome: results of a multicenter prospective study. Haematologica 2007;92:1173-1179.Â [CrossRef][ISI][Medline]
30. Cools J, DeAngelo DJ, Gotlib J, et al. A tyrosine kinase created by fusion of the PDGFRA and FIP1L1 genes as a therapeutic target of imatinib in idiopathic hypereosinophilic syndrome. N Engl J Med 2003;348:1201-1214.Â [FreeÂ FullÂ Text]
31. Graux C, Cools J, Melotte C, et al. Fusion of NUP214 to ABL1 on amplified episomes in T-cell acute lymphoblastic leukemia. Nat Genet 2004;36:1084-1089.Â [CrossRef][ISI][Medline]
32. Soda M, Choi YL, Enomoto M, et al. Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer. Nature 2007;448:561-566.Â [CrossRef][ISI][Medline]
33. Delattre O, Zucman J, Plougastel B, et al. Gene fusion with an ETS DNA-binding domain caused by chromosome translocation in human tumours. Nature 1992;359:162-165.Â [CrossRef][ISI][Medline]
34. Sorensen PH, Lessnick SL, Lopez-Terrada D, Liu XF, Triche TJ, Denny CT. A second Ewing's sarcoma translocation, t(21;22), fuses the EWS gene to another ETS-family transcription factor, ERG. Nat Genet 1994;6:146-151.Â [CrossRef][ISI][Medline]
35. Owen LA, Lessnick SL. Identification of target genes in their native cellular context: an analysis of EWS/FLI in Ewing's sarcoma. Cell Cycle 2006;5:2049-2053.Â [ISI][Medline]
36. Riggi N, Stamenkovic I. The biology of Ewing sarcoma. Cancer Lett 2007;254:1-10.Â [CrossRef][ISI][Medline]
37. Darnell JE Jr. Transcription factors as targets for cancer therapy. Nat Rev Cancer 2002;2:740-749.Â [CrossRef][ISI][Medline]
38. MrÃ³zek K, Heerema NA, Bloomfield CD. Cytogenetics in acute leukemia. Blood Rev 2004;18:115-136.Â [CrossRef][ISI][Medline]
39. Licht JD, Sternberg DW. The molecular pathology of acute myeloid leukemia. Hematology Am Soc Hematol Educ Program 2005:137-42.
40. Sanz MA. Treatment of acute promyelocytic leukemia. Hematology Am Soc Hematol Educ Program 2006:147-55.
41. Scaglioni PP, Pandolfi PP. The theory of APL revisited. Curr Top Microbiol Immunol 2007;313:85-100.Â [CrossRef][ISI][Medline]
42. Wang ZY, Chen Z. Acute promyelocytic leukemia: from highly fatal to highly curable. Blood 2008;111:2505-2515.Â [CrossRef][ISI][Medline]
43. KÃ¼ppers R. Mechanisms of B-cell lymphoma pathogenesis. Nat Rev Cancer 2005;5:251-262.Â [CrossRef][ISI][Medline]
44. O'Neil J, Look AT. Mechanisms of transcription factor deregulation in lymphoid cell transformation. Oncogene 2007;26:6838-6849.Â [CrossRef][ISI][Medline]
45. Perner S, Demichelis F, Beroukhim R, et al. TMPRSS2:ERG fusion-associated deletions provide insight into the heterogeneity of prostate cancer. Cancer Res 2006;66:8337-8341.Â [FreeÂ FullÂ Text]
46. Tomlins SA, Rhodes DR, Perner S, et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 2005;310:644-648.Â [FreeÂ FullÂ Text]
47. Liu W, Ewing CM, Chang BL, et al. Multiple genomic alterations on 21q22 predict various TMPRSS2/ERG fusion transcripts in human prostate cancers. Genes Chromosomes Cancer 2007;46:972-980.Â [CrossRef][ISI][Medline]
48. Helgeson BE, Tomlins SA, Shah N, et al. Characterization of TMPRSS2:ETV5 and SLC45A3:ETV5 gene fusions in prostate cancer. Cancer Res 2008;68:73-80.Â [FreeÂ FullÂ Text]
49. Tomlins SA, Laxman B, Dhanasekaran SM, et al. Distinct classes of chromosomal rearrangements create oncogenic ETS gene fusions in prostate cancer. Nature 2007;448:595-599.Â [CrossRef][ISI][Medline]
50. Tomlins SA, Mehra R, Rhodes DR, et al. TMPRSS2:ETV4 gene fusions define a third molecular subtype of prostate cancer. Cancer Res 2006;66:3396-3400.Â [FreeÂ FullÂ Text]
51. Demichelis F, Fall K, Perner S, et al. TMPRSS2:ERG gene fusion associated with lethal prostate cancer in a watchful waiting cohort. Oncogene 2007;26:4596-4599. [Erratum, Oncogene 2007;26:5692.]Â [CrossRef][ISI][Medline]
52. Laxman B, Morris DS, Yu J, et al. A first-generation multiplex biomarker analysis of urine for the early detection of prostate cancer. Cancer Res 2008;68:645-649.Â [FreeÂ FullÂ Text]
53. Nam RK, Sugar L, Yang W, et al. Expression of the TMPRSS2:ERG fusion gene predicts cancer recurrence after surgery for localised prostate cancer. Br J Cancer 2007;97:1690-1695.Â [CrossRef][ISI][Medline]
54. Perner S, Mosquera JM, Demichelis F, et al. TMPRSS2-ERG fusion prostate cancer: an early molecular event associated with invasion. Am J Surg Pathol 2007;31:882-888.Â [CrossRef][ISI][Medline]
55. Kim SY, Hahn WC. Cancer genomics: integrating form and function. Carcinogenesis 2007;28:1387-1392.Â [FreeÂ FullÂ Text]
56. Hudis CA. Trastuzumab -- mechanism of action and use in clinical practice. N Engl J Med 2007;357:39-51.Â [FreeÂ FullÂ Text]
57. Slamon DJ, Godolphin W, Jones LA, et al. Studies of the HER-2/neu proto-oncogene in human breast and ovarian cancer. Science 1989;244:707-712.Â [FreeÂ FullÂ Text]
58. Garraway LA, Widlund HR, Rubin MA, et al. Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature 2005;436:117-122.Â [CrossRef][ISI][Medline]
59. Kim M, Gans JD, Nogueira C, et al. Comparative oncogenomics identifies NEDD9 as a melanoma metastasis gene. Cell 2006;125:1269-1281.Â [CrossRef][ISI][Medline]
60. Zender L, Spector MS, Xue W, et al. Identification and validation of oncogenes in liver cancer using an integrative oncogenomic approach. Cell 2006;125:1253-1267.Â [CrossRef][ISI][Medline]
61. Chin K, DeVries S, Fridlyand J, et al. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 2006;10:529-541.Â [CrossRef][ISI][Medline]
62. Yao J, Weremowicz S, Feng B, et al. Combined cDNA array comparative genomic hybridization and serial analysis of gene expression analysis of breast tumor progression. Cancer Res 2006;66:4065-4078.Â [FreeÂ FullÂ Text]
63. Dutt A, Beroukhim R. Single nucleotide polymorphism array analysis of cancer. Curr Opin Oncol 2007;19:43-49.Â [ISI][Medline]
64. Pinkel D, Albertson DG. Array comparative genomic hybridization and its applications in cancer. Nat Genet 2005;37:Suppl:S11-S17.Â [CrossRef][ISI][Medline]
65. Holst F, Stahl PR, Ruiz C, et al. Estrogen receptor alpha (ESR1) gene amplification is frequent in breast cancer. Nat Genet 2007;39:655-660.Â [CrossRef][Medline]
66. Albertson D. Conflicting evidence on the frequency of ESR1 amplification in breast cancer. Nat Genet 2008;40:821-822.Â [CrossRef][ISI][Medline]
67. Weir BA, Woo MS, Getz G, et al. Characterizing the cancer genome in lung adenocarcinoma. Nature 2007;450:893-898.Â [CrossRef][ISI][Medline]
68. Sharma SV, Bell DW, Settleman J, Haber DA. Epidermal growth factor receptor mutations in lung cancer. Nat Rev Cancer 2007;7:169-181.Â [CrossRef][ISI][Medline]
69. Engelman JA, Zejnullahu K, Mitsudomi T, et al. MET amplification leads to gefitinib resistance in lung cancer by activating ERBB3 signaling. Science 2007;316:1039-1043.Â [FreeÂ FullÂ Text]
70. Sansal I, Sellers WR. The biology and clinical relevance of the PTEN tumor suppressor pathway. J Clin Oncol 2004;22:2954-2963.Â [FreeÂ FullÂ Text]
71. Cloughesy TF, Yoshimoto K, Nghiemphu P, et al. Antitumor activity of rapamycin in a Phase I trial for patients with recurrent PTEN-deficient glioblastoma. PLoS Med 2008;5:e8-e8.Â [CrossRef][Medline]
72. Neshat MS, Mellinghoff IK, Tran C, et al. Enhanced sensitivity of PTEN-deficient tumors to inhibition of FRAP/mTOR. Proc Natl Acad Sci U S A 2001;98:10314-10319.Â [FreeÂ FullÂ Text]
73. Yilmaz OH, Valdez R, Theisen BK, et al. Pten dependence distinguishes haematopoietic stem cells from leukaemia-initiating cells. Nature 2006;441:475-482.Â [CrossRef][ISI][Medline]
74. Hinds PW, Weinberg RA. Tumor suppressor genes. Curr Opin Genet Dev 1994;4:135-141.Â [CrossRef][Medline]
75. Knudson AG. Two genetic hits (more or less) to cancer. Nat Rev Cancer 2001;1:157-162.Â [CrossRef][Medline]
76. Okawa ER, Gotoh T, Manne J, et al. Expression and sequence analysis of candidates for the 1p36.31 tumor suppressor gene deleted in neuroblastomas. Oncogene 2008;27:803-810.Â [CrossRef][ISI][Medline]
77. Zabarovsky ER, Lerman MI, Minna JD. Tumor suppressor genes on chromosome 3p involved in the pathogenesis of lung and other cancers. Oncogene 2002;21:6915-6935.Â [CrossRef][ISI][Medline]
78. Curtiss NP, Bonifas JM, Lauchle JO, et al. Isolation and analysis of candidate myeloid tumor suppressor genes from a commonly deleted segment of 7q22. Genomics 2005;85:600-607.Â [CrossRef][ISI][Medline]
79. DÃ¶hner K, Brown J, Hehmann U, et al. Molecular cytogenetic characterization of a critical region in bands 7q35-q36 commonly deleted in malignant myeloid disorders. Blood 1998;92:4031-4035.Â [ISI][Medline]
80. DÃ¶hner H, Stilgenbauer S, Benner A, et al. Genomic aberrations and survival in chronic lymphocytic leukemia. N Engl J Med 2000;343:1910-1916.Â [FreeÂ FullÂ Text]
81. Cairncross G, Berkey B, Shaw E, et al. Phase III trial of chemotherapy plus radiotherapy compared with radiotherapy alone for pure and mixed anaplastic oligodendroglioma: Intergroup Radiation Therapy Oncology Group Trial 9402. J Clin Oncol 2006;24:2707-2714.Â [FreeÂ FullÂ Text]
82. Westbrook TF, Martin ES, Schlabach MR, et al. A genetic screen for candidate tumor suppressors identifies REST. Cell 2005;121:837-848.Â [CrossRef][ISI][Medline]
83. Mullighan CG, Goorha S, Radtke I, et al. Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature 2007;446:758-764.Â [CrossRef][ISI][Medline]
84. Mullighan CG, Miller CB, Radtke I, et al. BCR-ABL1 lymphoblastic leukaemia is characterized by the deletion of Ikaros. Nature 2008;453:110-114.Â [CrossRef][ISI][Medline]
85. Fodde R, Smits R. Cancer biology: a matter of dosage. Science 2002;298:761-763.Â [FreeÂ FullÂ Text]
86. Ebert BL, Pretz J, Bosco J, et al. Identification of RPS14 as a 5q- syndrome gene by RNA interference screen. Nature 2008;451:335-339.Â [CrossRef][ISI][Medline]
87. Boultwood J, Fidler C, Strickson AJ, et al. Narrowing and genomic annotation of the commonly deleted region of the 5q- syndrome. Blood 2002;99:4638-4641.Â [CrossRef][ISI][Medline]
88. List A, Dewald G, Bennett J, et al. Lenalidomide in the myelodysplastic syndrome with chromosome 5q deletion. N Engl J Med 2006;355:1456-1465.Â [FreeÂ FullÂ Text]
89. Rivera MN, Kim WJ, Wells J, et al. An X chromosome gene, WTX, is commonly inactivated in Wilms tumor. Science 2007;315:642-645.Â [FreeÂ FullÂ Text]
90. Calin GA, Sevignani C, Dumitru CD, et al. Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc Natl Acad Sci U S A 2004;101:2999-3004.Â [FreeÂ FullÂ Text]
91. Zhang L, Huang J, Yang N, et al. MicroRNAs exhibit high frequency genomic alterations in human cancer. Proc Natl Acad Sci U S A 2006;103:9136-9141.Â [FreeÂ FullÂ Text]
92. Calin GA, Dumitru CD, Shimizu M, et al. Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci U S A 2002;99:15524-15529.Â [FreeÂ FullÂ Text]
93. Cimmino A, Calin GA, Fabbri M, et al. miR-15 and miR-16 induce apoptosis by targeting BCL2. Proc Natl Acad Sci U S A 2005;102:13944-13949. [Erratum, Proc Natl Acad Sci U S A 2006;103:2464.]Â [FreeÂ FullÂ Text]