Review

# Cancer Genome Landscapes

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Science  29 Mar 2013:
Vol. 339, Issue 6127, pp. 1546-1558
DOI: 10.1126/science.1235122

## Abstract

Over the past decade, comprehensive sequencing efforts have revealed the genomic landscapes of common forms of human cancer. For most cancer types, this landscape consists of a small number of “mountains” (genes altered in a high percentage of tumors) and a much larger number of “hills” (genes altered infrequently). To date, these studies have revealed ~140 genes that, when altered by intragenic mutations, can promote or “drive” tumorigenesis. A typical tumor contains two to eight of these “driver gene” mutations; the remaining mutations are passengers that confer no selective growth advantage. Driver genes can be classified into 12 signaling pathways that regulate three core cellular processes: cell fate, cell survival, and genome maintenance. A better understanding of these pathways is one of the most pressing needs in basic cancer research. Even now, however, our knowledge of cancer genomes is sufficient to guide the development of more effective approaches for reducing cancer morbidity and mortality.

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Ten years ago, the idea that all of the genes altered in cancer could be identified at base-pair resolution would have seemed like science fiction. Today, such genome-wide analysis, through sequencing of the exome (click hlighlighted terms for definitions used in this Review) or of the whole genome, is routine.

### Challenges

One challenge of genome-based medicine in oncology is already apparent from the opportunities described above: All of the clinically approved drugs that target the products of genetically altered genes are directed against kinases. One reason for this is that kinases are relatively easy to target with small molecules and have been extensively studied at the biochemical, structural, and physiologic levels (129). But another reason has far deeper ramifications. The vast majority of drugs on the market today, for cancer or other diseases, inhibit the actions of their protein targets. This inhibition occurs because the drugs interfere with the protein’s enzymatic activity (such as the phosphorylation catalyzed by kinases) or with the binding of the protein to a small ligand (such as with G protein–coupled receptors). Only 31 of the oncogenes listed in tables S2 and S3 have enzymatic activities that are targetable in this manner. Many others participate in protein complexes, involving large interfaces and numerous weak interactions. Inhibiting the function of such proteins with small drugs is notoriously difficult because small compounds can only inhibit one of these interactions (130, 131).

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### Highlights

1. Most human cancers are caused by two to eight sequential alterations that develop over the course of 20 to 30 years.

2. Each of these alterations directly or indirectly increases the ratio of cell birth to cell death; that is, each alteration causes a selective growth advantage to the cell in which it resides.

3. The evidence to date suggests that there are ~140 genes whose intragenic mutations contribute to cancer (so-called Mut-driver genes). There are probably other genes (Epi-driver genes) that are altered by epigenetic mechanisms and cause a selective growth advantage, but the definitive identification of these genes has been challenging.

4. The known driver genes function through a dozen signaling pathways that regulate three core cellular processes: cell fate determination, cell survival, and genome maintenance.

5. Every individual tumor, even of the same histopathologic subtype as another tumor, is distinct with respect to its genetic alterations, but the pathways affected in different tumors are similar.

6. Genetic heterogeneity among the cells of an individual tumor always exists and can impact the response to therapeutics.

7. In the future, the most appropriate management plan for a patient with cancer will be informed by an assessment of the components of the patient’s germline genome and the genome of his or her tumor.

8. The information from cancer genome studies can also be exploited to improve methods for prevention and early detection of cancer, which will be essential to reduce cancer morbidity and mortality.

Though one can at least imagine the development of drugs that inhibit nonenzymatic protein functions, the second challenge evident from table S2 poses even greater difficulties: A large fraction of the Mut-driver genes encode tumor suppressors. Drugs generally interfere with protein function; they cannot, in general, replace the function of defective genes such as those resulting from mutations in tumor suppressor genes. Unfortunately, tumor suppressor gene–inactivating mutations predominate over oncogene-activating mutations in the most common solid tumors: Few individual tumors contain more than one oncogene mutation (Fig. 5).

The relatively small number of oncogene mutations in tumors is important in light of the intrametastatic heterogeneity described earlier. To circumvent the inevitable development of resistance to targeted therapies, it will likely be necessary to treat patients with two or more drugs. The probability that a single cancer cell within a large metastatic lesion will be resistant to two agents that target two independent pathways is exponentially less than the probability that the cell will be resistant to a single agent. However, if the cancer cell does not contain more than one targetable genetic alteration (i.e., an oncogene mutation), then this combination strategy is not feasible.

Given the paucity of oncogene alterations in common solid tumors and these principles, can targeted therapeutic approaches ever be expected to induce long-term remissions, even cures, rather than the short-term remissions now being achieved? The saviors are pathways; every tumor suppressor gene inactivation is expected to result in the activation of some growth-promoting signal downstream of the pathway. An example is provided by PTEN mutations: Inactivation of the tumor suppressor gene PTEN results in activation of the AKT kinase (Fig. 8). Similarly, inactivation of the tumor suppressor gene CDKN2A results in activation of kinases, such as cyclin-dependent kinase 4, that promote cell cycle traverse (132). Furthermore, inactivation of tumor suppressor gene APC results in constitutive activity of oncogenes such as CTNNB1 and CMYC (133135).

We believe that greater knowledge of these pathways and the ways in which they function is the most pressing need in basic cancer research. Successful research on this topic should allow the development of agents that target, albeit indirectly, defective tumor suppressor genes. Indeed, there are already examples of such indirect targeting. Inactivating mutations of the tumor suppressor genes BRCA1 or BRCA2 lead to activation of downstream pathways required to repair DNA damage in the absence of BRCA function. Thus, cancer cells with defects in BRCA1 or BRCA2 are more susceptible to DNA damaging agents or to drugs that inhibit enzymes that facilitate the repair of DNA damage such as PARP [poly(adenosine diphosphate–ribose) polymerase] (136). PARP inhibitors have shown encouraging results in clinical trials when used in patients whose tumors have inactivating mutations of BRCA genes (137).

Further progress in this area will require more detailed information about the signaling pathways through which cancer genes function in human cancer cells, as well as in model organisms. One of the lessons of molecular biology over the past two decades is that pathway functions are different, depending on the organism, cell type, and precise genetic alterations in that cell (138). A pertinent example of this principle is provided by results of treatment with drugs inhibiting mutant BRAF kinase activity. In the majority of patients with melanomas harboring (V600E; V, Val; E, Glu) mutations in the BRAF gene, these drugs induce dramatic (though transient) remissions (108). But the same drugs have no therapeutic effect in colorectal cancer patients harboring the identical BRAF mutations (139). This observation has been attributed to the expression of EGFR, which occurs in some colorectal cancers but not in melanoma and is thought to circumvent the growth-inhibitory effects of the BRAF inhibitors. With this example in mind, no one should be surprised that a new drug that works well in an engineered tumor in mice fails in human trials; the organism is different, the cell type is usually different, and the precise genetic constitutions are always different. The converse of this statement—that a drug that fails in animal trials will not necessarily fail in human trials—has important practical consequences. In our view, if the biochemical and conceptual bases for a drug’s actions are solid and the drug is shown to be safe in animals, then a human trial may be warranted, even if it does not shrink tumors in mice.

### Genome-Based Medicines of the Future

Cancer genomes can also be exploited for the development of more effective immunotherapies. As noted above, typical solid tumors contain 30 to 70 mutations that alter the amino acid sequences of the proteins encoded by the affected genes. Each of these alterations is foreign to the immune system, as none have been encountered during embryonic or postnatal life. Therefore, these alterations, in principle, provide a “holy grail” for tumor immunology: truly tumor-specific antigens. These antigens could be incorporated into any of the numerous platforms that already exist for the immunotherapy of cancer. These include administration of vaccines containing the mutant peptide, viruses encoding the mutant peptides on their surfaces, dendritic cells presenting the mutated peptide, and antibodies or T cells with reactivity directed against the mutant peptides (140).

To realize these sorts of therapeutics, several conditions must be met. First, the mutant protein must be expressed. As cancer cells generally express about half of the proteins that are encoded by the human genome (141), this condition is not limiting. Second, as most proteins affected by mutations are intracellular, these mutations will not be visible to the immune system unless the mutant residue is presented in the context of a human leukocyte antigen (HLA) protein. Based on in silico analyses of binding affinities, it has been estimated that a typical breast or colorectal cancer contains 7 to 10 mutant proteins that can bind to an individual patient’s HLA type (142). These theoretical predictions have recently gained experimental support. Studies of mouse tumors have identified mutant genes and shown that the corresponding peptides can induce antitumor immunity when administered as vaccines (143). Moreover, clinical trials of brain cancer patients immunized against a mutant peptide have yielded encouraging results (144).

As with all cancer therapies that are attractive in concept, obstacles abound in practice. If a tumor expresses a mutant protein that is recognizable as foreign, why has the host immune system not eradicated that tumor already? Indeed, immunoediting in cancers has been shown to exist, resulting in the down-regulation or absence of mutant epitopes that should have, and perhaps did, elicit an immune response during tumor development (145, 146). Additionally, tumors can lose immunogenicity through a variety of genetic alterations, thereby precluding the presentation of epitopes that would otherwise be recognized as foreign (147). Though these theoretical limitations are disheartening, recent studies on immune regulation in humans portend cautious optimism (148, 149).

### Other Ways to Reduce Morbidity and Mortality Through Knowledge of Cancer Genomics

When we think about eradicating cancer, we generally think about curing advanced cases—those that cannot be cured by surgery alone because they have already metastasized. This is a curious way of thinking about this disease. When we think of cardiovascular or infectious diseases, we first consider ways to prevent them rather than drugs to cure their most advanced forms. Today, we are in no better position to cure polio or massive myocardial infarctions than we were a thousand years ago. But we can prevent these diseases entirely (vaccines), reduce incidence (dietary changes, statins), or mitigate severity (stents, thrombolytic agents) and thereby make a major impact on morbidity and mortality.

This focus on curing advanced cancers might have been reasonable 50 years ago, when the molecular pathogenesis of cancers was mysterious and when chemotherapeutic agents against advanced cancers were showing promise. But this mindset is no longer acceptable. We now know precisely what causes cancer: a sequential series of alterations in well-defined genes that alter the function of a limited number of pathways. Moreover, we know that this process takes decades to develop and that the incurable stage, metastasis, occurs only a few years before death. In other words, of the one million people that will die from cancer this year, the vast majority will die only because their cancers were not detected in the first 90% of the cancers’ lifetimes, when they were amenable to the surgeons’ scalpel.

This new knowledge of cancer (Box 2) has reinvigorated the search for cures for advanced cancers, but has not yet permeated other fields of applied cancer research. A common and limited set of driver genes and pathways is responsible for most common forms of cancer (table S2); these genes and pathways offer distinct potential for early diagnosis. The genes themselves, the proteins encoded by these genes, and the end products of their pathways are, in principle, detectable in many ways, including analyses of relevant body fluids, such as urine for genitourinary cancers, sputum for lung cancers, and stool for gastrointestinal cancers (150). Equally exciting are the possibilities afforded by molecular imaging, which not only indicate the presence of a cancer but also reveal its precise location and extent. Additionally, research into the relationship between particular environmental influences (diet and lifestyle) and the genetic alterations in cancer is sparse, despite its potential for preventative measures.

The reasons that society invests so much more in research on cures for advanced cancers than on prevention or early detection are complex. Economic issues play a part: New drugs are far more lucrative for industry than new tests, and large individual costs for treating patients with advanced disease have become acceptable, even in developing countries (151). From a technical standpoint, the development of new and improved methods for early detection and prevention will not be easy, but there is no reason to assume that it will be more difficult than the development of new therapies aimed at treating widely metastatic disease.

Our point is not that strenuous efforts to develop new therapies for advanced cancer patients should be abandoned. These will always be required, no matter our arsenal of early detection or preventative measures. Instead, we are suggesting that “plan A” should be prevention and early detection, and “plan B” (therapy for advanced cancers) should be necessary only when plan A fails. To make plan A viable, government and philanthropic organizations must dedicate a much greater fraction of their resources to this cause, with long-term considerations in mind. We believe that cancer deaths can be reduced by more than 75% in the coming decades (152), but that this reduction will only come about if greater efforts are made toward early detection and prevention.

## Glossary

Adenoma: A benign tumor composed of epithelial cells.

Alternative lengthening of telomeres (ALT): A process of maintaining telomeres independent of telomerase, the enzyme normally responsible for telomere replication.

Amplification: A genetic alteration producing a large number of copies of a small segment (less than a few megabases) of the genome.

Angiogenesis: the process of forming vascular conduits, including veins, arteries, and lymphatics.

Benign tumor: An abnormal proliferation of cells driven by at least one mutation in an oncogene or tumor suppressor gene. These cells are not invasive (i.e., they cannot penetrate the basement membrane lining them), which distinguishes them from malignant cells.

Carcinoma: A type of malignant tumor composed of epithelial cells.

Clonal mutation: A mutation that exists in the vast majority of the neoplastic cells within a tumor.

Driver gene mutation (driver): A mutation that directly or indirectly confers a selective growth advantage to the cell in which it occurs.

Driver gene: A gene that contains driver gene mutations (Mut-Driver gene) or is expressed aberrantly in a fashion that confers a selective growth advantage (Epi-Driver gene).

Epi-driver gene: A gene that is expressed aberrantly in cancers in a fashion that confers a selective growth advantage.

Epigenetic: Changes in gene expression or cellular phenotype caused by mechanisms other than changes in the DNA sequence.

Exome: The collection of exons in the human genome. Exome sequencing generally refers to the collection of exons that encode proteins.

Gatekeeper: A gene that, when mutated, initiates tumorigenesis. Examples include RB, mutations of which initiate retinoblastomas, and VHL, whose mutations initiate renal cell carcinomas.

Germline genome: An individual’s genome, as inherited from their parents.

Germline variants: Variations in sequences observed in different individuals. Two randomly chosen individuals differ by ~20,000 genetic variations distributed throughout the exome.

Human leukocyte antigen (HLA): A protein encoded by genes that determine an individual’s capacity to respond to specific antigens or reject transplants from other individuals.

Homozygous deletion: Deletion of both copies of a gene segment (the one inherited from the mother, as well as that inherited from the father).

Indel: A mutation due to small insertion or deletion of one or a few nucleotides.

Karyotype: Display of the chromosomes of a cell on a microscopic slide, used to evaluate changes in chromosome number as well as structural alterations of chromosomes.

Kinase: A protein that catalyzes the addition of phosphate groups to other molecules, such as proteins or lipids. These proteins are essential to nearly all signal transduction pathways.

Liquid tumors: Tumors composed of hematopoietic (blood) cells, such as leukemias. Though lymphomas generally form solid masses in lymph nodes, they are often classified as liquid tumors because of their derivation from hematopoietic cells and ability to travel through lymphatics.

Malignant tumor: An abnormal proliferation of cells driven by mutations in oncogenes or tumor suppressor genes that has already invaded their surrounding stroma. It is impossible to distinguish an isolated benign tumor cell from an isolated malignant tumor cell. This distinction can be made only through examination of tissue architecture.

Metastatic tumor: A malignant tumor that has migrated away from its primary site, such as to draining lymph nodes or another organ.

Methylation: Covalent addition of a methyl group to a protein, DNA, or other molecule.

Missense mutation: A single-nucleotide substitution (e.g., C to T) that results in an amino acid substitution (e.g., histidine to arginine).

Mut-driver gene: A gene that contains driver gene mutations.

Nonsense mutation: A single-nucleotide substitution (e.g., C to T) that results in the production of a stop codon.

Nonsynonymous mutation: A mutation that alters the encoded amino acid sequence of a protein. These include missense, nonsense, splice site, translation start, translation stop, and indel mutations.

Oncogene: A gene that, when activated by mutation, increases the selective growth advantage of the cell in which it resides.

Passenger mutation (passenger): A mutation that has no direct or indirect effect on the selective growth advantage of the cell in which it occurred.

Primary tumor: The original tumor at the site where tumor growth was initiated. This can be defined for solid tumors, but not for liquid tumors.

Promoter: A region within or near the gene that helps regulate its expression.

Rearrangement: A mutation that juxtaposes nucleotides that are normally separated, such as those on two different chromosomes.

Selective growth advantage (s): The difference between birth and death in a cell population. In normal adult cells in the absence of injury, s = 0.000000.

Self-renewing tissues: Tissues whose cells normally repopulate themselves, such as those lining the gastrointestinal or urogenital tracts, as well as blood cells.

Single-base substitution (SBS): A single-nucleotide substitution (e.g., C to T) relative to a reference sequence or, in the case of somatic mutations, relative to the germline genome of the person with a tumor.

Solid tumors: Tumors that form discrete masses, such as carcinomas or sarcomas.

Somatic mutations: Mutations that occur in any non–germ cell of the body after conception, such as those that initiate tumorigenesis.

Splice sites: Small regions of genes that are juxtaposed to the exons and direct exon splicing.

Stem cell: An immortal cell that can repopulate a particular cell type.

Subclonal mutation: A mutation that exists in only a subset of the neoplastic cells within a tumor.

Translocation: A specific type of rearrangement where regions from two nonhomologous chromosomes are joined.

Tumor suppressor gene: A gene that, when inactivated by mutation, increases the selective growth advantage of the cell in which it resides.

Untranslated regions: Regions within the exons at the 5′ and 3′ ends of the gene that do not encode amino acids.

## References and Notes

1. Acknowledgments: We thank M. Nowak and I. Bozic for critical reading of the manuscript, S. Gabelli for assisting with the production of Fig. 8, and A. Dixon, V. Ferranta, and E. Cook for artwork. This work was supported by The Virginia and D.K. Ludwig Fund for Cancer Research; The Lustgarten Foundation for Pancreatic Cancer Research; and NIH grants CA 43460, CA 47345, CA 62924, and CA 121113. All authors are Founding Scientific Advisors of Personal Genome Diagnostics (PGDx), a company focused on the identification of genetic alterations in human cancer for diagnostic and therapeutic purposes. All authors are also members of the Scientific Advisory Board of Inostics, a company that is developing technologies for the molecular diagnosis of cancer. All authors own stock in PGDx and Inostics. The terms of these arrangements are being managed by Johns Hopkins University, in accordance with their conflict-of-interest policies.
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