Cancer II: Mutations and Cancer

Cancer Part II-Mutations and Cancer

It is generally believed now that cancer is mostly a genetic disease, caused by an accumulation of mutations in a cell. It’s thought that every gene in the human body probably undergoes billions of mutations during a person’s lifetime. Although there are fairly efficient systems to repair some damaged DNA and to kill cells with damaged DNA that cannot be repaired, it is highly likely that many mutations that occur cannot be repaired and the cell containing them continues to survive and to pass the damaged gene on to its descendants through mitosis. If mutation rates are so high, and cancer is caused by mutation, why don’t more people get cancer? Not everyone dies from cancer and even of those who do, many are quite elderly and have lived a long time before the cancer developed. So why isn't cancer even more prevalent than it is? Several things work in our favor. First of all, most cancers require several mutations in different genes in order to develop, and often both copies of a gene--the maternal and paternal copy--must be mutated to inactivate the protein that is made by the gene. Thus not just one but many mutations in combination are necessary for the development of cancer. Second, not all mutations will affect the function of a gene (i.e., they are in the non-coding region or don’t change the amino acid sequence). Third, many mutations cause a loss of cell viability and thus the cells that acquire these mutations die, so the mutations are not passed on. More important, all these mutations that lead to cancer must happen in the same cell. The human body has several trillion cells. Thus even if every gene is mutated several billion times in our bodies, the odds are that only about one cell is a thousand is mutant for any particular gene. If both copies of the gene must be mutated, then only one cell in a million has both mutations. And if several mutations are required, then the odds become increasingly smaller that any one cell will accumulate all the mutations necessary to make it cancerous. Finally, the body appears to have some mechanisms for detecting and destroying malignant cells, though these are obviously overcome fairly often. In other words, one of the key ingredients in the development of cancer is time, because the longer the organism lives, the more time there is for the necessary combination of mutations to occur.
So what are mutations? How many different kinds can you think of? While we haven’t talked much about the mechanisms of DNA, RNA and protein metabolism in this course, this knowledge underpins much of what we have discussed. In particular the structure of proteins is encoded in the nucleotide sequence of DNA. A particular sequence of nucleotides give rise to a particular sequence of amino acids, and that in turn determines the way that that protein will function. Many changes in the nucleotide sequence will alter the amino acid sequence of the protein, and perhaps will change its function. There are several different forms of mutations, with different causes.
1. Point mutations, where a single nucleotide is altered. This can happen if DNA polymerase mismatches two bases during replication. There are "proofreading" functions that correct most such errors, but about one in a million is not detected and becomes incorporated permanently (or "fixed") in the DNA. Some kinds of chemicals interact with DNA and greatly increase the chance of such mutations--because the chemicals react with the bases in the DNA and alter their structure, which can fool the DNA polymerase into putting an inappropriate base on the opposite strand.
2. Deletions--if all or part of the gene is removed, then of course either no protein or a severely altered protein will be produced. These are usually caused by mistakes in crossing over between homologous chromosome pairs during meiosis (germ cell formation).
3. Gene amplification--for reasons still not well understood, sometimes a gene is copied more than once in the same chromosome so that multiple copies exist. This usually results in overproduction of the protein rather than formation of a defective protein.
4. Chromosomal translocation. Parts of chromosomes can break and rejoin, sometimes with the same chromosome and sometimes with a different chromosome; this latter is called a translocation. Any gene that is at the break and rejoining site can be altered or joined abnormally to another gene or control region (e.g., promotor or enhancer). A large number of human cancers seem to be caused in part by such translocations, and processes that cause chromosome breaks, such as X-rays or cosmic rays, greatly speed up the rate of such translocations.
5. Tumor viruses. Tumor viruses are viruses that as part of their life cycle can insert their genetic material into the DNA of the chromosome of the host cell. Wherever these viruses insert into the host chromosome, (which appears to be a random process--i.e., the virus doesn’t go into any special place in the DNA), they can disrupt a gene. Either they can inactivate it, for example by plunking down in the middle of it, or, conversely, activate it excessively. RNA viruses in particular can activate a normally inactive gene by putting it next to a promoter for one of the viral genes. In some cases the RNA viruses pick up pieces of the host cells when they transcribe new genomic RNA, so that they now have not only viral genes but animal genes as well. Often these animal genes can mutate in the virus because 1. the virus doesn’t need the gene and 2. RNA virus replication is fairly error-prone. Such mutated versions of normal cellular genes sometimes can themselves cause cancer when the virus reinserts the mutated gene into a host cell. For example the src oncogene was first discovered as being essential for a chicken tumor virus--Rous sarcoma virus--to cause tumors in chickens. It has subsequently been shown to be a normal cellular product, a membrane bound tyrosine kinase. Similarly Ras means rat sarcoma--it was originally found when humans acted like viruses--injecting bits of DNA into cells to make them cancerous and then identifying the genes that could serve that function. Such genes were identified as "oncogenes"--i.e. genes whose protein product is more likely to make a cell cancerous. If they are found in viruses, the gene name is preceded by a "v"; the normal cellular counterpoint of the oncogene is designated by a "c", for cellular; e.g. v-src and c-src.
In contrast to RNA viruses which tend to activate a normal cellular gene so that it is expressed at an abnormally high level or is mutated into the v-oncogene form, DNA tumor viruses mostly cause cancer because of the activity of a normal viral gene (not a cellular gene). The DNA virus has to replicate rapidly to reproduce and DNA viral proteins often activate DNA replication--e.g., by inactivating proteins that normally inhibit replication. While this turns on viral DNA replication, it also turns on cellular DNA replication. Rarely, the viral DNA gets incorporated into the host chromosome, and its replication-inducing protein becomes part of the cell’s permanent makeup. This in turn gives a constant stimulus to the cell to divide which seems to promote the development of cancer. Thus, for example, almost all cases of cervical cancer in women are thought to be induced by the DNA virus that causes genital warts--a papillomavirus.
These various modes of mutation can turn genes on or off, or even create new genetic combinations of parts of two proteins, and all these processes can contribute to cancer
There are two ways in which a mutations can alter the function of a protein for which they code. These are called gain of function mutations and loss of function mutations. Gain of function mutations activate or overactivate some process that is normally not active or is tightly controlled in cells. The oncogenic form of Ras is a gain of function mutation--the mutation inactivates the GTPase that is a normal Ras function and thereby freezes the protein in its active state. Since every cells normally starts out with two Ras genes, one from each parent, how many of them would have to be mutated to cause an effect on a single cell--one or both? Why? In mendelian terminology, what kind of mutation exerts its effects if only one of a pair of genes is affected? Right--gain of function mutations are normally dominant; only one mutation is necessary. Loss of function mutations, as the name implies, result in the inactivation of some protein necessary for the cell to function normally. How many mutations--in one or both genes--would normally be necessary for to knock out such functions. And what kind of mutation, according to mendel, is only expressed if both copies of the gene in a cell are similarly affected? Recessive. Most loss of function mutations are recessive.
How does mutation of particular genes translate into the uncontrolled growth that causes cancer? As shown in Fig. 24-9 (Lodish et al.), there are 7 different classes of proteins that are typically found to be mutated in cancerous cells; all of these classes affect the proliferation of cells in one way or another. These include growth factor proteins, growth factor receptor proteins, signal transduction proteins, transcription factors, DNA repair enzymes, cell-cycle control proteins (like cyclins, cyclin-dependent kinsases, or cyclin kinase inhibitors), and apoptosis regulating proteins (like Bcl-2 or p53).
What kinds of proteins are involved in gain of function mutations? Usually proteins that are activators of cell division--that is, proteins encoded by oncogenes. These kinds of mutants normally affect growth factors, receptors, signal transduction pathways, transcription factors, or some kinds of cell cycle control proteins. The book provides many examples of these kinds of mutations, which I don't want to belabor. These include overproduction of growth factors (such as platelet derived growth factor--PDGF) (see Fig. 24-14); growth factor receptors that can be activated in the absence of growth factors (such as neu receptor or erb-B (EGF receptor) (Fig. 24-15); intracellular signal transduction proteins like Ras, which lead to constitutive activation of the MAP kinase pathway (Fig. 20-28); transcription factors such asmyc or jun/fos, that when overproduced or converted to a constantly active state promote transcription of proteins necessary for DNA replication and cell cycle progression (these transcription factors are normally activated by phosphorylation by MAP kinase, and so in a sense they are, like Ras, part of the MAP kinase signal transduction pathway); and overproduction of cell cycle promoting proteins, like cyclin D (Fig. 24-19). These are all common gain of function mutations found in cancers. That is, these are proteins that normally act in signaling pathways for growth factors that promote cell division or that are essential for the process of cell division itself, like cyclins or cdks. In fact a great deal of what we know about signaling and cell division actually comes from studies of cancer cells; when people tried to work out the function of the mutant genes, they learned a lot about the way normal cells work.
Loss of function mutations, in contrast, are usually in proteins that regulate the processes of cell growth or division--and it is said that these proteins are encoded bytumor suppressor genes. Loss of function mutations mostly affect inhibitors of cell division or proteins that repair damaged DNA--such as some cell cycle control proteins, anti-apoptosis proteins, or DNA repair enzymes. We already discussed the retinoblastoma protein, a cell cycle regulator, which was discovered because it was mutated in families with a high incidence of hereditary retinoblastoma, but Rb’s normal function is to inactivate a nuclear transcription factor, unless it has been phosphorylated. If it is mutated so that it cannot bind to the transcription factors ever, then those factors are permanently active, overstimulating the cell (Figs. 13-31 and 24-19). You can see that even one functional copy of the Rb gene might be enough to make sufficient amounts of the protein to inhibit transcription, but if both copies are defective, then the cell can begin to divide with impunity. Another loss of function mutations that has attracted a lot of interest lately is one in a protein named after its molecular weight--protein 53,000 or p53. This protein seems to be defective in over 3/4 of all human cancers. Another very recently discovered protein, p16, is often defective in the rest (Fig. 24-19). These are thus of interest not only because they are frequent, but because they have interesting mechanisms of action. They seem to prevent the cell from entering the S phase of the cell cycle, and in the case of p53, it may actually be activated in response to cell stress or damage to diminish the possibility that a defective cell will divide. p53, moreover, is also an important signaling protein that induces apoptosis.