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Vol. 96, Issue 26, 14675-14677, December 21, 1999
Department of Medicine and Cancer Center, University of California,
San Diego, School of Medicine, Veterans Administration Medical Center,
San Diego, CA 92093-0688
In this issue of PNAS, Stoler and
colleagues report that typical sporadic colorectal cancers on average
contain at least 11,000 genomic alterations per cell (1). Furthermore,
they report that the genomic instability responsible for generating
this number of mutations starts very early in the neoplastic process
and can be found in adenomatous polyps, which are known to be the
precursors of cancer in the colon and rectum. Should this conclusion be
emblazoned on the front page of the evening news, or does this serve to
confirm and extend concepts that we already accept? To grasp the
implications of this work, it will be helpful to briefly review the
historical background of genomic instability and place this submission
in that context. To do this, a series of questions must be posed. How
does one measure mutations, and how can one quantitate heterogeneous alterations? Is it possible that tumors simply generate a very large
number of alterations at genomic sequences that are irrelevant to
issues of tumor development? If there are many mutations and only a few
are biologically relevant, how does one determine whether mutations are
important? Let's see.
The Historical Context of Genomic Instability.
It has been known
Commentary
How many mutations does it take to make a tumor?
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References
for most of this century
that cancer is often
associated with visible derangements in the nucleus of the cell. Solid
tumors commonly have duplications, deletions, and rearrangements that
occur at the chromosomal level. These were difficult to categorize,
particularly before the organization of the human nucleus was understood.
How Does One Measure Mutations in a Tumor? The most obvious way to determine the number of point mutations in a cancer would be to sequence the entire normal genome, sequence the DNA from a cancer, and compare them. Because of the large size of the human genome, not to mention the variety of alterations in cancer that are not simple nucleotide substitutions, this is impractical. Furthermore, direct sequencing strategies might not detect many of the hemizygous chromosomal deletions (i.e., LOH events) and would probably miss many of the rearrangements. The identification of a small number of unique cytogenetic rearrangements in specific tumors (such as the Philadelphia chromosome in chronic myelogenous leukemia) led to the hope that a systematic cytogenetic characterization of tumors might permit one to understand the basis of tumor formation. However, the tools of cytogenetics were not sufficiently powerful to tackle the problem.
In 1990, Welsh and McClelland used an arbitrarily primed PCR (AP-PCR) to generate genomic "fingerprints" in bacteria and rice (7). Two years later, Peinado et al. used AP-PCR to characterize genetic alterations in colorectal cancers by comparing the fingerprints of normal tissue with that obtained from the tumors. The arbitrary primer sequences yielded reproducible and unbiased fingerprint patterns from template DNA; they literally threw dice to generate the primer sequences. When the PCR products of normal tissue and cancer were directly compared, they were able to estimate the global extent of genetic gains and losses in a single step. Moreover, this approach permitted the direct cloning of the deleted sequences by using the PCR product of the normal tissue to map the appropriate regions (8). This group, led by Manuel Perucho, made another critical observation (6) that was observed and confirmed in the same general time frame by two other groups (9, 10). In addition to seeing and quantitating chromosomal losses and gains by using AP-PCR, this technique detected subtle length variations in the PCR products in a subset of 12% of cancers that did not have chromosomal gains and losses. Instead, Perucho noted that these tumors had clonal somatic mutations in simple repeated sequences such as mononucleotide (always deletions) and dinucleotide (deletions and insertions) repeats. The unbiased nature of the technique permitted an estimate that tumors carried more than 100,000 such mutations, an astounding conclusion! These tumors did not have the widespread LOH events seen in most other cancers and displayed other distinctive phenotypic and genotypic features. By this observation, a novel pathway to tumorigenesis in 12-20% of cancers was detected, and within a year, the molecular basis of this pathway was definitively traced to inactivation of the human DNA mismatch repair system (11-13). Tumors with this phenotype are now said to have "microsatellite instability" (MSI), and these tumors are characterized by a very large number of single point mutations and in particular the accumulation of length alterations in simple repeated sequences, which are ubiquitous throughout our genome. The discovery of this alternate pathway for tumor development in the cancer fulfilled Loeb's prediction of a mutator phenotype, provided a mechanism to account for this, and showed that some tumors could have an extremely large number of mutations. AP-PCR was initially developed to improve on Southern analysis for LOH events. Continuing along this line, Perucho's group also published a study in 1998 using AP-PCR to compare primary and metastatic colorectal cancers (14). They deduced a molecular karyotype by assigning monochromosomal identities to the DNA fingerprints. They observed that gains of sequences were as frequent as losses in cancer. Gains of sequences from chromosomes 8 and 13 occurred in over 75% of tumors. Moreover, they found that losses of sequences from chromosome 4 were associated with metastasis, predicting the presence of a tumor suppressor gene that influences metastasis on that chromosome.What Mutations Are Important in Tumorigenesis? Most microsatellite sequences occur in introns or between genes; length variations at these loci in the progeny of a cell with microsatellite instability would be biologically irrelevant in most instances. It has subsequently been shown that a critical small number of genes contain simple repetitive sequences in critical coding regions, that insertion/deletion mutations occur in cancers, and that these length variations create frameshifts that inactivate those critical gene products. This last finding provided a biological story. Mutations occur in a large number of sequences throughout the genome, which will alter the products of a much smaller number of genes involved in regulating cell growth, which then accumulate in a stepwise manner in a developing neoplasm. In an interesting tangent, germ-line mutations in the DNA mismatch repair genes were found to be responsible for the hereditary cancer predisposition known as Lynch Syndrome (15).
So, How Many Mutations in a Tumor?
Returning to the work from Anderson's group, in 1997, Basik and
colleagues used an intersimple sequence repeat PCR (INTER-SSR-PCR) to
assess the degree of genomic instability among 57 colon cancers (16).
These investigators used a single PCR primer homologous to dinucleotide
repeats, anchored at the 3' end by two nonrepetitive nucleotides as
illustrated in Fig. 1. They were able to evaluate the
degree of genomic instability by observing the appearance (gains) or
disappearance (losses) of bands when comparing the amplifiable segments
obtained from tumors and matched normal colonic tissues. The use of
this primer has an intrinsic priming bias. Nonetheless, it allowed an
estimate of the number of events that occurred in each tumor cell and a
calculation of a rate of genomic instability, by using the following
formula:
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and this is an issue that bears careful consideration
the
authors reported a range of genomic instability indices that were
similar between sporadic cancers and polyps, including 11 adenomas
(benign neoplasms) and 2 hyperplastic polyps (which are not considered
neoplastic), suggesting that genomic instability is an early event in
multistep carcinogenesis and occurs in one possibly nonneoplastic
lesion.
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What Mechanisms Might Account for Genomic Instability in Non-MSI Cancers? A mechanistic explanation is available to account for MSI in tumors, namely loss of DNA mismatch repair activity. But how does one account for gains and losses (not to mention rearrangements) of large chromosomal segments that are demonstrated by LOH at Southern analysis and have been proposed by results with INTER-SSR-PCR? Several theories have been proposed to account for this common phenomenon. The p53 gene, as "guardian of the genome," was thought to be a candidate for this, but LOH of the wild-type p53 allele occurs as the adenoma becomes malignant in the colon (3, 18). Thus, it occurs too late to also account for CIN in benign neoplasms. Altered mitotic spindle checkpoint genes, such as hBub-1, have been proposed and are mechanistically attractive candidates (19), but the evidence to date indicates that this is a relatively rare event in colorectal neoplasia, and their functional significance remains to be established. Several other genetic alterations have been proposed, but the evidence supporting their role in human cancers remains thin.
A recent candidate with the ability to create chromosomal instability in human epithelial cells is the T antigen, which is a complex viral transforming gene found in the SV40 virus and in two human viruses: JC virus and BK virus. The work of Hahn et al. (2) indicates that T antigen is a candidate-transforming gene in a human cell model, and work from our group has recently demonstrated that JC viral sequences are present in normal human colons, in colon cancers, and in one colon cancer cell line with CIN (20). Understanding all of the varieties of genomic instability remains an unsolved problem and is likely to occupy the attention of cancer researchers for some time to come.| |
Acknowledgements |
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The authors are supported, in part, by the Research Service of the Veteran's Administration Medical Center, by the California Cancer Research Program, and by National Institutes of Health grant CA72851.
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Footnotes |
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See companion article on page 15121.
* To whom reprint requests should be addressed at: 9500 Gillman Drive, La Jolla, CA 92093-0688. E-mail: crboland{at}ucsd.edu.
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Copyright © 1999 by The National Academy of Sciences 0027-8424/99/9614675-3$2.00/0
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