Methods such as those we have described above shone a spotlight on a set of can-cer-critical genes that were identified in a piecemeal fashion. Meanwhile, the rest of the cancer cell genome remained in darkness: it was a mystery how many other mutations might lurk there, of what types, in which varieties of cancer, at what frequencies, with what variations from patient to patient, and with what consequences. With the sequencing of the human genome and the dramatic advances in DNA sequencing technology (see Panel 8–1, pp. 478–481), it has become possible to see the whole picture—to view cancer cell genomes in their entirety. This transforms our understanding of the disease.
Cancer cell genomes can be scanned systematically in several different ways. At one extreme—the most costly, but no longer prohibitively so—one can determine a tumor’s complete genome sequence. More cheaply, one can focus just on the 21,000 or so genes in the human genome that code for protein (the so-called exome), looking for mutations in the cancer cell DNA that alter the amino acid sequence of the product or prevent its synthesis (Figure 20–23). There are also efficient techniques to survey the genome for regions that have undergone
Figure 20–21 Six ways of losing the remaining good copy of a tumor suppressor gene through a change in DNA sequences. A cell that is defective in only one of its two copies of a tumor suppressor gene—for example, the Rb gene—usually behaves as a normal, healthy cell; the diagrams below show how this cell may lose the function of the other gene copy as well and thereby progress toward cancer. A seventh possibility, frequently encountered with some tumor suppressors, is that the gene may be silenced by an epigenetic change, without alteration of the DNA sequence, as illustrated in Figure 20–22. (After
W.K. Cavenee et al., Nature 305:779–784, 1983. With permission from Macmillan Publishers Ltd.) deletion or duplication, without the need for complete sequence information. The genome can be scanned for epigenetic changes. And finally, alterations in levels of gene expression can be systematically determined by analysis of mRNAs (see Figure 7–3). These approaches generally involve comparing cancer cells with normal controls—ideally, noncancerous cells originating in the same tissue and from the same patient.
Figure 20–22 The pathways leading to loss of tumor suppressor gene function in cancer involve both genetic and epigenetic changes. (A) As indicated, the changes that silence tumor suppressor genes can occur in any order. Both DNA methylation and the packaging of a gene into condensed chromatin can prevent its expression in a way that is inherited when a cell divides (see Figure 4–44).
(B) The frequency of gene silencing by hypermethylation observed in four different types of cancer. The five genes listed at the top can all function as tumor suppressor genes; BRCA1 and hMLH1 affect genome stability and are in the subclass known as genome maintenance genes. ND, no data. (Adapted from M. Esteller et al., Cancer Res. 61:3225–3229, 2001.)