(BQ) Part 2 book The biology of cancer has contents: Multi-Step tumorigenesis, maintenance of genomic integrity and the development of cancer, the rational treatment of cancer, crowd control - tumor immunology and immunotherapy,... and other contents.
Chapter p53 and Apoptosis: Master Guardian and Executioner To examine the causes of life, we must first have recourse to death Mary Shelley, Frankenstein, 1831 There cannot however be the least doubt, that the higher organisms, as they are now constructed, contain within themselves the germs of death August Weissmann, philosopher of biology, 1889 M etazoan organisms have a vital interest in eliminating defective or malfunctioning cells from their tissues Responding to this need, mammals have implanted a loyal watchman in their cells Within almost all cells in mammalian tissues, the p53 protein serves as the local representative of the organism’s interests p53 is present onsite to ensure that the cell keeps its household in order If p53 receives information about metabolic disorder or genetic damage within a cell, it may arrest the advance of the cell through its growth-and-division cycle and, at the same time, orchestrate localized responses in that cell to facilitate the repair of damage If p53 learns that metabolic derangement or damage to the genome is too severe to be cured, it may decide to emit signals that awaken the cell’s normally latent suicide program—apoptosis The consequence is the rapid death of the cell This results in the elimination of a cell whose continued growth and division might otherwise pose a threat to the organism’s health and viability The apoptotic program that may be activated by p53 is built into the control circuitry of most cells throughout the body Apoptosis consists of a series of distinctive cellular changes that function to ensure the disappearance of all traces of a cell, often within an hour of its initial activation The continued presence of a latent but intact apoptotic machinery represents an ongoing threat to an incipient cancer cell, since Movies in this chapter 9.1 p53 Structure 9.2 Apoptosis 331 332 Chapter 9: p53 and Apoptosis: Master Guardian and Executioner Figure 9.1 Large T antigen in SV40transformed cells Antibodies that bind the SV40 large T (LT) antigen can be used to detect LT in the nuclei of SV40transformed tumor cells In the present case, such antibodies were used to stain human mammary epithelial cells (MECs) that were transformed by introduction of the SV40 early region plus two other genes A similar image would be seen if such antibodies were used to stain SV40transformed mouse cells LT was detected by linking these antibody molecules to peroxidase enzyme, which generated the dark brown spots In this image of a tumor xenograft, the transformed MECs form ducts (seen in cross section), which are surrounded by normal stromal cells (light blue nuclei) (Courtesy of T.A Ince.) this machinery is poised to eliminate cells that are en route to becoming neoplastic This explains why p53 function must be disabled before a clone of pre-malignant cells gains a sure and stable foothold within a tissue Without a clear description of p53 function and apoptosis, we have no hope of understanding a fundamental component of the process that leads to the creation of virtually all types of human tumors 9.1 Papovaviruses lead to the discovery of p53 TBoC2 B9.01,n9.100/9.01 When murine cells that have been transformed by the SV40 DNA tumor virus are injected into a mouse of identical genetic background (that is, a syngeneic host), the immune system of the host reacts by mounting a strong response; antibodies are made that react with a nuclear protein that is present in the virus-transformed cells and is otherwise undetectable in normal mouse cells (Figure 9.1) This protein, the large tumor (large T, LT) antigen, is encoded by a region of the viral genome that is also expressed when this virus infects and multiplies within monkey kidney cells—host cells that permit a full infectious (lytic) cycle to proceed to completion (see Section 3.4) Large T is a multifunctional protein that the SV40 virus uses to perturb a number of distinct regulatory circuits within infected and transformed cells Indeed, large T was cited in the previous chapter because of its ability to bind and thus functionally inactivate pRb (see Section 8.5) Anti-large T sera harvested from mice and hamsters bearing SV40-induced tumors were used in 1979 to analyze the proteins in SV40transformed cells The resulting immunoprecipitates contained both large T and an associated protein that exhibited an apparent molecular weight of 53 to 54 kilodaltons (Figure 9.2A) Antisera reactive with the p53 protein were found to detect this protein in mouse embryonal carcinoma cells and, later on, in a variety of human and rodent tumor cells that had never been infected by SV40 However, monoclonal antibodies that recognized only large T immunoprecipitated the 53- to 54-kD protein in virusinfected but not in uninfected cells Taken together, these observations indicated that the large T protein expressed in SV40-transformed cells was tightly bound to a novel protein, which came to be called p53 (see Figure 9.2B) Antisera that reacted with both large T and p53 detected p53 in certain uninfected cells, notably tumor cells that were transformed by non-viral mechanisms, such as the F9 embryonal carcinoma cells analyzed in Figure 9.2A The latter observations indicated that p53 was of cellular rather than viral origin, a conclusion that was reinforced by the report in the same year that mouse cells transformed by exposure to a chemical carcinogen also expressed p53 These various lines of evidence suggested that the large T oncoprotein functions, at least in part, by targeting host-cell proteins for binding (The discovery that large Papovaviruses lead to the discovery of p53 (A) (B) 3T3 SV40 – F9 SV40 p53 – T N T N T N T N 90° 94 kD 54 kD large T hexamer T antigen is also able to bind pRb, the retinoblastoma protein, came seven years later.) In the years since these 1979 discoveries, a number of other DNA viruses and at least one RNA virus have been found to specify oncoproteins that associate with p53 or perturb its function (Table 9.1) (As we will discuss later in this chapter, and as is apparent from this table, these viruses also target pRb and undertake to block apoptosis.) Table 9.1 Tumor viruses that perturb pRb, p53, and/or apoptotic function Virus Viral protein targeting pRb Viral protein targeting p53 SV40 large T (LT)a large T (LT)a Adenovirus E1A E1B55K HPV E7 E6 Polyomavirus large T large T? Herpesvirus saimiri V cyclind HHV-8 (KSHV) K cyclind LANA-2 v-Bcl-2,e v-FLIPf Human cytomegalovirus (HCMV) IE72g IE86 vICA,h pUL37i HTLV-I Taxj Tax Epstein–Barr EBNA3C EBNA-1k aSV40 TBoC2 b9.02/9.02 Viral protein targeting apoptosis E1B19Kb middle T (MT)c v-Bcl-2e LMP1k LT also binds a number of other cellular proteins, including p300, CBP, Cul7, IRS1, Bub1, Nbs1, and Fbw7, thereby perturbing a variety of other regulatory pathways bFunctions like Bcl-2 to block apoptosis cActivates PI3K and thus Akt/PKB dRelated to D-type cyclins eRelated to cellular Bcl-2 anti-apoptotic protein fViral caspase (FLICE) inhibitory protein; blocks an early step in the extrinsic apoptotic cascade gInteracts with and inhibits p107 and possibly p130; may also target pRb for degradation in proteasomes hBinds and inhibits procaspase iInhibits the apoptotic pathway below caspase and before cytochrome c release jInduces synthesis of cyclin D2 and binds and inactivates p16INK4A kLMP1 facilitates p52 NF-κB activation and thereby induces expression of Bcl-2; EBNA-1 acts via a cellular protein, USP7/HAUSP, to reduce p53 levels EBNA3C interferes with p53 function Figure 9.2 The discovery of p53 and its association with SV40 large T (A) Normal BALB/c 3T3 mouse fibroblasts (3T3) transformed by SV40, as well as F9 mouse embryonal carcinoma cells, were exposed to 35S-methionine, and resulting cell lysates were incubated with either normal hamster serum (N) or hamster antiserum reactive with SV40-transformed hamster cells (T) The anti-tumor serum immunoprecipitated a protein of 94 kD from virus-infected but not uninfected 3T3 cells In addition, a second protein running slightly ahead of the 54-kD marker was immunoprecipitated from SV40transformed 3T3 cells but not from normal 3T3 cells Moreover, this same protein could be immunoprecipitated from F9 cells, whether or not they had been exposed to SV40 (arrow) These particular data, on their own, did not prove a physical association of SV40 large T (the 94-kD protein) with p53, but they did show that p53 was a cellular protein that was present in elevated amounts in two types of transformed cells Moreover, they suggested that the elevated levels of p53 in SV40transformed hamster cells cause the hamster immune system to mount an immune response against both large T and the hamster’s own p53 (B) As revealed by X-ray crystallography, SV40 large T molecules assemble into homohexamers, each subunit of which binds and thereby sequesters a single molecule of p53 (A, from D.I Linzer and A.J Levine, Cell 17:43–52, 1979 B, from D Li et al., Nature 423:512–518, 2003.) 333 334 Chapter 9: p53 and Apoptosis: Master Guardian and Executioner Figure 9.3 Effects of p53 on cell transformation A cDNA encoding a ras oncogene was co-transfected with several alternative forms of a p53 cDNA into rat embryo fibroblasts In the presence of a p53 dl mutant vector, which contains an almost complete deletion of the p53 reading frame (left), a small number of foci were formed In the presence of a p53 point mutant (middle), a large number of robust foci were formed However, in the presence of a p53 wild-type cDNA clone (right), almost no foci were formed (Courtesy of M Oren; from D Michalovitz et al., Cell 62:671–680, 1990.) ras + p53 deletion mutant ras + p53 val-135 point mutant ras + p53 wild type 9.2 p53 is discovered to be a tumor suppressor gene The initial functional studies of p53 involved a substantial scientific detour: transfection of a p53 cDNA clone into rat embryo fibroblasts revealed that this DNA could collaborate with a co-introduced ras oncogene in the transformation of these rodent cells Such activity suggested that the p53 gene (which is sometimes termed Trp53 in mice and TP53 in humans) might operate as an oncogene, much like the myc oncogene, which had previously been found capable of collaborating with the ras oncogene in rodent cell transformation (see Section 11.10) Like myc, the introduced p53 cDNA seemed to contribute certain growth-inducing signals that resulted in cell transformation in the presence of a concomitantly expressed ras oncogene But appearances deceived As later became the p53 cDNA had originally TBoC2 apparent, b9.03/9.03 been synthesized using as template the mRNA extracted from tumor cells (rather than normal cells) Subsequent manipulation of a p53 cDNA cloned instead from the mRNA of normal cells revealed that this p53 cDNA clone, rather than favoring cell transformation, actually suppressed it (Figure 9.3) Comparison of the sequences of the two cDNAs revealed that the two differed by a single base substitution—a point mutation—that caused an amino acid substitution in the p53 protein Hence, the initially used clone encoded a mutant p53 protein with altered function These results indicated that the wild-type allele of p53 really functions to suppress cell proliferation, and that p53 acquires growth-promoting powers when it sustains a point mutation in its reading frame Because of this discovery, the p53 gene was eventually categorized as a tumor suppressor gene By 1987 it became apparent that such point-mutated alleles of p53 are common in the genomes of a wide variety of human tumor cells Data accumulated from diverse studies indicated that the p53 gene is mutated in 30 to 50% of commonly occurring human cancers (Figure 9.4) Indeed, among all the genes examined to date in human cancer cell genomes, p53 is the gene found to be most frequently mutated, being present in mutant form in the genomes of almost one-third of all human tumors Further functional analyses of p53, conducted much later, made it clear, however, that p53 is not a typical tumor suppressor gene In the case of most tumor suppressor genes, when the gene was inactivated (that is, “knocked out”) homozygously in the mouse germ line (using the strategy of targeted gene inactivation described in Supplementary Sidebar 7.7), the result was, almost invariably, a disruption of embryonic development due to deregulated morphogenesis in one or more tissues These tumor suppressor genes seemed to function as negative regulators of proliferation in a variety of cell types; their deletion from the regulatory circuitry of cells led, consequently, to inappropriate proliferation of certain cells and thus to disruption of normal development In stark contrast, deletion of both p53 gene copies from the mouse germ line had no significant effect on the development of the great majority of p53–/– embryos Therefore, p53 could not be considered to be a simple negative regulator of cell proliferation during normal development Still, p53 was clearly a tumor suppressor gene, since mice lacking both germ-line copies of the p53 gene had a short life span (about months), dying most often from lymphomas and sarcomas (Figure 9.5) This behavior provided Mutant p53 acts as a dominant-negative TP53 mutation prevalence by tumor site Figure 9.4 Frequency of mutant p53 alleles in human tumor cell genomes As indicated in this bar graph, mutant alleles of p53 are found frequently in commonly occurring human tumors This data set includes 26,597 somatic mutations of p53 and 535 germ-line mutations that had been reported by November 2009 The bars indicate the percentage of each tumor type found to carry a mutant p53 allele More recent research indicates that virtually all (119/123) of high-grade ovarian serious carcinomas carry mutant p53 alleles (From International Agency for Research on Cancer, TP53 genetic variations in human cancer, IARC release R14, 2009.) ovary colorectum head & neck esophagus lung skin pancreas stomach liver bladder brain breast uterus soft tissues lymph nodes prostate endocrine glands bones kidney hematop system cervix 10 15 20 25 30 35 % of tumors with p53 mutation 40 45 50 the first hints that the p53 protein does not operate to transduce the proliferative and anti-proliferative signals that continuously impinge on cells and regulate their proliferation Instead, p53 seemed to be specialized to prevent the appearance of abnormal cells, specifically, those cells that were capable of spawning tumors 9.3 Mutant versions of p53 interfere with normal p53 function The observations of frequent mutation of the p53 gene in tumor cell genomes suggested that many incipient cancer cells must perturb or eliminate p53 function before they can thrive This notion raised the question of precisely how these cells succeed in shedding p53 function Here, another anomaly arose, because the p53 gene did not seem to obey Knudson’s scheme for the two-hit elimination of tumor suppressor genes For example, the finding that a cDNA clone encoding a mutant version of p53 was able to alter the behavior of wild-type rat embryo fibroblasts (as described above) ran directly counter to Knudson’s model of how tumor suppressor genes should operate (see Section 7.3) TBoC2 b9.04/9.04 According to the Knudson scheme, an evolving pre-malignant cell can only reap substantial benefit once it has lost both functional copies of a tumor suppressor gene that has been holding back its proliferation In the Knudson model, such gene inactivation events are caused by mutations that create inactive (“null”) and thus recessive alleles p53 + / + 100 90 % survival 80 p53 + / – 70 60 50 40 30 p53 – / – 20 10 0 100 200 300 age (days) 400 500 Figure 9.5 Effects of mutant p53 alleles in the mouse germ line This Kaplan–Meier plot indicates the percent of mice of the indicated genotype that survived (ordinate) as a function of elapsed lifetime in days (abscissa) While the absence of p53 function in the p53–/– mice (carrying two p53 null alleles) had relatively little effect on their embryonic development and viability at birth, it resulted in a greatly increased mortality relatively early in life, deriving largely from the development of sarcomas and leukemias All p53–/– homozygotes succumbed to malignancies by about 250 days of age (red line), and even p53+/– heterozygotes (blue line) began to develop tumors at this time, while wildtype (p53+/+) mice (green line) showed virtually no mortality until almost 500 days of age (Adapted from T Jacks et al., Curr Biol 4:1–7, 1994.) 335 336 Chapter 9: p53 and Apoptosis: Master Guardian and Executioner Therefore, a pre-malignant cell may benefit minimally from inactivation of one copy of a tumor suppressor gene—due to the halving of effective gene function—or not at all, if the residual activity specified by the surviving wild-type gene copy suffices on its own to mediate normal function As we learned in Chapter 7, substantial change in cell phenotype usually occurs only when the function of a suppressor gene is eliminated through two successive inactivating mutations or through a combination of an inactivating mutation plus a loss-of-heterozygosity (LOH) event (see Section 7.4) Knudson’s model was hard to reconcile with the observed behavior of the mutant p53 cDNA introduced into rat embryo fibroblasts (see Figure 9.3) The mutant p53 cDNAs clearly altered cell phenotype, even though these embryo fibroblast cells continued to harbor their own pair of wild-type p53 gene copies This meant that the introduced mutant p53 cDNA could not be functioning as an inactive, recessive allele It seemed, instead, that the point-mutated p53 allele was actively exerting some type of dominant function when introduced into these rat embryo cells Another clue came from sequence analyses of mutant p53 alleles in various human tumor cell genomes These analyses indicated that the great majority of tumor-associated, mutant p53 alleles carry point mutations in their reading frames that create missense codons (resulting in amino acid substitutions) rather than nonsense codons (which cause premature termination of the growing polypeptide chain) To date, more than 26,000 tumor-associated p53 alleles originating in human tumor cell genomes have been sequenced, 74% of which have been found to carry such missense mutations (Figure 9.6A) Furthermore, deletions of sequences within the reading frame of the p53 gene are relatively uncommon Consequently, researchers came to the inescapable conclusion that tumor cells can benefit from the presence of a slightly altered p53 protein rather than from its complete absence, as would occur following the creation of null alleles by nonsense mutations or the outright deletion of significant portions of the p53 gene A solution to the puzzle of how mutant p53 protein might foster tumor cell formation arose from two lines of research First, studies in the area of yeast genetics indicated that mutant alleles of certain genes can be found in which the responsible mutation inactivates the normal functioning of the encoded gene product At the same time, this mutation confers on the mutant allele the ability to interfere with or obstruct the ongoing activities of the surviving wild-type copy of this gene in a cell Alleles of this type are termed variously dominant-interfering or dominant-negative alleles A second clue came from biochemical and structural analyses of the p53 protein, which revealed that p53 was a nuclear protein that normally exists in the cell as a homotetramer, that is, an assembly of four identical polypeptide subunits (see Figure 9.6B and C) Together with the dominant-negative concept, this observed tetrameric state suggested a mechanism through which a mutant allele of p53 could actively interfere with the continued functioning of a wild-type p53 allele being expressed in the same cell Assume that a mutant p53 allele found in a human cancer cell encodes a form of the p53 protein that has lost most normal function but has retained the ability to participate in tetramer formation If one such mutant allele were to coexist with a wild-type allele in this cell, the p53 tetramers assembled in such a cell would contain mixtures of mutant and wild-type p53 proteins in various proportions The presence of only a single mutant p53 protein in a tetramer might well interfere with the functioning of the tetramer as a whole Figure 9.7A illustrates the fact that 15 out of the 16 equally possible combinations of mutant and wild-type p53 monomers would contain at least one mutant p53 subunit and might therefore lack some or all of the activity associated with a fully wild-type p53 tetramer Consequently, only one-sixteenth of the p53 tetramers assembled in this heterozygous cell (which carries one mutant and one wild-type p53 gene copy) would be formed purely from wild-type p53 subunits and retain full wildtype function In an experimental situation in which a mutant p53 cDNA clone is introduced by gene transfer (transfection) into cells carrying a pair of wild-type p53 alleles (see Figure 9.3), the expression of this introduced allele is usually driven by a highly active p53 alterations largely affect DNA binding transcriptional promoter, indeed, a promoter that is far more active than the gene promoter controlling expression of the native p53 gene copies As a consequence, in such transfected cells, the amount of mutant p53 protein expressed by the introduced (A) 9% 2%2% 4% 8% 54% 56% 74% 4% 9% frameshift 2% 5% ATM (n = 617) in frame deletions/insertions missense 30% 28% 4% APC (n = 15,451) p53 (n = 26,597) 11% 14% 32% 51% (B) BRCA1 (n = 3,703) nonsense silent splice site (C) transactivation sequence-specific DNA binding proline rich tetramerization 175 distribution of mutations 248 245 249 C-terminal 273 282 COOH H2N 1.7% 95.1% tetramerization 3.2% flexible linker DNA DNA-binding transactivation tetramerization Taz2 co-activator DNA binding and the tetramerization domain are shown below (C) The overall Figure 9.6 Nature of p53 mutations (A) As indicated in these structure of the DNA-bound p53 tetramer is shown here The four pie charts, point-mutated alleles of p53 leading to amino acid DNA-binding domains are shown in green and blue, while the four substitutions (green) represent the great majority of the mutant tetramerization domains are seen as red and dark red α-helices p53 alleles found in human tumors, while other types of mutations are seen relatively infrequently In contrast, the mutations striking (above) The DNA double helix is shown in yellow Each of the four other tumor suppressor genes (APC) or “caretaker” genes involved DNA-binding domains associates with half of a binding site in the in maintenance of the genome (ATM, BRCA1) represent readingDNA; two copies of the binding site are present in the DNA with frame shifts (yellow) or nonsense codons (blue) in the majority of a small number of base pairs separating them (see Figure 9.12B) cases; both of these types of mutation disrupt protein structure, Each of the four transactivating domains (dark pink) is shown TBoC2 b9.06,n9.101/9.06 usually by creating truncated versions of proteins that are often interacting with the Taz2 domain of the p300 co-activator (light degraded rapidly in cells (B) The locations across the p53 reading purple), which functions to stimulate transcription through its frame of the point mutations causing amino acid substitutions ability to acetylate histones and p53 itself The C-terminal domain are plotted here (above) As is apparent, the great majority of p53 (yellow) plays important roles in regulating transcription mutations (95.1%) affect the DNA-binding domain of the p53 (A, from International Agency for Research on Cancer, TP53 genetic protein The numbers above the figure indicate the residue numbers variations in human cancer, IARC release R14, 2009; and A.I Robles of the amino acids that are subject to frequent substitution et al., Oncogene 21:6898–6907, 2002 B, from K.H Vousden and in human tumors The transactivation domain enables p53 to X Lu, Nat Rev Cancer 2:594–604, 2002; and A.C Joerger and interact physically with a number of alternative partners, including A.R Fersht, Annu Rev Biochem 77:557–582, 2008 C, from the p300/CBP transcriptional co-activator and Mdm2, the p53 A.C Joerger and A.R Fersht, Cold Spring Harb Perspect Biol antagonist The detailed structures of the DNA-binding domain 2:000919, 2010.) 337 338 Chapter 9: p53 and Apoptosis: Master Guardian and Executioner (A) wild-type p53 subunit (B) p53 function point mutation mutant p53 subunit Figure 9.7 p53 structure and p53 function as a dominant-negative allele (A) In cells bearing a single mutant p53 allele, the mutant protein usually retains its ability to form tetramers but loses its ability to function normally because of a defective DNA-binding domain Consequently, mixed tetramers composed of differing proportions of wild-type (blue) and mutant (red) p53 subunits may form, and the presence of even a single mutant protein subunit may compromise the functioning of the entire tetramer Therefore, in a cell that is heterozygous at the p53 locus, fifteen-sixteenths of the p53 tetramers may lack fully normal function (B) Perhaps the most direct demonstration of the dominant-negative mode of p53 action has come from “knocking in” (see Supplementary Sidebar 7.7) mutant p53 alleles into the genome of mouse embryonal stem (ES) cells In cells in which a point mutation in the DNA-binding domain (above) was knocked into one p53 gene copy, almost all p53 function was lost In contrast, when one p53 gene copy was completely inactivated (yielding a null allele), p53 function was almost normal p53wt/wt knock-in mutations wild-type embryonic stem cell deletion wt/pt.mut p53 p53wt/null almost none almost normal gene will be vastly higher than the amount of normal protein produced by the cells’ endogenous wild-type p53 gene copies Therefore, far fewer than one-sixteenth of the p53 tetramers in such cells will be formed purely from wild-type p53 subunits This explains how an introduced mutant p53 allele can be highly effective in compromising virtually all p53 function in such cells The above logic might suggest that many human tumor cells, which seem to gain some advantage by shedding p53 function, should carry one wild-type and one mutant p53 b9.07b,n9.102/9.07 allele Actually,TBoC2 in the great majority of human tumor cells that are mutant at the p53 locus, the p53 locus is found to have undergone a loss of heterozygosity (LOH; see Section 7.4), in which the wild-type allele has been discarded, yielding a cell with two mutant p53 alleles Thus, in such a cell, one copy of the p53 gene is initially mutated, followed by elimination of the surviving wild-type copy through some type of loss-ofheterozygosity mechanism It is clear that an initial mutation resulting in a mutant, dominant-negative (DN) allele is far more useful for the incipient tumor cell than one resulting in a null allele, which causes total loss of an encoded p53 protein (see Figure 9.7B) The dominant-negative allele may well cause loss of fifteen-sixteenths of p53 function, while the null allele will result, at best, in elimination of one-half of p53 function (Actually, if the levels of p53 protein in the cell are carefully regulated, as they happen to be, then this null allele will have no effect whatsoever on a cell’s overall p53 concentration, since the surviving wild-type allele will compensate by making more of the wild-type protein.) Why, then, is elimination of the surviving wild-type p53 allele even necessary? The answer seems to lie in the residual one-sixteenth of fully normal p53 gene function; even this little bit seems to be more than most tumor cells care to live with So, being most opportunistic, they jettison the remaining wild-type p53 allele in order to proliferate even better The observations described in Figure 9.7B of genetically altered embryonic stem (ES) cells provide further evidence for p53’s dominant-negative mode of action 9.4 p53 protein molecules usually have short lifetimes Long before the DNA-binding domain of p53 was discovered, the nuclear localization of this protein in many normal and neoplastic cells suggested that it might function as a transcription factor (TF) At least three mechanisms were known to regulate the activity of transcription factors (1) Concentrations of the transcription factor in the nucleus are modulated (2) Concentrations of the transcription factor in the nucleus are held constant, but the intrinsic activity of the factor is boosted by some type of covalent modification (3) Levels of certain collaborating transcription factors may be modulated In some instances, all three mechanisms cooperate In the case of p53, the first mechanism—changes in the level of the p53 protein—was initially implicated Measurement of p53 protein levels indicated that they could vary drastically from one cell type to another and, provocatively, would increase rapidly when cells were exposed to certain types of physiologic stress These observations raised the question of how p53 protein levels are modulated by the cell Many cellular protein molecules, once synthesized, persist for tens or hundreds of hours (Some cellular proteins, such as those forming the ribosomal subunits in p53 normally turns over rapidly exponentially growing cells, seem to persist for many days.) Yet other cellular proteins are metabolically highly unstable and are degraded almost as soon as they are assembled One way to distinguish between these alternatives is to treat cells with cycloheximide, a drug that blocks protein synthesis When such an experiment was performed in cells with wild-type p53 alleles, the p53 protein disappeared with a half-life of only 20 minutes This led to the conclusion that p53 is usually a highly unstable protein, being broken down by proteolysis soon after it is synthesized This pattern of synthesis followed by rapid degradation might appear to be a “futile cycle,” which would be highly wasteful for the cell Why should a cell invest substantial energy and synthetic capacity in making a protein molecule, only to destroy it almost as soon as it has been created? Similar behaviors have been associated with other cellular proteins such as Myc (see Section 6.1) The rationale underlying this ostensibly wasteful scheme of rapid protein turnover is a simple one: a cell may need to rapidly increase or decrease the level of a protein in response to certain physiologic signals In principle, such modulation could be achieved by regulating the level of its encoding mRNA or the rate with which this mRNA is being translated However, far more rapid changes in the levels of a critical protein can be achieved simply by stabilizing or destabilizing the protein itself For example, in the case of p53, a cell can double the concentration of p53 protein in 20 minutes simply by blocking its degradation Under normal conditions, a cell will continuously synthesize p53 molecules at a high rate and rapidly degrade them at an equal rate The net result of this is a very low “steady-state” level of the protein within this cell In response to certain physiologic signals, however, the degradation of p53 is blocked, resulting in a rapid increase of p53 levels in the cell This finding led to the further question of why a normal cell would wish to rapidly modulate p53 levels, and what types of signals would cause a cell to halt p53 degradation, resulting in rapidly increasing levels of this protein 9.5 A variety of signals cause p53 induction During the early 1990s, a variety of agents were found to be capable of inducing rapid increases in p53 protein levels These included X-rays, ultraviolet (UV) radiation, certain chemotherapeutic drugs that damage DNA, inhibitors of DNA synthesis, and agents that disrupt the microtubule components of the cytoskeleton Within minutes of exposing cells to some of these agents, p53 was readily detected in substantial amounts in cells that previously had shown only minimal levels of this protein This rapid induction occurred in the absence of any marked changes in p53 mRNA levels and hence was not due to increased transcription of the p53 gene Instead, it soon became apparent that the elevated protein levels were due entirely to the post-translational stabilization of the normally labile p53 protein In the years that followed, an even greater diversity of cell-physiologic signals were found capable of provoking increases in p53 levels Among these were low oxygen tension (hypoxia), which is experienced by cells, normal and malignant, that lack adequate access to the circulation and thus to oxygen borne by the blood Still later, introduction of either the adenovirus E1A or myc oncogene (see Sections 8.5 and 8.9) into cells was also found to be capable of causing increases in p53 levels By now, the list of stimuli that provoke increases in p53 levels has grown even longer Expression of higher-than-normal levels of the E2F1 transcription factor, widespread demethylation of chromosomal DNA, and a deficit in the nucleotide precursors of DNA all trigger p53 accumulation Exposure of cells to nitrous oxide or to an acidified growth medium, depletion of the intracellular pool of ribonucleotides, and blockage of either RNA or DNA synthesis also increase p53 levels These various observations made it clear that a diverse array of sensors are responsible for monitoring the integrity and functioning of various cellular systems When these sensors detect damage or aberrant functioning, they send signals to p53 and its regulators, resulting in a rapid increase in p53 levels within a cell (Figure 9.8) 339 Chapter 9: p53 and Apoptosis: Master Guardian and Executioner Figure 9.8 p53-activating signals and p53’s downstream effects Studies of p53 function have revealed that a variety of cell-physiologic stresses can cause a rapid increase in p53 levels The resulting accumulated p53 protein then undergoes post-translational modifications and proceeds to induce a number of responses A cytostatic response (“cell cycle arrest,” often called “growth arrest”) can be either irreversible (“senescence”) or reversible (“return to proliferation”) DNA repair proteins may be mobilized as well as proteins that antagonize blood vessel formation (“block of angiogenesis”) As an alternative, in certain circumstances, p53 may trigger apoptosis lack of UV ionizing oncogene blockage of hypoxia nucleotides radiation radiation signaling transcription p53 cell cycle DNA block of apoptosis arrest repair angiogenesis OR senescence return to proliferation The same genotoxic (that is, DNA-damaging) agents and physiologic signals that provoked p53 increases were already known from other work to act under certain conditions in a cytostatic fashion, forcing cells to halt their advance through the cell cycle, a response often called “growth arrest.” In other situations, some of these stressful signals might trigger activation of the apoptotic (cell suicide) program These observations, when taken together, showed a striking parallel: toxic agents that induced growth arrest or apoptosis were also capable of inducing increases in p53 levels TBoC2 b9.08/9.08 Because such observations were initially only correlations, they hardly proved that p53 was involved in some fashion in causing cells to enter into growth arrest or apoptosis following exposure to toxic or stressful stimuli Figure 9.9 p53 and the radiation response Exposure of cells to X-rays serves to strongly increase p53 levels (A) Once it is present in higher concentrations (8, 24 hours) and is functionally activated via various covalent modifications (not measured here), p53 induces expression of the p21Cip1 protein (see Section 8.4) p21Cip1 acts as a potent CDK inhibitor of the cyclin–CDK complexes that are active in late G1, S, G2, and M phases and can thereby halt further cell proliferation at any of these phases of the cell cycle The actin protein is included in all three samples as a “loading control” to ensure that equal amounts of protein were added to the three gel channels prior to electrophoresis (B) Thymocytes (leukocytes derived from the thymus) of wild-type mice show an 80% loss of viability relative to untreated control cells during the 25 hours following X-irradiation (green), while thymocytes from p53+/– heterozygous mice (with one wild-type and one null allele) show almost as much loss of viability (red) In contrast, thymocytes prepared from p53–/– homozygous mutant mice exhibit less than a 5% loss of viability during this time period (blue) In all cases, the loss of viability was attributable to apoptosis (not shown) (A, courtesy of K.H Vousden B, from S.W Lowe et al., Nature 362:847–849, 1993.) The definitive demonstrations of causality came from detailed examinations of p53 functions For example, when genotoxic agents, such as X-rays, evoked an increase in cellular p53 levels, the levels of the p21Cip1 protein (see Section 8.4) increased subsequently; this induction was absent in cells expressing mutant p53 protein This suggested that p53 could halt cell cycle advance by inducing expression of this widely acting CDK inhibitor (Figure 9.9A) Indeed, the long-term biological responses to irradiation were often affected by the state of a cell’s p53 gene Thus, cells carrying mutant p53 alleles showed a greatly decreased tendency to enter into growth arrest or apoptosis when compared with wild-type cells that were exposed in parallel to this stressor (see Figure 9.9B) These various observations could be incorporated into a simple, unifying mechanistic model: p53 continuously receives signals from a diverse array of surveillance systems If p53 receives specific alarm signals from these monitors, it calls a halt to cell proliferation or triggers the apoptotic suicide program (see Figure 9.8) (A) (B) 100 p53 p53 – / – p21Cip1 actin 24 hours post radiation viability (% of untreated) 340 80 60 p53 + / – 40 20 p53 + / + 10 15 time (h) 20 25 Index familial appearance 16SS heterotypic signaling 88SS in immunocompromised patients 746 persistence of episomal genome 12SS karyotypes chromosome alterations in cancer cells 555–558 chromosome numbers in cancer cells 558–564 euploidy 11 keratin 15F keratinocytes carcinomas of 37 response to PKC-α 491–492 response to ultraviolet 344S, 456F, 535 keratoses 527 kidney carcinomas 265, 267F, 701F kinetics multi-step tumorigenesis 468, 475, 498–501 retinoblastomas 236 signal transduction 222 tumor progression 441–442, 443S kinetochores 408F, 560–561, 564T kinome 874, 138–139SS KIR (killer inhibitory receptor) 766F Kirsten sarcoma virus 94, 108 KISS1 protein 710T, 711 kit gene 152F, 152S, 154S, 171, 842F Kit growth factor receptor 470, 617S, 828F, 839 ‘knock-out’ mice 83, 270, 334, 423–429, 494, 41–42SS ‘knocked-down’ gene expression 4SS ‘knocked-in’ mice 117, 338 Knudson, Alfred 236, 237F, 238, 259S Knudson model for TSGs 335–336 Kostmann syndrome 485 Krebs cycle see citric acid cycle KSHV see Kaposi’s sarcoma L L-myc genes 28S, 323 Lacks, Henrietta 394 lactate generation 53, 61SS ‘lagging-strand synthesis”’ 410, 412F LAK (lymphokine-activated killer) cells 789–790 lamellipodia 199, 690, 691F, 692–694, 697F laminin 35F laminins as basement membrane component 583, 585F, 593F cleavage by MMPs 590T, 685, 688 in extracellular matrix 161–162, 163T in muscle 609F lamins 370 LAN1 cells 775F Langerhans, islets of 616–618, 631–632, 737F Langerhans cells 729–730F lapatinib 780 large T antigen (SV40) avoiding senescence 400, 423 crisis and 404–405 immortalization by hTERT and 476 p53 discovery via 332–334 p53 sequestration by 353, 373S large T oncogene (polyomavirus) 470, 472, 473S, 473T large T oncoprotein (SV40) 758 latency 475, 717 LCM (laser capture microdissection) 603, 805, 83SS LDH-A (lactate dehydrogenase-A) 54F, 55 leiomyomas 51 Let-7 miRNA 26, 123 leukapheresis 787 leukemias 39, 41F acute leukemias see ALL; AMLs; APL in animals see feline; MLV childhood leukemias 470, 471F chronic leukemias see CLL; CML CNL (chronic neutrophilic leukemia) 835 endogenous retroviruses and 104 erythroleukemias 41F fusion proteins 835 HTLV-I and 97 in Li-Fraumeni syndrome 360 megakaryoblastic leukemias 516S transmission of virus-induced 72 leukemogenesis by ALV 97 leukocytes 604 recruited to tumors 750 role in tumorigenesis 750, 751T see also macrophages Lewis lung carcinoma (LLC) 586F, 611F, 613F, 623F Li-Fraumeni syndrome 360–361, 428 licensing of drugs 832 life expectancy and cancer mortality 440 life span, cells 364, 399–400, 513, 516 number of cell divisions 221, 382, 393, 423, 478 life span, proteins see half-life lifestyle as a cancer risk factor 58–59, 60T, 67 ligand-independent dimerization 150– 152 ligand-independent firing 142–143, 150– 151, 152S, 154S, 156, 169, 212 EGF receptor 218 lineage marking 99SS lineage tracing 51 lineages defined 392 founding cell 42T transdifferentiation 466 and tumor growth 396F lipophilic nuclear receptor ligands 159– 161 Lisch nodules 255, 256F liver colon metastases 701 dormant micrometastases 656 liver cancer see HCCs LMO2 proto-oncogene 100S lncRNA (long non-coding RNAs) 26 LOH (loss of heterozygosity) 239–245 in breast cancer pathogenesis 455 in colon cancer pathogenesis 452, 454 in Darwinian model 458 in human tumor progression 499 identifying TSGs using 243–247, 449–450 in neurofibromas 258, 259S, 269–270 NF1 gene 256 p53 gene 336, 338 promoter methylation and 252–253 PTCH gene 857 rate of 249S Rb gene 241–243 secondary mutation alternative and 33SS ‘long patch repair’ 542 longitudinal studies 446 loss of heterozygosity see LOH lumina 36F, 37, 206F capillaries 648, 649F mammary glands 367, 368F lung carcinomas Lewis lung carcinoma (LLC) 61`3F, 586F, 611F, 623F lifestyle effects 58 mouse 33F and smoking 59T, 441F see also NSCLCs; SCLC lungs breast cancer metastases 702 CTC trapping 648–649 lupus erythematosus 737, 784 lymph nodes breast cancer metastases 677 micrometastases detection in 652, 653F sentinel nodes 698, 699S site of antigen presentation 726, 731F specialization of metastases in 700, 719F lymphangiogenesis 611S, 696 lymphatic cells as therapeutic targets 638F lymphatic ducts defective tumor drainage 614, 615F endothelial cells in 583, 610, 611S metastasizing cells in 695–699 lymphocytes 39 adoptive cell transfer 791 antigen-specific 757 auto-reactive 736–737 breast cancer and 565F, 565S recruitment by carcinomas 582, 774 tumor counterattacks 769–773 see also T lymphocytes; TILs lymphokine-activated killer (LAK) cells 789–790 lymphomas 39 anti-CD47 therapies 122SS first cure 807 germinal-center B-cell-like 805–806 lysine residues, histone H3 23F lysosomes 143S, 172, 380 lytic cycles 80, 85 M M-CSF (macrophage colony-stimulating factor) see CSF-1 M phase, cell cycle 233 chromatid duplication and alignment 279 M-to-G1 transition 295F, 299 macrophages in angiogenesis 604, 605F in apoptosis 356F, 357 breast cancer reciprocal stimulation 673F immunoevasion 768–769 and invasiveness 645, 672F as MMP source 686F, 688 monocyte differentiation to 604 in Nude mice 741 as ‘professional’ APCs 742 recruitment by carcinomas 582, 604– 606, 647F recruitment in extravasation 650, 686 TAMs (tumor-associated macrophages) 605F, 606, 669, 672F as therapeutic targets 638F tumor-associated stroma activation 604–606 tumor progression and 752F tumoricidal 606 in wound healing 591F, 752F Mad protein see Mxd Maden-Darby cells 661F, 674F malaria and Burkitt’s lymphoma 120, 121S males, as biologically disadvantaged malignancy basement membrane breach and 644, 645F EMT-TF and 680–685 heterotypic signaling and 685 MALT (mucosa-associated lymphoid tissue) I:15 I:16 Index tissues 490 mammals body size and cell transformation 478, 479F body size and metabolic rate 527F interspecies differences 475–476 master signaling circuitry 506F similarities 8S, 27, 28S mammary glands alveoli 707 formation of lumina 367, 368F involution 358 lymphatic drainage 697 MAPK (mitogen-activated protein kinase) pathway 191–192 EGF-R inhibition and 831 kinetics 222 mdm2 transcription and 345 mitogen independence and 504 negative feedback 219 pRb phosphorylation and 304 MAPKK and MAPKKK 191 mass action effects 143S mast cells angiogenic switching role 617S neurofibromatosis and 258–259 as therapeutic targets 638F in wound healing 592 Max protein 307F, 308, 309–311F, 317F maximum tolerated dose (MTD) 829, 831 3-MC (3-methylcholanthrene) 106–107, 480, 484, 741, 743, 744F, 757–758, 119SS MC29 myelocytomatosis virus 93–94 McClintock, Barbara 406, 409 MCP-1 (macrophage chemoattractant protein; MCP-1) 604 mCRPs (membrane-bound complement regulatory proteins) 774, 775F MDCF (Maden-Darby canine kidney) cells 661F, 674F Mdm2 as an oncoprotein 345 ARF proteins and 346, 821 complex formation with p53 820 overexpression in cancer cells 376 as p53 antagonist 337F, 341–348, 48SS MdmX (Mdm4) 344, 360S MDR1 gene 833, 834F Mdr1 (multi-drug resistance 1) protein 518 MDS (myelodysplastic syndrome) 536–537 MDV (Marek’s disease virus) 86 meat cooking and HCAs 532, 534F, 537S, 76SS as a tumor promoter 65–66SS MECs (mammary epithelial cells) 332F, 362F, 399F in breast cancer 486 EMT in mice 663F EMT of human mice 678 transformation rate 475, 600, 601F transformed subpopulations 715F medulloblastomas 40, 43F, 215, 451F, 857F, 858–860 megakaryoblastic leukemias 516S megakaryocytes 155 MeIQx (2-amino-3,8-dimethylimidazo[4,5-f ]quinoxaline 534F, 537S MEK kinase 190–191, 817F, 866 melanin 535 Melanoma Molecular Map Project 3SS melanomas 33F, 40 antigenicity 120SS APAF1 methylation 376–377 B-Raf and 192, 202, 864–866 cancer-specific antigens 753, 755, 763S differentiation antigens 759 FasL in 771F incidence and mortality 869F melanocytes and 44F N-cadherin and 660–662 organ transplant patients 748 p16INK4A in familial 319 STAT3 in 203–204 TATAs of 121SS TILs and outcomes 750 uveal 701 Melphalan 852F membrane attack complex (MAC) 775F Mena protein 648F, 695, 696–697F, 755 menarche 485 Mendel, Gregor 2, 20SS Mendelian genetics applicability to metazoa and metaphyta chromosome behavior and 7–11 in the ‘modern synthesis’ 456 pea plant traits 3F meningiomas 215 6-mercaptopurine 808T, 809F merotely 560–561 mesenchymal cell types 38, 421 in carcinomas 581 tumors of 40F see also EMT; fibroblasts mesenchymal stem cells (MSCs) 596, 597F, 636–637 mesoderm, embryonic 35, 37F, 38–39, 657, 675 mesothelioma 442, 444F, 488T, 11SS MET (mesenchymal-epithelial transition) 592, 594–595F reversing EMT 663–664, 669 Met receptor 140T, 145T, 150, 151F, 154S, 636 as HGF receptor 689 metaphase 278F, 279, 280F, 284, 325 metaphase plate 60, 80F, 566 metaphase spindle 566 metaphyta, genetics metaplasia 46, 74 metastases cancer mortality and 642 as cause of death 34 contralateral 701S development timescale 103SS difficulty of investigations 480, 716–717 distinction from primary tumor 33 epithelial cell presence 666 favored organ sites 699–703 macrophage effects on 672F4F melanomas 44F non-epithelial 716 osteotropic metastases 703–709 parallel progression and 703S primary tumor reseeding 464 reactive stroma formation 665 Rho family proteins 695 ‘seed and soil’ hypothesis 701, 709, 105SS specialization required 700 stromal support 585, 587F see also invasion-metastasis cascade; micrometastases metastasis potential 711–714 metastasis-specific alleles 108SS metastasis suppressor genes 709–711 see also tumor suppressor metastatic inefficiency 652, 711, 107SS metastatic shower 654S metastatic site access 643–651 metastatic tropism 642, 699–700, 701– 702, 717, 718F metazoa apoptosis as common to 362 applicability of Mendelian genetics cancer protection evolution 439 cell-to-cell communication 132–133 common ancestor 24SS conserved components 8S, 27–28, 24SS, 138SS growth factor receptors in 141 morphogenesis 31–32 telomerase expression in 416–417 methionine aminopeptidase-2 enzyme 629 methyl-CpG-binding proteins 25 methylated CpG sequence 249–252, 254 methylation DNA bases 526–527, 528F, 539F gene repression and 23–24, 376–377 hypermethylated genes and tumor types 251T promoters see promoter methylation of Rb promoters 318 and tumor type 254F methylation-specific polymerase chain reaction (MSP) 35SS 5-methylcytosine 524F, 525 deoxy- 526F mFISH (multicolor fluorescence in situ hybridization) 12F, 13F MGMT (O6-methylguanine-DNA methyltransferase) 538–539, 540S, 568 MHC (major histocompatibility complex) allograft rejection and 739 polymorphism 739S, 740F role in adaptive immune response 726 MHC class I CTVS transmission and 113SS display 730–735 NK cells and 766 repression or blocking 762–764, 765F, 792, 112SS MHC class II molecules cancer-specific antigens 753 suppression of 770 MICA and MICB proteins 762T, 766–768 mice see mouse microfluidic devices 96–97SS micrometastases in bone marrow 699, 712 detection 652–656 dormant micrometastases 644, 653, 656, 703, 711–713 evolution 654F filopodia in formation 690 indolent micrometastases 745 lymph node 698F metastatic tropism and 717–718 occult micrometastases 652, 711–713 organ transplantation and 98SS and reactive stroma 666 surgery and 598S micronuclei 64S microsatellite instability (MIN) CIN and 559–560 detection of 523F mismatch repair system and 521, 522– 523F, 547–549 mutant Bax gene 377 polymerase β overexpression and 543 TGF-β receptors 313, 547F and tumor immunogenicity 758S, 765F microscopy, multiphoton 614F, 729F microscopy, two-photon 598F, 614F microthrombi 651F, 651S, 768, 93–95SS microtubule antagonists 406F, 565S, 810, 811T microtubule assembly 807, 808T microvessels see capillaries middle T (polyomavirus) oncogene 470– Index 472, 473S, 496F, 604F, 664F MIN see microsatellite instability ‘minimum residual disease’ 654F, 654S, 713S miRNAs (microRNAs) 19, 25–26, 268 chromosomal translocations and 122–123 Dicer gene and 710 regulatory circuits 3SS and RNA interference 5SS mismatch repair system 421 and cancer susceptibility 544–549 inactivated genes and proteins in cancers 548T see also MMR enzymes mitochondria aerobic glycolysis and 53–55 role in apoptosis 361–371 see also reactive oxygen mitogenic growth factors 275–277, 281, 298, 304, 306, 323 cyclin D and 286 human cancer attributes and 504 mitogenic pathways cytoplasmic and nuclear 472 GPCR stimulation 210 in human cell transformation 476 influencing Mdm2 and p53 345 most important 217–220 organization of 220–226 see also Ras signaling mitogens growth factors as 134, 138 NFκBs as 213 PDGF as 594 R point control by 298 short-term responses as atypical 180S as tumor promoters 484–486 Wnt-β-catenin pathway 206–208 mitoses in the cell cycle 277–, 325 in dysplastic epithelium 47F fate of syncytia 233 histone effects 22 multipolar apparatuses 562F nondisjunctive 240 number of genes involved 563 preservation of viral genomes 12–13SS subphases of 277–278 see also BFB; cell divisions; M phase; microtubule mitotic catastrophe 382, 815 mitotic recombination 238–240 mitotic spindles 264, 326F, 371 metaphase spindle 566 mlh1 gene 563 MLH1 protein 546–549 MLL1 HMT 23F MLL1 (mixed-lineage leukemia) gene 126 MLV (murine leukemia virus) 75F, 94, 97, 98S, 98T, 99, 100S, 251S, 489 MM (multiple myelomas) 9T, 11F, 41F, 52F, 783F, 844S, 851–852 MMP1 gene 718F MMPs (matrix metalloproteinases) 376, 590–592, 598 antagonists 626 MMP-1 687F MMP-2 606, 645, 663F, 686, 687F, 688 MMP-3 594F, 689 MMP-9 605F, 606, 617, 618F, 624T, 645, 688 MT1-MMP 685–686, 687–688F role in invasiveness 685–686, 688F MMR (mismatch repair) enzymes 520–521, 522–523F, 538, 546–549, 77SS MMTV (mouse mammary tumor virus) 98S, 98T, 99, 157, 474–475, 604F MMTV-PyMT transgenic mice 664F, 686F MNU (methylnitrosourea) 538, 539F, 540S mobilization of the immune system 786–791 ‘modern synthesis’ in genetics 456 molecular biology 1–2 central dogma 25 creation of phenotypes 14–15 prevention strategies and 800 molecular cloning 122, 135, 138, 544 molecular markers 800, 802, 847 molecular medicine concept 873 monocarboxylate transporter (MCT1) 61SS monoclonal antibodies (MoAbs) anti-bFGF 629 anti-BrdU 357F anti-CD20 844S anti-CD47 769F, 122SS anti-CTLA-4 789, 790F anti-E1A 296F, 297S anti-EGF-R 830F, 142SS anti-pRb 296F anti-VEGF 629, 89SS B-cell tumors 781–785 bispecific antibodies 124SS breast cancer passive immunization 778–781 chimeric MoAbs 782 denosumab 708–709 enhancing cytotoxicity 784–785 Herceptin (trastuzumab) 598S, 778, 779F, 780, 781F, 782S labeling using 459 production using FACS 57–59SS resistance involving CDCs 774, 776S Rituxan (tiuximab) 776S, 777F, 778, 782–784 against RTKs 782F, 782S staining using 84F, 332 monocyte chemotactic protein-1 604 monocytes 592, 604, 787 Monod, Jacques monolayers, cell culture 77 monomeric growth factors 147 mononucleosis 121S monozygotic (identical) twins 470, 471F, 485 Mormons 260F, 260S morphogenesis anoikis and 206F and cyclopamine 856 and the nature of cancer 31–32 Wnt proteins as morphogens 98S, 208 morphology cancer cells 76 phenotype and 14 mortality see deaths motogenic growth factors 689 mouse embryonic EMTs 657T in genetic experiments 3, 475 genetically engineered mouse models 827 germ line 41–42SS HAMA antibodies 779 limitations as models 475–476, 478, 632, 872 Pax-6/small eye gene 8F ready transformation 478 skin cancer induction 481F, 482–483F telomeres of laboratory 423–425 mouse mammary tumor virus (MMTV) 98S, 98T, 99, 157 mouse strains allograft rejection 739 genetically altered 742–743 immunocompromised 83, 740–741, 114SS mTR-negative 423–433 NCI 60 682F, 827 Nude mice 83, 486–487, 587, 601, 629 see also knock-out mice; Rip-Rag mice MRI (magnetic resonance imaging) 799F mRNA (messenger RNA) 6F, 17S, 18F, 19 complementary DNA in vitro from 29 effects on miRNAs 25–26 expression and gene copy number 112 number from a single gene 17S see also pre-mRNA MSCs (mesenchymal stem cells) 596, 597F, 636–637 MSH2 protein 546, 548–549 MT1-MMP (membrane type- MMP) 685–686, 687–688F MTD (maximum tolerated dose) 829, 63SS mTERT reverse transcriptase 424F, 424S, 425 mTOR (mammalian target of rapamycin) 246–247T, 272, 861–866 Akt/PKB and 193F, 198, 862 targeting 817F mTORC1 kinase 267 mTR RNA subunit 423 mucosa, intestinal 445 mucus 36, 38F, 46, 133F, 514 multi-drug protocols 810, 833, 871 disincentives to testing 871S multi-drug resistance 811, 833, 834F multi-step tumorigenesis chromosomal aneuploidy 559 cumulative changes 449–453 Darwinian perspective on 457–463, 467–468 epidemiological evidence 441–442 FAP and 443–455 field cancerization and 453–455, 456F genetic diversification 463–466 heterotypic signaling in 582, 634 histopathological evidence 442–449 immune system involvement 793, 117SS kinetics 468, 103SS modifications to the hierarchical scheme 59–60SS parallel progression 703S promotion and rate of 498–501 redundant mutation puzzle 479S stem cell hierarchies 462 tendency to metastasize 713, 714F multiple myelomas (MM) 9T, 11F, 41F, 52F, 783F, 844S, 851–852 mural cells 583, 584F, 586F, 632 murine leukemia virus (MLV) 75F, 94, 97–99, 100S, 251S, 489 Mus musculus see mouse muscle development 315 mustard gas 807 mutagenesis assays Ames tests as 62 other tests 64S mutagens 3-MC as 106–107 dose-response curves 63SS electrophiles and alkylating agents as 528 endogenous 523–527, 542 ENU (ethylnitrosourea) mutagen 150 exogenous 527–535 in food 64–66 initiators as 484S insertional mutagenesis 96F, 97, 98S whether carcinogens are mutagens 60–66 mutations chromosome abnormalities and 11 I:17 I:18 Index collaboration for cell transformation 470–474, 479S colon carcinoma accumulations 449 de novo mutations and retinoblastoma 236 defenses against accumulation 512–515 defined deliberately introduced 543 driver and passenger mutations 459S, 531 endogenous mutations 502 in germ line and soma 11–14, 132– 133SS missense and nonsense 152F, 152S, 167, 336 mitotic recombination alternative 239 neutral mutations 5–6 numbers to create human cancers 468 predicting effects 222 rate of accumulation 566–567 redundant and exclusive mutations 479S stem cell targeting 515–517 submicroscopic 239, 241 tumor maintenance role 503 and tumor suppressor genes 234–235, 33SS see also point mutations mutator phenotype 512 Mxd protein 307F, 308, 311F, 315, 316F myc gene double minutes 119 NFκB induction 213 STATs targeting 203 synergy with bcl-2 363–364 transgene in hepatocytes 318 myc-like oncogenes 472 Myc-Max heterodimers 307F, 308, 309F myc oncogene ARF and apoptosis 349F copy number amplification 13F, 118– 119 hTERT expression and 417S in human cell lines 109 mechanism of creation 117–124 mRNA levels after mitogen addition 178 as non-addictive 818, 848S oncogene activation 116–117, 120 p53 induction 339 pro-apoptotic function 250 myc protein as anti-pausing protein 22 beyond the cell cycle 311F as a bHLH transcription factor 307 cell cycle clock interaction 308 changes in human cancers 320T, 323 choice between proliferation and differentiation 306–311, 316 fusion with estrogen receptor 310 nuclear signaling role 178, 306 myc proto-oncogene 121, 313 myelodysplasia 117T, 123 myelogenous leukemias 255 myeloid cells NF1 and 257 tumor-associated stroma activation 604–606 see also monocytes myelomas antibody formation by 51–52 invasiveness and cadherins 662F multiple 9T, 11F, 41F, 52F, 783F, 844S, 851–852 osteolytic metastases 706 myeloproliferative diseases 839 myoblasts 315, 316F, 317 MyoD transcription factor 315, 317 myofibroblasts 600–603 in CAFs 598, 601 liberation of SDF-1 by 620 origins 590, 591F, 596, 597F, 599, 636–637 and patient survival 600 and PGE2 678–680 recruitment 619–620, 621F, 622, 628T tumor growth acceleration 601, 82SS and VEGF 610 in wound closure 594–596 myxomas 73 N N-myc genes 28S, 118–119 N-Myc protein 317, 323 N-ras genes 116, 192 N-ras protein 202 nasal cancer and lifestyle 58 nasopharyngeal carcinomas (NPCs) 81, 121S NAT-1 (N-acetyltransferase 1) 537S natural products as drugs 807–808, 809F, 855, 858–859, 861 numbers available 855 natural selection and genetic diversity 5, necrosis and autophagy 379–381 choice of apoptosis or 362 tumor vasculature and 606–607, 608–609F NEDD8 protein 223, 37SS negative feedback in angiogenesis 626 β-arrestin 210 CTLA-4 receptor 789 in gene expression 180S in p53 level control 342F, 347F, 352 PTP/SHP1/EPO 184S Ras oncoprotein in 167–168 in Ras signaling 256–257 SH2-containing proteins 186 in signaling pathways 216–217, 219, 864 neoangiogenesis 592, 616, 622, 626–627 neoplasms definition 47–49 histology of 32F see also cancers; tumors neovasculature 602–603, 605, 607–611, 620, 623F, 626F, 635 as dynamic 86SS NER (nucleotide-excision repair) 540–542, 544S, 545, 567 NETs (pancreatic neuroendocrine tumors) 801, 864 Neu receptor 150 see also HER2 Neu5Gc (N-glycolylneuraminic acid) 65SS neural crest, embryonic 40, 42, 657 neuroblastomas 40, 43F, 118, 315, 317, 379, 420F neuroectoderm EMT-TFs and 716 tumors 39–40, 42T, 43F, 118S, 167S, 540S neurofibromatosis 219, 255–259 neuron apoptosis 357–358 neuropeptides 210–211 neurosecretory cells and SCLCs 42 neutral mutations 5–6 neutralization, immune system 724, 726F neutrophils induced differentiation 813 recruitment by carcinomas 582 as therapeutic targets 638F in wound healing 592 NF-κBs (nuclear factor-κBs) B-cell lymphomas 804–805 BRMS-1 and 711 in carcinomas 854 EMT maintenance and 668 in inflammation and apoptosis 371, 378–379, 491, 493–494 Velcade and multiple myelomas 852, 853–854F VHL and 268 NF-κBs signaling pathway 212–214 NF1 (neurofibromin) protein 167S, 217, 219F Ras signaling regulation 255–259 NGF (nerve growth factor) 140F, 140T, 150 NHEJ (nonhomologous end joining) 546T, 552–553, 554F, 558 NHL (non-Hodgkin’s lymphoma) 642, 776S, 783, 808T NIH 3T3 cell line 15F, 106–107, 108F, 113, 114S 137F, 143S revealed as not normal 469 Nijmegen breakage syndrome 546T, 552 nitrogen mustard analogs 802T nitrosamines 76SS NK (natural killer) cells FcγRIII receptors 727F Herceptin and 780 IFN-γ and 742, 780 immunoevasion 765–769 in the innate immune response 725, 727F, 734F, 736 LAK cells as 789 in Nude mice 741 physiologic stress and 766 triggering apoptosis 375 NKG2D receptor/pathway 762T, 766–768 NLS (nuclear localization signals) 345F, 350F nomenclature genes and proteins 118 tumor types 8–9SS non-canonical Wnt 158, 209, 222, 668, 30SS non-coding DNA see ‘junk DNA’ non-small-cell lung carcinomas see NSCLCs nonchromosomal replication 84–85 nondisjunction 560 nonepithelial tumors 39, 581, 716, 9SS nonmutagens in tumorigenesis 480–484 nonpermissive host cells 80–81, 85 nonpermissive temperatures 78 nonviral oncogenes 105–107 Noonan syndrome 249S normoxia 265–267 Northern blot procedure 286F, 21SS notation chromosomal translocations 125 genes and proteins 118 Notch protein and Skp2 321 Notch receptor in dual address signaling 213F, 214–215 heterotypic signaling 582 imposition of post-mitotic state 294F in transmembrane signaling 156 NOXA protein 348, 354T, 855 NPCC (hereditary non-polyposis colon cancer) 246T, 458, 522–523F, 545–546, 571 NSAIDs (nonsteroidal anti-inflammatory drug) cancer therapies derived from 502–503 COX-2 and 494, 495F inflammation-dependent tumor promotion 490–491, 496F, 497 NSCLCs (non-small-cell lung carcinomas) 254, 465F, 605F, 628–629, 749F Index response to Iressa 846–848 nuclear factor-κB see NF-κBs nuclear membrane phosphorylation 283 nuclear receptors ER as 221 hormone receptors as druggable 819 lipophilic ligands 159–161 nucleated cells see eukaryotic cells nucleoplasm 346, 349F nucleosomes 22, 252 572S nucleotides, rate of chemical alteration 524–525 nucleus Jak-STAT pathway 202–204 micro-and macronuclei 414F as non-deformable 686 see also transcription factors Nude mice 83, 486–487, 587, 601, 629, 114SS immunocyte retention by 740–741 null alleles 335–336, 338, 340F, 355, 360S, 536 NURF (nucleosome remodeling factors) 23F Nutlin-2 820F nutrient starvation 379–381 O obesity 385–386, 387F objective responses 851 ofatumumab 776S, 777F off-target effects 823–824, 4SS, 140SS 4-OHT (4-hydroxytamoxifen) 160F oligodendrogliomas 43F ommatidia 181, 277F oncogene addiction 818, 844, 848F, 848S, 862 oncogenes acquired by retroviruses 95T activation by point mutation 116 activation by protein structural changes 124–126 altered growth factor genes as 144–146 bcr-abl as 125 cloning of transfected 114F, 114S collaboration 470–475 continuing dependence on 816–818 see also oncogene addiction detection of nonviral 105–107 endogenous and retroviral 108–113 growth promotion by 94 homology between transfected and retroviral 108 HPV 86 and hTERT expression 417S most often mutated 200 multiple, in tumor viruses 470 naturally carried by retroviruses 97–99 pleiotropy 474 proposed carcinogen activation 104– 105 rel oncogene 212, 214 retroviral, in human cancers 109T sequencing 864 shutdown in transgenic mice 817T sis oncogene 144–146 TSG importance compared with 231 v-src as 91 see also erbB; large T; middle T; myc; proto-oncogenes; Ras ‘oncoMiRs’ 26, 3SS oncoproteins altered growth factor receptors as 141–143 DNA viruses and p53 332–333 DNA viruses and pRb 295–296 as drug targets 816, 818 mitogenic signaling and 145 pRb cell cycle effects 294–298 as transcription factors 306S oocytes 381, 2SS, 55SS OPG (osteoprotegerin) 706, 708 Opisthorcis viverrini 500 OPN (osteopontin) gene 718F opsonization 724, 727F oral cancers lymphocyte depression 770, 771F oral metastases 106SS organ transplants immunocompromised humans from 745 melanoma in 748 micrometastases and 98SS organismic generations 428–429 orthologous protein 27 orthologs and homologs 28S orthotopic sites 589S OSI-774 see Tarceva osteoblasts 40F, 704–707, 709 osteoclasts 704–707, 709 osteolytic lesions 851 osteolytic metastases 668, 703–709, 718F osteoprotegerin (OPG) 706, 708 osteosarcomas 236, 243, 246T, 264F osteotropic metastases 703–707, 717, 718F outcomes research 806 ovarian carcinomas 197F, 200, 211T, 220, 748–750, 776F overexpression cyclin D in myoblasts 315 DNA methyltransferase 3B 252 DNA polymerase β 543 receptor proteins 142F, 143S, 150, 218–219 8-oxo-dG (8-oxo-deoxyguanosine) 501, 526, 543, 75SS oxygen diffusion 607–609 oxygen tensions 399, 402 tumor angiogenesis and 610, 615, 623 see also anoxia; hypoxia; reactive oxygen P P14ARF 346, 347F, 348, 349F, 351S, 377T, 821 p15INK4B gene as CDK inhibitor 289–290, 309, 312–313, 319, 320–321T target of TGF-β 312 as tumor suppressor 255 p16INK4A gene ARF proteins and 346, 347F as a CDK inhibitor 289, 302, 315, 319 changes in human tumor types 320–321T, 451F in familial melanoma 319 and senescence 398–400, 401F, 418F suppressing in mice 427 suppression in normal tissue 455 as a tumor suppressor 246T, 251T, 252, 253F, 254F, 255 p16INK4A/CDKN2A gene 251, 817 p18INK4C gene 289 p19ARF gene 255, 259S P19ARF 346, 347F, 349F, 351 gene encoding 347F, 349F, 351 as mdm2 antagonist 346 suppressing in mice 427 p19INK4D gene 289 p21Cip1 309, 312–313, 315, 320T, 323 CDK inhibition and 289–290, 291F, 292, 293F cytostatic action 353, 355 p53 induction 353 response to p53 and 340 and senescence 398, 400 p21Waf1 gene 192 p27Kip1 gene 305, 315, 316F, 319–324 CDK inhibition and 289–293, 294F changes in human tumor types 320–321T loss in G1 phase 305, 309, 319–320 phosphorylation 47SS Skp2 suppression of 321, 322F ubiquitylation 303, 309, 321 p53 gene (also TP53) centrosome number and 562F DNA damage and 340–342 importance as TSG 255, 271, 334–335, 710 inactivation by human cancers 341, 359, 376, 429, 450 inactivation in mice 428 mouse pancreatic adenocarcinoma 827 mutations and normal p53 function 335–338 mutations in human cancers 334, 335F, 530, 531F, 752, 54SS mutations in mouse papillomas 483 mutations in smokers 533–534 papovaviruses and discovery of 332–334 polymorphism and drug-induced apoptosis 132–133SS reading frame mutations 359 restoration of function 383 stromal cell mutations of 603 transformation requiring Ras activation and 473S VHL gene and 268 p53 protein as apoptosis mediator 348–352, 355–359, 375F carcinoma EMT and 667 concentration in cancer cells 352 control by kinases 347F correcting mutant stereochemistry 816 cytostatic and apoptotic roles 359 downstream targets 358 factors causing induction 339–341 importance in cell cycle control 327, 340–341 inactivation by ras 404S lability 339 possible immunogenicity of mutants 116SS premature aging and 343F, 343S and senescence 398, 400, 404S, 418F short lifetime 338–339 specialized domains 345F as a transcription factor 338, 344, 352–355 ubiquitylation 342 Kip2 gene 289, 293, 294F, 315 p57 p63 gene 345F, 360S, 368, 710, 53SS p73 gene 345F, 348, 360S, 53SS p107 protein E1A inactivation of 308 E2F represison and 302, 312F, 3131 effects of phosphorylation 315, 327 influence in G1 phase 299, 324 as a pocket protein 301 relationship to pRb 297F, 297S, 299 p130 protein 296–297F, 297S, 299, 301–302, 308, 315, 324–325 p300/CBP transcriptional activator 337F, 344 P-glycoprotein 834F PA2024 787 paclitaxel (taxol) in chemotherapy 807, 808T, 809F, 810T, 811 induction of senescence by 401F I:19 I:20 Index plus trastuzumab 779F rate of clearance 828F TIL detection after therapy with 749F Paget, Stephen 701, 709 PAHs (polycyclic aromatic hydrocarbons) 59, 61F, 525, 534 pancreas β cells 198, 326, 616, 737F exocrine 616 islets of Langerhans 616–618, 631–632 pancreatic adenocarcinoma genetically engineered mouse models 827 Hedgehog signaling 860F pancreatic cancer cells 12F, 224, 430, 451F pancreatic cancers antgiogenesis inhibitors and 631 aspirin protective effect 491 Hedgehog overexpression 858 metastatic tropism 700F ras oncogene requirement 816 survival rates 801, 832 see also Rip-Tag mice pancreatic exocrine adenocarcinoma 801 pancreatic intraepithelial neoplasias (PanINs) 451F, 817 pancreatic neuroendocrine tumors (NETs) 801, 864 Paneth cells 133F, 514F PAP (prostate acid phosphatase) 787–788 papillary thyroid carcinomas 801 papillomas 47, 480–484, 492F, 497 papillomaviruses see BPV; HPV papovaviruses 81, 84 Paracelsus 797 paracrine signaling and the EMT 669, 680F defined 145 in epithelial-stromal interactions 636–637 in GPCRs 211 by Hedgehog protein 216, 860 involving PGE2 497, 498F involving Schwann cells 258 pro-inflammatory cytokines 404 by TGF-β 770 by THF-α 492–493 Wnt proteins 208, 261F, 680F parallel progression 703S paralogs 176 paraneoplastic syndromes 118SS parenchyma 596F, 608F, 613–614, 615F micrometastases in 652 parenchymal cells 609 PARP (poly(ADP-ribose) polymerase]) 356, 569–570 passenger mutations 459S, 531, 741, 753, 119SS passive immunization bone marrow transplantation as 785 monoclonal antibodies and B-cell tumors 781–785 monoclonal antibodies and breast cancer 778–781 rituximab in 778 Patched gene 271F Patched receptor (Ptc) 156–157, 213F, 215–216 Patched-Smoothened pathway 856, 857F pathogenesis, molecular explanation 66 patient prognoses and biochemical indicators 226, 326– 327 and bone marrow DTCs 652 and cell differentiation 318 and DCIS in breast cancer 380F and gene expression signatures 714F and genetic heterogeneity 872F and lymph node effects 699 and macrophage density 604 and MGMT in glioblastomas 538 and MHC class I repression 763–764 and myofibroblasts 600, 82SS and N-myc copy number 420S and neuroblastoma type 379 and occult micrometastases 711–713 and p27Kip1 levels 321 and regulatory T cell concentration 776F and retinoblastoma type 236 and telomerase activity 420F, 420S, 430 and TGF-β levels 668 and TIL concentration 748–750 and tumor anoxia/HIF-1 level 635–636 and tumor vascularization 619, 622F and vitiligo 759 see also breast cancer prognoses; survival times patients complete responses 839, 848, 852 immunocompromised 745–746, 748, 761, 792 indications for inclusion in trials 831 Pax-6/small eye gene 8F PCNA (proliferating-cell nuclear antigen) 290, 541F, 550, 551F PCR (polymerase chain reaction) 244, 253–254F, 413F, 466, 34SS methylation-specific (MSP) 35SS use in ChIP 45SS use in TRAP assay 56SS PDEs (phosphodiesterases) 158, 159F PDGF inhibitors 632, 839 see also Gleevec PDGF (platelet-derived growth factor) in angiogenesis 611 in bone ECM 707 in carcinoma recruitment 594, 80SS in cultured cells 586 expression and HIF-1 265, 268 growth factor oncogene functions 140T, 142F, 144–146, 148F in heterotypic signaling 581, 583, 600, 79SS interstitial fluid expression 614 in monocyte recruitment 604 PDGF-R autocrine loops 839 proteins attracted to ligand-activated 184–185 in serum-starved cells 180F TGF-β ανδ 668 in wound healing 134, 589–591 PDGF receptors 163 autophosphorylation 147–148 on mesenchymal cell surfaces 142F, 144–145 PDGF-α receptor 145T, 157F, 839 PDGF-β receptor 839 role in wound healing 135F RTKs related to 152 structure 140F SU6668 as antagonist 629–632 PDK1 and PDK2 197F, 220, 143SS PDM (mean population doubling) see population doublings pediatric tumors childhood leukemias 470, 471F mutation accumulation problem 478 mutation densities 531 telomerases and 419, 420F, 420S see also retinoblastomas penetrance 4, 236F, 554, 556S PEP (phosphoenolpyruvate) 55 peptidase inhibitors 851 peptide boronic acids 851F perforin 732, 734F, 742 pericytes growth factors expressed by 584, 597, 632 in normal tissue and tumors 612, 613F PDGF in recruitment 632, 79SS recruitment and origin 583–584, 617, 632 resitance to anti-angiogenics 628T, 631F as therapeutic targets 638F in tumor vacularization 586F, 610, 628T peripheral neuropathy 811 peritoneovenous shunts 105SS perlecan 583, 585F, 624T permeability see capillaries peroxiredoxin (Prdx5) 741F peroxisomes 525 pertuzumab (Omnitarg) 782F, 782S pesticides 537–538 PET (positron emission tomography) 54F PFS (progression-free survival) see survival times PGDH (15-hydroxyprostaglandin dehydrogenase) 494, 495F, 497F PGE2 (prostaglandin E2) 494–497, 498F, 503 carcinoma EMT and 666, 669–670 myofibroblasts and 678–680 PH (pleckstrin homology) domains 185F, 188T, 194T, 196–198 phagocytic cells distinction between APCs and B cells 730F see also APCs; dendritic cells; macrophages phagocytosis 356F, 357, 526S pharmacodynamics (PD) 811, 828F, 829–831 pharmacokinetics (PK) 811, 828, 830F, 831, 850 see also half-life Phase I clinical trials 829–831 Phase II and III clinical trials 831–833 phenocopies 44F, 498 phenotypes cancer as recessive 232–235, 238S control by gene expression 19–21 defined distinct, within a tumor 61SS distinction from genotypes 5F, 505F dominant and recessive genetic determination of 9, 14–19 immortalization as 392 mutator phenotype 512 phenotypic plasticity 833 pheochromocytomas 255, 265 Philadelphia chromosome (Ph1) 61, 62F, 516, 834–835, 837 PhIP (2-amino-1-methyl-6phenylimidazo[4,5-b]pyridine) 532, 534F phorbols see TPA phosphatases PI3K regulation 197 PTPs 172 phosphatidylserine 768 phosphoinositol, IP3 194 phospholipase C see PLC phospholipids as amphipathic 193 inositol, PIK3 and 194–195 phosphorylation anti-apoptotic proteins 374 cross-phosphorylation 25SS histones 22, 23F kinase cascade activation by 192 p53 protein 344, 352 pRb protein 294, 311–315 Index proteins 17S Skp2 protein 323 phosphotyrosine 137, 138F, 147, 149, 203 SH2 interactions 26–27SS phosphotyrosine binding (PTB) 188, 26–27SS phosphotyrosine phosphatases (PTPs) 172 photosensitivity 544–545 physiologic stresses to cancer cells 376 cell cycle progression 290, 298 NK cells and 766, 768 p53 levels and 338, 340F, 344 and replicative capacity 398–404 and senescence 418S and stromal cell evolution 603 PI3 kinase pathway Bcr-Abl protein 836 in cell motility 692–693 downstream Ras signaling 193–201 Herceptin action and 781 hyperactivation in cancer cells 378 Mdm2 and cell survival 345 in mitogenic pathways 220, 290, 305 mutations in cancer cells 451 PI3K (phosphatidylinositol 3-kinase) activated PDGF-R and 184, 186 activation by HIFs 267 activation by Ras and other GFs 195F, 196–197 defective inactivation 220 mutations and TKI unresponsiveness 850 SH2 domain 183 PIN (prostatic intraepithelial neoplasia) 536F, 600F, 621F PINCH antigen 578F, 580F PIP2 (phosphatidylinositol 4,5-diphosphate) 194F, 195 PIP3 (phosphatidylinositol 3,4,5-triphosphate) and cell motility 693 PH docking 197F in the PI3 kinase pathway 193F, 196 PK (pyruvate kinase) 54F, 55 PKA (protein kinase A) 823F PKB (protein kinase B) see Akt PKC (protein kinase C) 188T, 194, 219F, 480F, 484, 491–492, 499F pathways activated by PKC-α 485F, 491 plasma cells 728 plasma membrane apposed, tethering of 592, 593F asymmetry 357 drug efflux pumps 833 signal transduction requirement 131 platelets PDGF and 134 role in cancer cell dissemination 647, 768, 93–95SS role in EMT 664 PLC (phospholipase C) 183 PLC-β (phospholipase C-β) 158–159 PLC-γ (phospholipase C-γ) activated PDGF-R and 184, 186 pleiotropy 21, 83, 93 EMT-TFs 685 HER2/Neu receptor 171 miRNAs 26, 268 of oncogenes 474, 504 Ras proteins 202 Src protein 137 pleural effusions 634, 81SS pluripotency, embryonic stem cells 44, 516, 42SS, 43SS plutonium exposure 12F, 13F PLX4720 B-Raf inhibitor 865 PLX4032 (vemurafenib) 866, 868 PMA (phorbol-12-myristate-13-acetate) see TPA PMBLs (primary mediastinal B-cell lymphomas) 804, 805F PML-RARα fusion protein 813–814 PND (paraneoplastic neurological degeneration) 118SS pocket proteins differentiation and 315 pRb, p107 and p130 as 297F, 297S R point control and 299–302 podosomes (invadopodia) 686, 687F point mutations from 3-MC 758 in B-Raf 192, 864 C-T transition mutations 525 CDK4 gene 319 in immunoglobulins 543 Kit oncogene 842F Met oncogene 154T p53 gene 334, 336, 337F, 360–361 proliferative advantage and 169 Ras oncogenes 115–116, 117T, 167 resistance to transformation 468–470 RTKs 150 in TSHR 212 pol gene 75F, 89F, 145S poliovirus 74S, 79–80 polychromatic flow cytometry 580 polykaryons 232F, 233 polymerase chain reaction (PCR) 244, 253F, 254F, 413F, 466 polymorphisms genetic markers 244 human gene pool 32SS MHC 739S, 740F p53 gene 132–133SS single-nucleotide 244–245, 361S, 34SS polyomavirus 79, 84, 165S, 470 collaboration of large T and middle T 473S see also large T; middle T polyps 47, 48F, 446 polyubiquitylation 267, 285, 342, 344, 850, 852 population doublings (PD) 393–394, 395– 396F, 397, 398F, 419F population genetics 456 positive feedback loops 217, 219F, 292, 302–303, 668–669 Rac activation 693 post-mitotic state 277, 292–294 see also differentiation; senescence postoperative therapy 598S, 780, 806 posttranslational modifications HER2 781 histones 22–23 introduced 16–17 MHC class I repression 764 other than phosphorylation 223 p53 stabilization 339, 340F, 384 pre-mRNA 26 proteins 17S Ras proteins 817F, 134SS see also phosphorylation Pott, Percivall 58–59 pox viruses 81 PP1 (protein phosphatase type 1) 295, 299 PP2A (protein phosphatase type 2A) 476– 477, 478F pRb gene 271–272 pRb protein (retinoblastoma protein) deregulation in cancer 299, 318–323, 350 and differentiation control 314–318 E7 oncoprotein and 563 E1A oncoprotein and 308 hypo- and hyperphosphorylation 294, 304–306, 311–315 inactivation and human cancers 668 inactivation and senescence 400F influences on R point transition and 318F monitoring by ARF/p53 348–349 transcription factors interactions 299– 304, 325 as a transcriptional repressor 302 transformation requiring Ras activation and 473S see also cell cycle pre-clinical testing 811, 825–829 pre-malignant cell attrition 396F, 397, 427F pre-mRNA 17S, 19, 21–22 K-ras alternative splicing 166 posttranslational modification 26 processing 18F Twist transcription factor and 695 predisposition see cancer susceptibility pregnancy 69–71SS premalignant cells precursor-product relationship 446 progression from 439 premalignant changes 46 PRI-724 822 primary cells 469–470 primary tumors cell travel to potential metastatic site 643–651 development timescale 103SS distinguished from metastases 33, 50 EMT within 683 genetic similarity with metastases 718, 719F metastatic tropism and 700F re-seeding from metastases 464, 702 subpopulations and metastatic propensity 713 surgery and metastases 598S, 625 volume and number of cells 641 see also tumor masses primase enzymes 410 primers, DNA 410 pro-apoptotic genes 549 pro-drug therapy 785 pro-enzymes 591, 685–686, 688 procarcinogens 62–63, 529F procaspases 367, 369F, 372F, 374F, 375 ‘professional’ APCs 726, 728–729, 730F, 733F, 742 progenitor cells see transit-amplifying cells progeria 571 progesterone 160, 467F, 485, 486F, 500T, 503 prognoses see patient prognoses ‘prognosis genes’ 804F progression stage, tumorigenesis 482 prokaryotic cells, transcription 16 prolactin 485, 486F proliferation see cell proliferation proline and SH3 domains 183F, 186–187 proline hydroxylases (PHD) 266F, 267 promoter independence 482, 490, 497 promoter methylation in cancer pathogenesis 451F, 452, 455, 480 and CDH1 repression 659 gene silencing 253, 468, 538, 547 in immunoevasion 761, 792 MSP technique 35SS and TSG inactivation 249–252, 319, 457 and VHL inactivation 265 promoters, nonmutagenic carcinogens 65 promoters, of tumorigenesis 481–482 endogenous 486 I:21 I:22 Index humans 484–486, 498–501 insulin and IGF-1 as 503 mice 481–484 viral 490 promyelocytic leukemia 107, 109 proofreading by DNA polymerases 519, 520F, 521 prophase 278F, 279, 284 prostate cancers androgen deprivation therapy 787, 788F β-catenin in 208 BRCA2 and 550 chromosomal translocations in 557 desmoplastic stroma 598F examples of necrosis 608–609F GST-π and 536 IGF-1 and 386S metastatic tropism 700F mitogenesis 221S mTOR suppressors and 272 proportion unlikely to cause death 802, 128SS RSGs and 259S stromal fibroblasts and 600F transcription factor deregulation 122 treatment with sipuleucel-T/Provenge 787–789 proteases cathepsin B protease 669, 673F in human genome 104SS introduced 16, 17S pro-enzyme forms 591 role in invasiveness 645, 685–689 see also caspases; granzymes; MMPs proteasome inhibitors 850–855 proteasomes 730, 733F, 764, 26SS see also ubiquitylation protein binding domains 188 protein conformation changes 182 protein kinases amino acid targets 137 downstream signaling from Ras 189– 192 drug screening against 140–141SS human kinome 874, 138–139SS immunoblot analysis 137F number in human genome 28S, 224, 138SS structural similarity 823F see also phosphorylation; PKC; tyrosine kinases protein-protein interactions as drug targets 820, 822 transcription factors 216 protein relocalization model 182, 222 protein synthesis Akt/PKB and 198 cycloheximide blocking 177 phenotype creation through 14–19 proteins accumulation of misfolded 853F denaturation 78 enzymes as 15 enzymes devoted to DNA repair 538 notation for genes and 118 number in a single cell 176 number in human body 17S oncogene activation by structural changes 124–126 posttranslational modification 16–17 proto-oncogene activation mechanisms 113–117 signaling function 15–16, 132–133 similarities among metazoans 138SS telomere-binding 409–410, 411F proteoglycans 583, 591, 597, 606, 685 proteolysis, Notch receptor 215 proteomic analysis 803S, 806 proto-oncogenes abl as 125 activation mechanisms 113–117, 122 c-src as 92–93 common cellular 108–113 deregulation by translocation 122T detection by insertional mutagenesis 97, 98S exploitation by retroviruses 94–97 germ line and 249S LMO2 and Bmi-1 as 100S mutation of 105 in vertebrate genome 93–94 protozoa absence of TK receptors 141 biochemical parallels with mammals 27 Provenge (sipuleucel-T) 787–789 proviruses 88–89, 96, 97–99, 351S endogenous 104, 18–19SS provirus integration 120 PS-341 see Velcade PS (phosphatidylserine) 357 PTB (phosphotyrosine binding) 26–27SS PTB domains 188 Ptc gene 157, 213F, 215, 271F, 582F cyclopamine action and 856, 859 PTCH gene 215, 856 PTEN gene mutations 603 PTEN phosphatase 197, 200–201, 220, 222, 259S, 820 inactivation and Iressa 846 see also Akt/PKB PTHrP (parathyroid hormone-related peptide) 706F, 707, 708F, 708S PTPs (phosphotyrosine phosphatases) 172, 184S, 223 PUMA protein 348, 354T, 371 purines 484S, 524–525 pVHL protein 265–268 pyknosis 356, 370 PyMT transgenic mice 672–673F, 680F pyrimidine dimers 527, 528F, 542–543, 544S, 545 pyrimidines cross-linking 344S, 353 transitions and transversions 484S, 535 R R point (restriction point) 281F, 282, 294, 298S events influencing the transition 318F Myc and 311 positive feedback control 302–303 pRb control 298–299 Rac protein 198–199, 201F, 202, 690, 692–693 RAD50 protein 548T, 550 RAD51 protein 546T, 550, 552, 553F, 555F radiation exposure age as a factor 443S cancer risk and 58, 60, 344S irradiated tumor cell vaccination 741, 789 p53 levels after 353 plutonium 12F, 13F sensitivity of asmase-deficient mice 363 ultraviolet light 344S see also X-ray exposure radical mastectomy/prostatectomy 129SS radiolabeling glucose 53 nucleosides 90S radionuclides 12–13F, 783, 807 radiotherapy 633, 806 Rae1 ligands 766F, 767–768 RAET1 subfamily 766F Raf kinase B-Raf 864–866 in mitogenic pathways 220 p53 expression and 352 targeting 817F Ral-A and Ral-B 201 Ral-GEFs 201 RalBP1 protein 201F, 202 RANK receptor/RANKL ligand 706–708 rapamycin (sirolimus) 861–864 Raptor protein 862–864 RAR-α (retinoic acid receptor-α) 813 RAR-β (retinoic acid receptor-β) 455, 814 RARβ2 gene 254 Ras effectors 190, 202, 224–225, 692 Ras family proteins activation by growth factor receptors 188–189, 692 activation by Sos 181, 189 apoptosis induction 350F defective inactivation 219 as downstream signalers 165–169, 351–352 inhibition and FTIs 134SS lipid groups 16 pleiotropy 202 see also Rho family proteins; small G proteins Ras GAP proteins activated PDGF-R and 184, 186 negative feedback 217 NF1 and 167S, 256, 257F, 259 ras-like oncogenes 472 Ras-like proteins 689–695 ras oncogene carcinoma EMT and 667–668 cell proliferation and 163, 171F continuing requirement 816 E1A collaboration 308 expression suppressed by Let-7 26 nature of mutations 167 proteins encoded by 117T, 166 senescence and tumor progression 404, 422–423 see also H-ras; K-ras; N-ras Ras oncoproteins as cancer-specific antigens 751–754 unsuitable as a drug target 819 Ras protein importance of Raf pathway 192 in a signaling cascade 180–182 switch domains 168F, 190 TSP1 gene shutdown 624–625 Ras signaling cycle 166F, 191F Bcr-Abl protein 836 and cell motility 692 and human cell transformation 476–477, 478F, 505 NF1 regulation 255–259 PI3K pathway 193–201 pRb phosphorylation 304–306 Ra pathway 201–202 Ras-Raf-MAPK 190–192 and viral transformation 473S rational drug design 822–824, 834, 839, 866 Rb gene cloning 242–243 and haploinsufficiency 259S in human cancers 255, 321T loss of heterozygosity 241–243, 33SS in mice 270, 271F promoter methylation and 251 retinoblastoma puzzle 48–49SS as tumor suppressor 235F, 236–244, 296 VHL compared to 265 whether dominant or recessive 238S see also pRb RB protein see pRb protein Glossary RCC (renal cell carcinoma) 630T, 864 reactive nitrogen species (RNS) 499 reactive oxygen species (ROS) 283, 370, 394, 398, 402, 499 oxidative DNA damage 525 superoxide dismutase and 535 ‘reactive stroma’ 664–666, 670–671, 680, 685, 702 reading frames, defined 116 receptor dimerization growth factor triggering 143, 147–149, 169 heterodimers 149 ligand-independent 150–151 receptor firing deregulation 142F see also ligand-independent firing receptors co-activators and co-repressors 161 nuclear receptors 159 other than RTKs 153–159 protein overexpression 142F, 143S serpentine receptors 157, 159 see also cell adhesion receptors; cell surface receptors; growth factor receptors; tyrosine kinase receptors recessive phenotypes 4, 232–235, 238S reciprocal translocations 12F, 362–363, 835 recombinant DNA technology 66 recombinant endostatin 628 recombinant PAP 787 recombinant vectors 404S, 6SS redheads 535F reductionism in cancer research 577–578, 874 refractory tumors 627, 783, 832, 846, 847F regulatory circuits see signaling cascades/ pathways regulatory sequences 117 regulatory T cells (Treg) 755, 774–778, 792–794 adaptive immune suppression 737–738 cancer cell immunoevasion with 774–778 proportion of GTLs and 778 rel oncogene 212, 214 remission in APL 813 replication forks 542, 567 fragility 521, 523F, 550, 556, 569, 570F stalled 543, 550, 551F, 555F replication stress 567–568 replicative doublings see population doublings replicative immortality see immortalization replicative senescence see senescence reproductive cloning 449, 2SS resorption of bone ECM 704 restriction enzymes 108F, 110F, 113, 115F, 244 restriction point see R point ret gene 154S retinoblastomas 43F, 235–238, 241 familial 236–237, 249S, 251 incidence and age 443F, 443S RB gene and 48–49SS sporadic and familial 236–238 retinoic acid 254, 315, 814 ATRA (all-trans-retinoic acid) 813–814 retinoic acid receptor-α (RAR-α) 813 retinoic acid receptor-β (RAR-β) 455, 814 retroviral vectors 14–15SS retroviruses activation of endogenous 104–105 alternatives to RSV 93–94, 98S cell-type specific 144 endogenous 18–19SS exploitation of cellular genes 91–92, 94–97 gene therapy using 100S integration into host chromosomes 87–89 oncogenes acquired by 95T oncogenes carried by 97–99 oncogenes in human cancers 109T RSV as 75F, 88 see also ALV; MLV; RSV reverse transcriptases (RT) complementary DNA in vitro from 29 rare in human tumors 105 RNA virus transmission and 88 RSV encoding 89 in telomerases 413, 421, 434 revertants 64F RFLP (restriction fragment length polymorphism) markers 244, 245F RGD receptors 162F rheumatoid arthritis 609, 737, 784 Rho family proteins 198 cell motility and 690, 692, 694 RhoA and RhoB 693 RhoC 695 see also Cdc42; Rac Rho-GEFs (guanine nucleotide exchange proteins) 193F, 198, 691–692 rhodopsin signaling 210 RhoGDI-2 711 ribbon diagrams 17F ribosomes 16, 862 Rip-Tag mice cathepsin release 647, 669, 673 described 616–619 EMT illustrated in 661, 669 macrophage recruitment in 647, 669, 673 metastases in 643 MMP-9 release 617 pancreatic tumors of 605F tumor angiogenesis 619, 628, 631, 635 as tumorigenesis model 618, 629 RISC (RNA-induced silencing complex) nucleoprotein 25 risk factors lifestyle as 58–59, 60T, 67 obesity 385–386 radiation exposure 58, 60, 344S see also tobacco rituximab (Rituxan) 776S, 777F, 778, 782–784, 844S RNA antisense 417 enzyme function 16 hTR template in telomerases 413–415, 416F, 417, 426F, 426S, 436 mTR template in telomerases 423 synthesis in eukaryotic cells 17–19 see also hnRNA; lncRNA; miRNAs; mRNA; shRNAs; siRNA RNA interference (RNAi) 781F, 4SS RNA polymerases RNA polymerase II (Pol II) 18F, 21–22, 161, 308 transcription factors and 21 RNA primers 412F RNA viruses genome structure 87 genomic transmission 87–89 RNA replication by 74S rodents genetic similarity with humans 475 see also Ames test; mouse Rottweilers 154S Rous, Francis Peyton 31, 59, 71, 72–74 RSV (Rous sarcoma virus) cell transformation in vitro 75–77, 474 discovery and origins 72–73, 17SS life cycle and transmission 87–89 mechanism of Src transformation 188 replication and transformation genes 89 temperature-sensitive mutant 78 virion 75F see also src gene RTKs see tyrosine kinase receptors Rubin, Harry 75–78 RUNX gene 247T, 351S Runx3 gene 270 RXR (retinoid X receptor) 160F S saccharine 66S, 64SS Saccharomyces cerevisiae amino acid sequence 8F elements of cell cycle clock in 323 in genetic experiments IRA1 and IRA2 proteins 256 SH3 domains in 186 telomerases and 413F, 419–420 Saccharomyces pombe 8F SAHFs (senescence-associated heterochromatic foci) 402–403S, 403F, 418S absence from mice 423 senescence and 432 Salmonella sp 61–62, 63F sarcomas 38, 39T ALT mechanism in 421 see also RSV SASP (senescence-associated secretory phenotype) 404 satellite sequences 521 scatter factor (SF) see HGF SCCs (squamous cell carcinomas) 37, 38F adenoma/papilloma progression 448F, 480 age and 443F carcinogen exposure duration 444F field cancerization 456FF head-and-neck (HNSCCs) 119T, 145T, 319F, 557F 765F HPV and 344S, 746F, 50–51SS immunoevasion 123SS inflammation and 488T invasiveness and fibroblasts 92SS myofibroblasts and prognosis 82SS ultraviolet radiation and 527, 50–51SS xeroderma pigmentosum and 544 SCE (sister chromatid exchange) 64S SCF (stem cell factor) 140T, 144–145T, 146, 149F, 152S, 258F, 617S Schwann cells 256F, 258 schwannomas 40 SCID mouse strain 11S, 19S, 83S, 460F, 587, 589F SCID (severe combined immunodeficiency) 100S, 553 SCLC (small-cell lung carcinomas) 42, 146, 150, 210–211 ABT-737 effects on 820F Hedgehog ligands and 216 SDF-1 (stroma-derived factor-1) 601–602 SDF-1/CXCL12 chemokine 583, 591F, 601– 602, 620, 638F SDH (succinate dehydrogenase) 268, 38SS sea anemone 675, 676F Sec5 protein 201 second messengers 194, 210 second-site cancers 802, 807 ‘seed and soil’ hypothesis 701, 709, 105SS E-selectin 773, 123SS selectivity 823, 826, 829 I:23 I:24 Index biological and biochemical 826 drugs and drug candidates 808, 810T, 823, 826, 829 Herceptin, for overexpressed proteins 779 ‘self and non-self’ see immune tolerance Sendai virus 232F, 233 senescence 340F, 345, 382–383 biochemistry 402S in culture and in vivo 400–403 distinguished from crisis 398 physiologic stress and 398 preferred to immortalization 476 telomeres and 417, 418F, 422–423, 435 senescence-associated heterochromatic foci see SAHFs senescence-associated secretory phenotype (SASP) 404 sentinel nodes 698, 699S sequence information analysis in tumor progression 468 exchange between telomeres 420, 422F tumor genomes 865–866 see also genome sequencing sequence motifs 21, 301, 352 sequence similarity, Src and EGF-R 139 serial passaging 393 SERMs (selective estrogen receptor modulators) 161 serpentine receptors 157, 159 serum distorting factor in cell culture 586–587 as source of growth factors 134 withdrawal during the cell cycle 281–282 ‘serum starvation’ 177, 180F, 304, 310, 598–599 sevenless gene 181 Seventh-Day Adventists 57 sex chromosomes 9, 10F SFRP1 protein 668, 670F SH1 (src homology domain) 181–182, 840 SH2 function 183–184 phosphotyrosine binding 26SS Ras activation and 188–189 in STATS transcription factors 203 SH3 origins 186 Ras activation and 188–189 structure and function 183F, 186–187 Shc adaptor protein 181, 221S sheep 855 Shelley, Mary 331 shelterin complex 411F, 422F SHH gene 856 Shope, Richard 79 Shope papillomavirus 79F, 81 SHP1 protein 183, 184S SHP2 protein 184 shRNAs (short hairpin) 478F, 670F, 683F, 769F, 4SS Siah-1 gene 354T, 355 sialic acid derivatives 65SS side-effects of anti-cancer drugs 816, 829, 864 clinical trial design and 829 and intervention 802 signal transduction 16 actions of the TPA promoter 484 and cancer-associated genes 506F in cancer cells 217–220 integrin signaling 204–206 Jak-STAT pathway 202–204 kinetics of 222 in normal cells 131 proteins attracted by phosphorylated receptors 184F Ras proteins as downstream signalers 165–169 receptors other than RTKs 153–159 small lipophilic ligands 159–160 three methods available 221–222 signaling contextual signals and EMT 662–669 heterotypic signaling 581–589, 595F, 609–610, 617, 628, 634–636, 638F signaling cascades/pathways activated by PKC-α 485F afferent and efferent signals 221 ancient origins 181–182 apoptosis signaling cascade 349, 367, 385 caspase cascade 367, 369F, 371, 372F control by tyrosine phosphorylation 182–188 convergence on p53 341–342 for cyclin D induction 286–287 downstream of p53 340F, 350F, 352, 358, 368F downstream of Ras 189–202 dual address signaling 212–216 EGF-mediated cell motility 694 extent of pathway 177–180 feedback control 216–217, 219F inflammation-dependent tumor promotion 490–498 interaction and complexity 223–224 MAPK 191–192 mTOR regulatory circuit 863F mutli-kinase cascades 29SS needed for human cell transformation 476, 506F Patched-Smoothened pathway 856, 857F PI3 kinase pathway 193–201 possible organization 182, 188–189 proteasome role 851 Ral pathway 201–202 Ras protein role 180–182 RTK, complexity of 28SS siRNA-based regulatory circuits 3SS specificity 176, 188–189 TKI responsiveness and 850 triggering EMT 674F visualization from crystallography 226F in wound healing 589 see also mitogenic pathways; Wnt signaling signaling proteins as drug targets 816–817 simian sarcoma virus 144 sipuleucel-T (Provenge) 787–789 SIR (standardized incidence ratio) 746F siRNA (small interfering RNA) 264F, 681, 848F ‘knocked-down’ gene expression 4SS sirolimus see rapamycin sis oncogene/Sis protein 144–146 site-directed mutagenesis 204F S6K1 kinase 862 skin cancers induction in mice 481F, 482–483F lifestyle effects 58 sunlight and 344S, 535 see also SCCs skin rashes, anti-EGF-R therapy 850, 142SS Skp2 gene 303, 47SS Skp2 protein 303, 321, 322F, 323 SKY (spectral karyotype) analysis 12F, 62F, 280F, 434F Sky1 (SR-protein-specific kinase of budding yeast,) 823F Slug transcription factor 662F, 675, 676F, 677–678, 679F, 680–681, 683F, 684 α-SMA (α-smooth muscle actin) 595–596, 597F Smac/DIABLO 369F, 370 Smad transcription factors 216, 259S, 312–313, 606 Smad4/DPC4 gene 452, 817 small G proteins 199F small T oncoprotein (SV40) 476, 477F, 477S smoking see tobacco Smoothened protein (Smo) 157, 213F, 215 acquired drug resistance 812T cyclopamine actions 856–859, 860F SNAI2 see Slug transcription factor Snail transcription factor (SNAI1) 636, 675, 676F, 677–678, 679F, 680– 681, 683, 684F SNPs (single-nucleotide polymorphisms) 244–245, 361S, 34SS sodium bisulfite 35SS solubility, drug candidates 826 somatic mutations 11, 14 Sonic Hedgehog ligand 216 Sos gene (son of sevenless) FAK and 204 Ras activation 181, 188–189 Rho activation 691 Southern blot procedure (Edwin Southern) 108, 21SS Sox9 transcription factor 658F, 678, 679F S1P (sphingosine-1-phosphate) 16F space-filling models 17F spectral karyotype (SKY) analysis 12F spindle assembly checkpoint (SAC) 561 spleen 383F, 513, 701, 772 splicing 17 see also alternative splicing sporadic cancers promoter methylation in 251 retinoblastomas 236–238 Sprouty protein 219F src gene 89F antibodies against 23SS evolutionary conservation 91F in human tumors 113 presence in uninfected cells 89–91 pronunciation 90 structure 823F viral version, v-src 91, 135, 144 Src homology domains in signaling pathways 182 see also SH1; SH2; SH3 Src kinase activated PDGF-R and 184, 187S functions of SH2 and SH3 domains 187S structure of 182, 187F substrate specificity 137–138 as a tyrosine kinase 135–138 SSBs (single-strand breaks) 569–570 STATs (signal transducers and activators of transcription) 203–204, 287 staurosporine 356F, 366F stem cell compartments 512, 516, 680, 74SS stem cell pools 69SS stem cell state 677–680 stem cells and adenomatous polyposis 261–262, 264 adult mouse, mTERT in 424F autocrine signaling and 146 differentiating within a tumor 464 gene therapy using 100S genome protection 512–513, 72–74SS identification in tissues 514F and inflammatory conditions 431S mesenchymal cancer cells resembling 666 Glossary mesenchymal stem cells 596, 597F, 636–637 minimizing accumulated mutations 517–518 as mutagenesis targets 515–517 organ size and proliferation 31SS and retinoblastomas 235F telomere length 433–434 see also cancer stem cells; embryonic stem (ES) cells stereochemistry, drug design 822 steroid hormones 160, 485, 486F, 503 STI-571 see Gleevec stomach cancer 127, 270, 491, 529, 780 stratification of cancers 803, 804–805F, 806, 846–847, 131SS Streptomyces spp 855, 861 stress fibers 694 stroma 34–35 stromal cells contribution to invasiveness 669–671 contribution to tumorigenesis 600–603 drug responsiveness and 873 reactive or desmoplastic stroma 596–597, 598F stromal components of epithelial tumors 578–579, 581, 585 stromalization 594 stromelysin-1 (MMP-3) 594F, 689F SU5416 629, 631F, 632 SU6668 629, 631F, 632 SU11248 839 sulindac 490, 494 SUMO protein/sumoylation 223, 352, 384, 37SS sunitinib 630T, 635F sunlight 344S, 544S, 545 supernumerary centrosomes 561 superoxide dismutase 535 surgery and adjuvant chemotherapy 806 and adjuvant radiotherapy 806 radical mastectomy 129SS and tumor growth 598S, 625 surrogate markers 242, 699, 829, 850 survival times five year APL 813 comparative 859 trends 798, 870F five year progression free lymphomas 810 NSCLCs 846 pancreatic tumors 801 five year relapse rate 838 six month progression free 866 see also age-adjusted mortality; KaplanMeier plots; patient prognoses survivin 820F, 822 SUV39H1 HMT writer 23F SV40 virus 79–82, 84–85, 87F, 87S, 88–89 genome integration 86F mesothelioma and 11SS pRb complex formation 296, 297F see also large T antigen; small T oncoprotein switch domains, Ras protein 168F, 190 symbiotic tumor subpopulations 466, 61SS symmetrical cell division 461, 515 synchronous growth cultured cells 177 embryos 285 syncytia 233, 356F, 609F syndromes retinoblastomas as 235 see also familial syndromes synergies bcl-2 and myc 363–364, 475 HBV and aflatoxin-B1 490 HPV and ultraviolet radiation 344S rapamycin and other immunosuppressives 861 see also collaboration; multi-drug protocols syngeneic hosts 83, 84F, 332, 478 histocompatibility 739–740 tumor transplantation 756–757 systemic lupus erythematosus 737, 784 systems biology concept 874 T T-ALL (T-cell acute lymphocytic leukemias) 215 t-loops 409, 410F, 411F, 412, 418F, 422F T lymphocytes biphasic response to APCs 89 controlling CRCs 750 E-selectin and 773, 123SS immunoediting and 743 see also CTLs; helper T cells; regulatory T cells; TCRs T3151 protein 839 tamoxifen 161, 221S, 310, 350F, 819 4-hydroxy- (4-OHT) 160F TAMs (tumor associated macrophages) 605F, 606, 669 TAP (transporter associated with antigen presentation) proteins TAP1 and TAP2 764, 765F Tarceva 824F, 845–847, 848S, 850 TAS (tumor-associated stroma) 578F, 598, 604–606 TATAs (tumor associated transplantation antigens) 756–761, 778 evoking immune responses 758–761 melanoma antigens 121SS tax gene 99 taxol see paclitaxel taxonomy of tumors 49F Taxus brevifolia 807 TC cells (cytotoxic T-lymphocytes) see CTLs Tcf/Lef proteins 208, 263F, 305 Tcf4 transcription factor 262 TCR (transcription-coupled repair) 542 TCRs (T-cell receptors) antigen recognition by 725, 728F, 733F, 789 origins of diversity 109–111SS translocations in lymphomas 557 tea 820F, 821 telomerase-negative mice 423–425 cancer susceptibility 425–429, 434 as model for human tumors 429–433 telomerases and cancer cell proliferation 417–419 expression by incipient cancers 412–417 hTERT catalytic subunit 413F hTR RNA subunit 414–415, 416F, 417, 426F, 426S, 436 inhibition as a potential therapy 435 and interspecies differences 476 isolation 414F and pediatric tumors 419, 420S prevention and escape from crisis 416 structure of the holoenzyme 413, 415F suppression of tumor growth 419F TRAP assay 412, 413F, 416F, 420S, 56SS telomere collapse 259, 499 telomeres 3’ overhang 409–410, 414 ALT mechanism maintenance 420 and crisis 409–411, 428, 435 cultured cell proliferation limitation 404–409 defects and dyskeratosis congenita 426F, 426S in embryos and stem cells 433–434 erosion in mTR negative mice 425F, 427F function in chromosomal DNA 405 maintaining without telomerases 419–423 nucleotide sequence 406, 409 number in various cells 414S and senescence 417, 418F, 418S, 422– 423, 435 shortening with cell proliferation 407F, 428 species differences 423–425 structure 409–411 telophase 279 Temin, Howard 76–78, 87–88, 96, 105, 469 temozolomide 523F, 528, 538–539, 568, 809F temperature-sensitive RSV mutant 78 teratogens 855–860 teratomas 42–44, 478 TERC gene 414, 434 see also hTR RNA subunit terminal deoxyribonucleotide transferase (TdT) enzyme 357F, 52SS testes 755, 759F, 760 testicular cancer 808 Tet (ten eleven translocation) enzymes 24 Tetrahymena spp 414F TGF-α (transforming growth factor-α) expression and HIF-1 265, 268 growth factors as oncoproteins 142F, 145–146, 149F, 150, 170, 171F, 172 in heterotypic signaling 581, 618 Myc and 309 TGF-β (transforming growth factor-β) 146, 155–156, 259S in angiogenesis 611 bone metastases and 706F, 707, 708F, 708S cell cycle progression 290, 311–315 conflicting influence in tumor development 100SS EMT-TFs 677 in heterotypic signaling 581 immunosuppressive action 770 inactivation in colonic tumors 450, 487 inactivation in mice 600 inhibitors 871F microsatellite instability 547 myofibroblast production 596 pRb effects 311 release by regulatory T cells 738 senescence and 404 suppression of proliferation 275, 100SS in wound healing 589–592 TGF-β signaling pathways 213F, 216 autocrine signaling 667 carcinoma EMT and invasiveness 666–668, 670 TH cells see helper T cells therapeutic indices 810T, 816, 826, 829, 855 therapeutic resistance 870, 872F see also drug resistance therapeutic window 830F, 831 therapies see cancer therapies; drug therapy Thomas, Lewis 511, 739 3-MC (3-methylcholanthrene) see MC thrombin, in extravasation 651S thrombopoietin (TPO) 155, 202–203 thrombospondin-1 359, 382 thymus immune tolerance 754 lymphoma survival in 826 I:25 I:26 Index T cells and 736–737, 740–741 thyroid cancers 154S, 212 Tiam1 protein 692–694 TILs (tumor-infiltrating lymphocytes) 748–750, 758S, 763F, 774, 777, 791, 792T adoptive cell transfer using 791 FasL and 771F MHC class I and 764 regulatory T cells among 774, 777 timescales, human tumor development 440–442 TIMPs (tissue inhibitors of metalloproteinases) 251F, 254F, 624T, 626, 688, 710T, 711 tissue architecture 132F Tissue Factor 591F, 596F tissue-of-origin 453S see also cells-of-origin tissue sections 32, 33F tissue-specific genes 20–21 tissues preferentially colonized see metastatic tropism TMEM cell triads 645, 648F TNF-α (tumor necrosis factor) 491–494, 499F TNF (tumor necrosis factor) proteins 373, 374T, 379 TNF-α (tumor necrosis factor) carcinoma EMT and 666, 668–670, 681 TNP-470 630 tobacco smoking 58, 59T and cancer mortality 440, 441F, 867 carcinogens in smoke 59–60, 66S chromosomal translocations 557F G-to-T transversions 533 methylation of p16INK4A 455 topoinhibition see contact inhibition topoisomerase inhibition 808T, 809F, 871S TORC2 complex 862, 143SS toxicity clinical trial design and 829 cyclopamine 859 multi-drug therapies and 811 see also side-effects Tp53/Trp53 gene see p53 gene TPA (12-O-tetradecanoylphorbol-13acetate) 480–484, 485F, 486, 497, 499F inflammatory pathway 491–492 TPO (thrombopoietin) 155, 202–203 TRAIL ligands 372F, 373, 374T, 377T TRAMP transgenic mice 766F transcription 16 histone modification and 23–24 transcription factors (TFs) activation without protein synthesis 177–178 AP-1 transcription factor 192, 304 bHLH 307–308, 317 β-catenin 208 C2H2 transcription factors 675 EMT programming by 672–677 ERG transcription factor 122 Erk kinase phosphorylation 192 ETV1 122 Forkhead 320T, 323 Fos 286F, 304, 305F FOXC2 675F, 676F, 679F FOXP3 737, 751T, 776F fused domains 126 gene expression and 21–24, 124 Gli 157, 215–216, 856–858, 860F Goosecoid 675T, 676F, 677 HIF-1, and 265–268, 610, 623, 636 MyoD 315, 317 Notch receptor signaling and 156, 213F, 214 oncoproteins as 306S p53 protein as 338, 344 in prostate cancer 122 Smad 216, 259S, 312–313, 606 small lipophilic ligands 160 Sox9 658F, 678, 679F specified by IEGs 178 STATs 203–204, 287 Tcf/Lef 208, 262, 263F YAP 31SS ZEB1 and ZEB2 675T, 676F, 679F 681, 682–683F, 99SS zinc finger 675, 856 see also E12; E2F; EMT-TFs: Id: Slug; Snail; Twist transcriptional pausing 22 transcriptional promoters 113, 121–122, 680 transcriptomes 806 transdifferentiation EMT as 19, 42 fibroblasts 90SS between lineages 466 of T cells 777 in tumor cells 42, 596, 603 transduction see signal transduction transfection see DNA transfection transferrin 759–761 transformants nonpermissive host cells 81 persistence of virus genomes 83–87 properties 82T in vitro behavior 77 transformation 19, 76 collaboration requirement 470–474 genetic changes required 476–477 relationship to invasiveness 685 requirement for maintenance of 77–79 resistance to 468–470, 475–480 RSV use of cellular genes 91–93 transgenes, oncogenic 165F, 165S, 363 transgenic mice COX-2 carcinoma inhibition 596 oncogene collaboration 474–475 TRAMP model 766F, 767 see also mouse strains; Rip-Rag mice transit-amplifying cells (progenitor cells) dedifferentiation 844S, 872, 59SS Gleevec effectiveness 841–842, 843F in multi-step tumorigenesis 59–60SS as mutation targets 517S in stem-cell division 461–462, 466F, 512–513 transitions, C-to-T 525, 527 transitions, G-to-A 484S translation, RNA 16 translation initiation factors 192 translocations see chromosomal translocations transmembrane domains 139 transmembrane pumps see drug efflux pumps transphosphorylation 146–153, 155F transplantation autologous transplantations 582, 583F, 787, 788F see also bone marrow transplantation; organ transplants; tumor transplantation transposable elements 452 transversions, G-to-T 484S, 526, 531F, 532, 533 TRAP (telomeric repeat amplification protocol) assay 412, 413F, 416F, 420S, 56SS trastuzumab see Herceptin TRFs (telomeric restriction fragments) 407F, 410F, 411, 419F TRF1 411F TRF2 406F, 411F tricarboxylic acid cycle see citric acid trichostatin A (TSA) 254 triosephosphate isomerases 753 TrkA kinase 120, 121F trophic signals 376 α-tropomyosin pre-mRNA 18F Trp53 gene see p53 gene trypsin 490 TSC1 gene/protein (and TSC2) 199T, 246, 277F, 862, 864 TSGs see tumor suppressor genes TSHR (thyroid-stimulating hormone receptor) 212 Tsp-1 (thrombospondin-1) 163T, 354T, 359, 382 angiogenesis and 598, 623, 624T, 625F TSS (transcription start sites) 23F TSTAs (tumor-specific transplantation antigens) 756–758, 778, 119SS tuberous sclerosis 864 tubulin 15F tumor-associated proteins 84 tumor-associated stroma (TAS) 578F, 598, 604–606 tumor cells see cancer cells tumor development/progression altered energy metabolism 53–55 angiogenesis barrier 615–618, 622, 632 BFB cycles and 430–431 and blocked differentiation 314S cell cycle checkpoints and 280 chronic inflammation in 486–490 colon carcinoma 446 complexity of 439–442 DNA damage in 382–383 dominance and recessiveness in immortalization requirement 394–398 Immunoevasion and 750, 792 indolent tumors 569, 743, 745, 801, 803 kinetics 441–442 microarchitecture 33–34 mutation frequency 531 necrosis and autophagy 379–381 NK cells and 767 from normal tissue 32–34 number of genes implicated 112 p53 inactivation 359, 404S as progressive 45–50 TGF-β conflicting roles 100SS timescales 440–442 see also invasion-metastasis cascade; malignancy tumor-initiating cells (TICs) see cancer stem cells; cells-of-origin tumor masses absence of lymphatic vessels within 696 effects on nearby tissue 641 hydrostatic pressures within 614, 84SS lymphocyte infiltration 748 polymorphism within 459–460, 466F proportion of non-neoplastic cells 579 refractory tumors 627, 783, 832, 846, 847F replicative generations to form 395–397 see also primary tumors; tumor vasculature; tumors tumor rejection 83 tumor self-seeding 702 tumor stem cells see cancer stem cells tumor suppressor genes (TSGs) APC gene 245F, 246T, 251T, 254F, 259–265 cloned human TSGs 246–247T confirmation of existence 234 and familial cancers 248–249 Glossary function of derived proteins and 254–255 and hTERT expression 417S identifying using LOH 243–247 importance compared with oncogenes 231 importance of p53 255, 271, 334–335 inactivation through promoter methylation 249–252 mechanism of elimination 238–241 p63 and p73 as 360S p14ARF as 348 resistance in human cancers 503 role of LOH 33SS species differences 428 TSC1 gene 277F VHL gene 246T, 251T, 265, 266F, 267–268 vulnerability of genetic locus 348 tumor transplantation 756–757 tumor transplantation antigens TSTAs and TATAs 756–758 tumor types/locations biochemical characterization ALT state association 421 altered PI3K pathways in 200T anti-apoptotic alterations 377T cell cycle clock deregulation 320– 321T and EMT transcription factors 675T and GPCRs 211T having altered RTKs 144T, 152F, 152S Id overproduction 323 making autocrine growth factors 145–146 truncated EGF receptors in 141, 143 cancer-specific antigens 753F and clinical trials design 831–832 epithelial cancers and age 440F etiological differences geographic variations and 55–58, 535 tumor promoters 500T tumors with viral causes 103 genetic differences 14F, 44, 571 BFB cycles 432–433 classification by gene expression 20F gene activation frequencies 224–225 gene methylation 254F, 538 ‘genetic biography’ 452–453 hypermethylated genes and 251T, 252, 254, 264 K-ras mutations in 224–225 in Li-Fraumeni syndrome 360–361 in mice and humans 270, 433 mismatch repair defects 548T, 549 point mutated ras oncogenes 117T point mutation densities 532F histopathological classification 49F, 801 anaplastic tumors 45 benign and malignant 34, 49F classified by tissue type 34–40 distinct cell populations within 459–460 nomenclature of tumors 8–9SS metastatic propensity 642, 700 see also cancer cells; pediatric tumors tumor vasculature defects in 592, 596F, 613–614, 615F endothelial cell role 607–615 heterogeneity 622 and prognosis 619 vascular mimicry and independence 628T tumor viruses cancer as a replication side-effect 127 classes of 127, 128T DNA-based 79–82, 295–296 see also DNA viruses genome sizes 79T, 81–82 immunocompromised patients and 746–748 induction of apoptosis 371 induction of dominant phenotype 232, 233 latent infections 86 multiple oncogenes 470 as one of three causative agents 60 perturbing pRb, p53 and apoptosis 333T transmission without reinfection 87–89 TSTAs resulting 758 varying views of importance 71–73, 100, 103–104 see also EBV; HPV; RSV tumorigenesis epidemiological evidence 442 initiation and promotion 481 leukocyte role 750, 751T multi-step see multi-step tumorigenesis nonmutagenic agents in 480–484 parallels with wound healing 587–600 progression stage 482 stromal cell contribution 600–603 tumors discovered only at autopsy 442 as monoclonal 50–53 p53 gene inactivation 341 symbiosis within 466 transmission of virus-induced 72 TUNEL assay 357–358F, 396F, 496F, 625F, 633F, 52SS turnover number 55 Twist transcription factor anti-apoptotic action 684 association with other EMT-TFs 680–681 in breast cancer CTCs 683F in canine kidney cells 661F effects of siRNA against 683F embryonic development role 675, 676F, 677 expression by human mammary cells 651F, 670F, 678, 679F invadopodia formation and 687F melanoma progression and 684F mesenchymal transition 670F metastases and 681 mRNA alterations from 695 in palatal morphogenesis 102SS tyrosine kinases (TKs) EGF receptor as 138–141 Jak kinase as 202 nonreceptor 182–183, 204 see also Src Src protein as 135–138 tyrosine kinase inhibitors (TKIs) as drug candidates 824, 844 Gleevec as 836 tyrosine kinase receptors (RTKs) altered in tumors 144T, 152F, 152S complexity of signaling 28SS evolutionary origins 24SS monoclonal antibodies against 782F, 782S number of genes encoding 152–153 SH2 domain-containing proteins and 185–186, 26SS structure and classification 140 transphosphorylation and 146–153 tyrosinase vaccination 762 tyrosine phosphorylation 182–188 U ubiquitin ligases 246T, 285, 322F, 554, 36SS, 47SS ubiquitin-proteasome system 262, 850, 36SS ubiquitylation cyclins 285 deubiquitylation 46SS HIF-1α 266F, 267 histone H2A 554 p53 protein 342 p27Kip1 gene 303, 309, 321 PML-RARα complex 813 polyubiquitylation 267, 285, 342, 344, 850, 852 pRb protein 296 tagging for endocytosis 143S, 208, 296, 304, 36SS ULBP4 protein 766F ulcerative colitis 431F, 431S, 487, 540, 737 ultimate carcinogens 62, 63 ultraviolet radiation 353, 427, 527, 535, 544 HPV synergy in SCCs 344S, 50SS uPA (urokinase plasminogen activator) 597–598 UPR (unfolded protein response) 853F, 855 uracil DNA glycosylate 540 V v-ErbB protein 141F v-myc gene 113, 117–118 v-sis gene 144 v-src gene 91, 135 vaccination autologous tumor cells 789 and immunization 786 melanoma-associated antigen 789 prostate cancer 788F against tumor viruses 800, 115SS vaccine contamination 80, 11SS vacuoles 80 Valery, Paul 577 vandetanib (ZD6474) 612F, 630T Varmus, Harold 90, 91F, 93 ‘vascular ZIP code’ theory 702–703 vasculature see tumor vasculature vasoactive factors 589 VEGF-C 696 VEGF receptor-1 and -2 610, 618 VEGF receptor antagonists/inhibitors 612F, 629, 631F, 635F, 86SS VEGF (vascular endothelial growth factor) angiogenesis promoted by 602–604, 605F, 618F capillary leakage and 613, 615F, 84–85SS cell motility and 16F ECM sequestered 617 EPC mobilization 622 expression and HIF-1 265–268, 610 growth factors as oncogenes 140F, 140T, 145T, 149F in HHV-8 infection 212 lymphangiogenesis and VEGF-C and -D 611S in monocyte recruitment 604 pericyte release of 584 release following surgery 598S synthesis by myeloma cells 854 in wound healing 592 Velcade (bortezomib, PS-341) 808T, 809, 850–855 vemurafenib (PLX4032) 866, 868 venules see capillaries Veratrum californicum 856 VHL gene and pVHL 246T, 251T, 265–268, 610 ‘vicious cycle’ of osteolytic metastases 706F, 707–708 vimentin 370, 498F, 507F, 594F, 596, 621F I:27 Index I:28 as mesenchymal cell characteristic 659, 663F, 666, 667F, 682 vinblastine and vincristine 808, 809F Vinca rosea 808 virions 74S viruses distinguishing from bacteria 72 in immunocompromised patients 746 immunological response 724–725, 728–735, 112SS life cycle 74F, 74S virus-like particles (VLPs) 115SS viruses as a cause of cancer see tumor viruses vitiligo 759–760 VLPs (virus-like particles) 115SS Voltaire 797 von Hansemann, David 105 Von Hippel-Lindau syndrome 265–268 von Recklinghausen, Friedrich 255 W Warburg, Otto (Warburg effect) 53–55, 268, 61SS Weissmann, August 331, 391 wild type alleles defined in teratomas 44 Wilms tumor 120, 360, 377T Wnt-1 gene 98S, 98T Wnt-β-catenin pathway 206–209, 262 Wnt proteins 157–158 Wnt signaling canonical Wnt 158, 206–209, 668 carcinoma EMT and 666, 670 myofibroblasts and 680 non-canonical Wnt 158, 209, 222, 668, 30SS Wolpert, Lewis 641 wound healing 134, 135F, 474, 490 angiogenesis termination 622–623 EMT-TFs in 675, 677F flowchart 591F heterotypic signaling in 595F postoperative tumor growth 780, 106SS as tumor model 587–600, 637–638, 658–659 X Y X chromosomes 9, 10F X-inactivation 9–10, 51, 554, 1SS X-ray crystallography the apoptosomes 369F cyclin-CDK complexes 284F e immunoglobulin γ 725F EGF receptor kinase plus Tarceva 824F EGF to β-catenin pathway visualization 226F growth factor binding 147, 149F MHC class II antigen presentation 730F monoclonal antibody binding 782S p53 protein 345F Ras GTP binding 168 SH2 and SH3 domains 183F Src kinase 182F X-ray exposure apoptosis response 518 asmase or p53 deficient mice 383, 633–634 DNA damage 341, 403S, 527 hypersensitivity 565F, 565S increased cancer rates 58, 104, 807 mutations from 60–61, 63, 154S p53 response 340, 347F xenobiotics 529F, 537, 76SS xenografts 587 anti-angiogenic MoAb 89SS dietary restriction effects 386S inadequacy of 588–589S phenotypic diversity 466F pre-clinical testing 811, 827 SV40 large T in 332F transdifferentiation in 603 usefulness 872 vascularization in 612F, 614F, 635F Xenopus laevis 676F XIAP anti-apoptotic protein 370F, 377T, 379, 852 XP (xeroderma pigmentosum) 544–545, 570 XPV gene 543, 545, 546T xtracellular animals see metazoa Y chromosomes 9, 10F Yamagiwa, Katsusaburo 59, 104 YAP transcription factor 31SS yeasts 336, 413m 563 see also Saccharomyces Yervoy (ipilimumab) 789, 790F Z ZD1839 see Iressa ZD6474 see vandetanib ZEB1 (δEF1) transcription factor 675T, 676F, 681, 682–683F, 99SS ZEB2 (SIP1) transcription factor 675T, 676F, 679F, 681, 682F zinc, in matrix metalloproteinases 590 zinc finger transcription factors 675, 856 zoledronic acid 707 zTERT (zebra fish) enzyme 434 ... one or another of these cancers, and two-thirds of these developed some type of cancer by the time they reached age 22 Some family members were even afflicted with several types of cancer concurrently... 95% of the erythroblasts the precursors of mature red cells—are eliminated as part of the routine operations of the bone marrow However, in the event that the rate of oxygen transport by the. .. example of the contribution of apoptosis to normal physiology is provided by the regression of the cells in the mammary gland following the weaning of offspring As many as 90% of the epithelial