19. Neoplasia IV (The Molecular Genetics of Cancer)

What is APC's role in tumor suppression? What cancer is most often associated with it?

APC gene is a member of the class of tumor suppressors that function by downregulating growth promoting signaling pathways. Germline loss-of-function mutations of the APC gene (5q21) are associated with familial adenomatous polyposis, an autosomal dominant disorder in which individuals born with one mutant allele develop thousands of adenomatous polyps in the colon during their teens or 20s. Almost invariably, one or more of these polyps undergoes malignant transformation, giving rise to colon cancer. As with other tumor suppressor genes, both copies of the APC gene must be lost for an adenoma to arise. APC is also mutated in 80% of sporadic colorectal carcinomas. APC is a component of the WNT signaling pathway, which has a major role in controlling cell fate, adhesion, and cell polarity during embryonic development. The WNTs are secreted glycoproteins and comprise a large family of 19 proteins in humans. The main signaling molecule of the WNT signaling is β-catenin, a dual function protein, playing a role in cell-cell adhesion machinery as well as gene transcription. β-catenin is part of a protein complex that forms adherens junctions, which are necessary for the creation and maintenance of epithelial cell layers. In the absence of Wnt protein, the levels of cytoplasmic free β-catenin are kept low. If not bound to E-cadherin in the adherens junctions, β-catenin is phosphorylated in the cytoplasm by the activity of a multiprotein destruction complex, marking β-catenin for degradation. The destruction complex includes Axin, APC protein, protein phosphatase 2A (PP2A), glycogen synthase kinase 3 (GSK3) and casein kinase 1α (CK1α). GSK3 and CK1α target β-catenin for ubiquitination and subsequent proteolytic destruction by the proteasomal machinery. A major function of the APC protein, in the absence of WNT signaling, is to regulate proteasomal degradation of β-catenin, preventing its accumulation in the cytoplasm. No transcription of Wnt genes occur under normal conditions. When WNT protein is present it interacts with a cell surface receptor called frizzled (FRZ, a seven- transmembrane-span protein). After binding of WNT to the receptor complex, the signal is transduced to cytoplasmic phosphoprotein Dishevelled (Dsh). Dsh is activated. Once activated Dsh inhibits the destruction complex enzyme. β-catenin is now free to dissociate from the APC protein, enter the nucleus and binds to and activates the WNT responsive genes such as MYC and cyclin D1, promoting the proliferation of colonic epithelial cells. APC gene mutations result in truncation of the APC protein and loss of the all binding sites to components of the destruction complex. APC truncation also causes loss of the domain required for binding to β-catenin. APC mutations lead to β-catenin dissociation, accumulation of nuclear β-catenin, and activation of the WNT responsive genes.

Describe the two different ways that activate apoptosis?

Apoptosis is now widely accepted to play a role tumorigenesis. In the normal organism, apoptosis serves to eliminate cells with genomic injury. Mutations in the genes that regulate apoptosis allow cancer cells to escape suicide. As discussed in Block 1, there are two distinct programs that activate apoptosis, the extrinsic and intrinsic (mitochondrial) pathways. It is the intrinsic apoptotic pathway that is most frequently disabled in cancer. Recall that the activation of intrinsic pathway of apoptosis leads to permeabilization of the mitochondrial outer membrane, with resultant release of cytochrome c that initiates apoptosis. The integrity of the mitochondrial outer membrane is regulated by pro-apoptotic and anti-apoptotic members of the BCL2 family of proteins. The pro-apoptotic proteins Bad, Bax and Bak are required for apoptosis. Their action is inhibited by the anti-apoptotic members of this family, which are exemplified by Bcl-2, Bcl-X and Mcl-1. Pro-apoptotic proteins sense death-inducing stimuli and promote apoptosis by neutralizing the actions of anti-apoptotic proteins. BAX and BAK are activated and form pores in the mitochondrial membrane. Cytochrome c leaks into the cytosol, where it binds to APAF1 activating caspase 9. Caspase 9 then activates downstream caspases such as caspase 3, an executioner caspase that cleaves DNA and other substrates to cause cell death.

What happens in DNA hypomethylation? What type of cancer is caused by this?

Cancer cells are characterized by global genomic hypomethylation and focal hypermethylation of CpG islands, which are generally unmethylated in normal cells. DNA hypomethylation may lead to the upregulation of certain genes, and studies in mice have shown that hypomethylated genomes also exhibit chromosomal instability. Acute myeloid leukemia is a neoplasm commonly exhibiting abnormal DNA methylation. Focal hypermethylation in the promoters of critical tumor suppressors, despite global hypomethylation elsewhere, leads to transcriptional silencing of the downstream genes.

What is the difference between driver and passenger mutations?

Carcinogenesis results from the accumulation of complementary mutations in a stepwise fashion over time. The hallmarks of cancer comprise several biological capabilities acquired during mutations of key genes include sustained proliferation, local invasiveness and the ability to form distant metastases. The first driver mutation that starts a cell on the path to malignancy is the initiating mutation, which is typically maintained in all of the cells of the subsequent cancer. However, because no single mutation appears to be fully transforming, development of a cancer requires that the "initiated" cell acquire a number of additional driver mutations, each of which also contributes to the development of the cancer. Driver mutation is a mutation that gives a selective advantage to a clone in its microenvironment, through either increasing its survival or reproduction. Driver mutations tend to cause clonal expansions. The time over which this occurs is unknown in most cancers, but appears to be lengthy. Mutations that lead to genomic instability not only increase the likelihood of acquiring driver mutations, but also greatly increase the frequency of mutations that have no effect on the fitness of a clone, so-called passenger mutations.

What are the hallmarks of cancer?

Genomic and epigenomic alterations impart cancer cells with common fundamental phenotypic properties which are considered the hallmarks of cancer. These changes consist of the following: 1. Sustained proliferation. Tumors have the capacity to proliferate without external stimuli, usually as a consequence of oncogene activation. 2. Insensitivity to growth-inhibitory signals. Tumors do not respond to molecules that inhibit the proliferation of normal cells, usually because of inactivation of tumor suppressor genes that encode components of these growth inhibitory pathways. 3. Altered cellular metabolism. Tumor cells undergo a metabolic switch to aerobic glycolysis. 4. Evasion of apoptosis. Tumors are resistant to programmed cell death. 5. Immortality. Tumors have unrestricted proliferative capacity, a stem cell-like property that permits tumor cells to avoid cellular senescence. 6. Sustained angiogenesis. Tumor cells are not able to grow without a vascular supply. Hence, tumors must induce angiogenesis. 7. Ability to invade and metastasize. Tumor metastases arise from the spread of cancer cells to new areas of the body (often by way of the lymph system or bloodstream). 8. Ability to evade the host immune response. Cancer cells exhibit a number of alterations that allow them to evade the host immune response, which eliminates cells displaying abnormal antigens (e.g., a mutated oncoprotein).

Which genes are growth factor receptor tyrosine kinases? What kind of mutations in this pathway lead to cancer?

Growth receptor tyrosine kinases. The epidermal growth factor receptor (EGFR) is the prototype of G-protein-coupled growth receptors. EGFR mediates cell proliferation in response to a variety of different ligands, including epidermal growth factor (EGF) and transforming growth factor α (TGFα). G-protein-coupled growth receptors have intrinsic protein kinase activity due to a cytoplasmic tyrosine kinase domain. Normally, the receptor's kinase activity is activated transiently by binding of a specific growth factor to the extracellular domain. This event induces a rapid change in receptor conformation to an active dimeric state; the activated receptor then autophosphorylates tyrosine residues in its own intracellular tail. Tyrosine residues serve as sites for recruitment of a number of signaling molecules, including RAS and PI3K, which are key players in receptor tyrosine kinase signaling. (A) Growth factors and their receptors in malignancies. G-protein-coupled growth receptors can be activated in tumors by multiple mechanisms. Many cancer cells acquire the ability to synthesize the same growth factors to which they are responsive, creating an autocrine loop. Many sarcomas overexpress both TGF-α and EGFR receptors. The oncogenic versions of growth receptors are associated with mutations that lead to constitutive, growth factor-independent tyrosine kinase activity. Hence, the mutant receptors deliver continuous mitogenic signals to the cell, even in the absence of growth factor in the environment. Here are some examples of clinical importance: • Certain lung adenocarcinomas are characterized by mutations of the ERBB1 gene, which encodes the epidermal growth factor receptor (EGFR). These mutations result in constitutive activation of the EGFR tyrosine kinase. • The ERBB2 gene encodes HER2, a different member of the G-protein-coupled growth receptor family. In certain breast carcinomas the ERBB2 gene is amplified (i.e., by production of multiple copies of the gene), leading to overexpression of the HER2 receptor and constitutive tyrosine kinase activity. • Gene rearrangements activate ALK (anaplastic lymphoma kinase) gene, which codes for another G- protein-coupled growth receptor. An inversion within chromosome 2p fuses part of the ALK gene with part of another gene called EML4 in certain lung adenocarcinomas. The resulting EML4-ALK fusion gene encodes a chimeric EML4-ALK protein, again with constitutive tyrosine kinase activity. (B) Downstream components of growth receptor signaling pathway. As mentioned, receptor tyrosine kinase activation stimulates RAS and two major downstream signaling" arms," the RAF cascade and the PI3K/AKT pathway. RAF, PI3K, and other components of these pathways are frequently involved by gain-of-function mutations in different types of cancer. RAS MUTATIONS. There are three types of RAS genes, HRAS, KRAS, and NRAS. Point mutations of RAS family genes constitute the most common type of abnormality involving proto-oncogenes in tumors. RAS proteins are members of a family of membrane-associated small G proteins that bind guanosine nucleotides (guanosine triphosphate [GTP] and guanosine diphosphate [GDP]), similar to the larger trimolecular G proteins. They normally flip back and forth between an excited signal-transmitting state in which they are bound to GTP and a quiescent state in which they are bound to GDP. Stimulation of receptor tyrosine kinases by growth factors leads to exchange of GDP for GTP and subsequent conformational changes that generate active RAS, which in turn stimulates both the MAPK and PI3K/ AKT arms of the receptor tyrosine kinase signaling pathway. These downstream kinases phosphorylate and activate a number of cytoplasmic effectors as well as several transcription factors that turn on genes that support rapid cell growth. Activation of RAS is transient because RAS has an intrinsic GTPase activity that is accelerated by GTPase-activating proteins (GAPs), which bind to the active RAS and augment its GTPase activity by more than 1000-fold, thereby terminating signal transduction. Thus, GAPs prevent uncontrolled RAS activity. Several gain-of-function mutations in RAS genes have been identified in cancer cells that markedly reduce the GTPase activity of the RAS protein. As a result, these mutated forms of RAS are trapped in the activated GTP-bound form and the cell receives pro-growth signals continuously. BRAF MUTATIONS. BRAF gene is a member of the RAF family that encodes a serine/ threonine protein kinase that sits at the top of the MAPK signaling cascade. Mutations in BRAF gene have been detected in hairy cell leukemias and melanomas. MUTATIONS OF THE PI3K FAMILY OF PROTEINS. PI3K, like BRAF, activates a cascade of serine/threonine kinases, including AKT, which is a key signaling node. Like RAS, PI3K is negatively regulated by an important tumor suppressor gene called PTEN.

How are cyclins and cyclin-dependent kinases involved in cancer?

Cyclins and cyclin-dependent kinases. Growth factors transduce signals that stimulate the cell cycle. Progression of cells through the cell cycle is orchestrated by cyclin-dependent kinases (CDKs), which are activated by binding to cyclins. CDK inhibitors (CDKIs) are tumor suppressor genes that exert negative control over the cell cycle. Gain-of-function mutations in genes that encode cyclin D protein or CDK4, and loss-of-function mutations in CDK inhibitors, such as p16, a tumor suppressor gene, both facilitate cell cycle progression.

How do malignant tumors occur? How many mutations must occur to cause cancer?

Malignant tumors arise from a protracted sequence of events. Given that malignant tumors must acquire multiple "hallmarks" of cancer, it follows that cancers result from the stepwise accumulation of multiple mutations that act in complementary ways to produce a fully malignant tumor. How many mutations does it take to establish a fully malignant tumor? Genome-wide sequencing of cancers has revealed as few as 10 or so mutations in certain leukemias, to many thousands of mutations in lung cancers associated with cigarette smoking, most of which are passengers rather than drivers. These mutations presumably never occur simultaneously during the natural development of a human cancer, but instead occur in a stepwise fashion. A classic example of incremental acquisition of the malignant phenotype is found in colorectal carcinoma. Many of these cancers evolve through a series of morphologically identifiable stages: colon epithelial hyperplasia followed by formation of adenomas that progressively enlarge and ultimately undergo malignant transformation. Molecular analyses of proliferations at each of these stages have indeed shown that precancerous lesions have fewer mutations than adenocarcinomas and suggest a tendency to acquire particular mutations in the adenoma-carcinoma sequence. The adenoma-carcinoma sequence refers to a stepwise pattern of mutational activation of oncogenes (e.g. KRAS) and inactivation of tumor suppressor genes (e.g. APC and TP53) that results in cancer. Last but not least, constitutive expression of telomerase directly grants cells immortality. Most somatic cells do not express telomerase, the enzyme that is responsible for the maintenance of telomeres, and with each cell division their telomeres shorten. When the telomeric DNA is completely eroded, the functional p53 triggers cell apoptosis. But cells that reactivate telomerase can restore their telomeres and survive. Such cells are at high risk for malignant transformation.

What type of cancer is associated with NF1 gene mutations?

Neurofibromin 1 gene (NF1) is a tumor suppressor located on chromosome 17q11.2 and encodes neurofibromin. The NF1 gene is a negative regulator of the RAS signal transduction pathway. It stimulates the GTPase activity of RAS. Mutations in the NF1 gene cause neurofibromatosis type 1, a disorder characterized by development of numerous benign neurofibromas.

What type of cancers are associated with NF2 mutations?

Neurofibromin 2 gene (NF2), located on chromosome 22q11-13.1, gives rise to a product called merlin or schwannomin. Merlin is a membrane cytoskeleton-associated protein. Cells lacking merlin do not establish stable cell-to-cell junctions and are insensitive to normal growth arrest signals generated by cell-to-cell contact. Mutations in the NF2 gene cause neurofibromatosis type 2, a disorder characterized by development of numerous tumors such as schwannoma, meningioma, and glioma.

What are the functions of proto-oncogenes?

Proto-oncogenes function in the regulation of normal cell growth and differentiation. Proto-oncogenes encode proteins involved in the response of cells to stimulation by growth factors. The following are the steps of growth factor signaling in normal cells. • The binding of a growth factor to its specific receptor; • Transient activation of the growth factor receptor activates cytoplasmic signal-transducing proteins. • Transmission of the transduced signal to the nucleus via second messengers or by a cascade of signal transduction molecules; • Activation of nuclear regulatory factors that initiate DNA transcription; • Expression of factors that promote entry of the cell into cell division cycle and replication

What types of cancers are associated with PTCH mutations?

Patched (PTCH) is a tumor suppressor gene that encodes a cell membrane protein called protein patched homolog 1 (PATCHED1). PATCHED1 is transmembrane protein receptor that is a negative regulator of the Hedgehog signaling pathway. In the absence of PATCHED1, there is unopposed Hedgehog signaling that increases the expression of a number of pro-growth genes, including NMYC and D cyclins. Germline loss-of-function mutations in PTCH cause Gorlin syndrome, an inherited condition also known as nevoid basal cell carcinoma syndrome that is associated with greatly increased risks of basal cell carcinoma of the skin and of medulloblastoma of cerebellum.

What are oncogenes and proto-oncogenes?

Protooncogenes and oncogenes. Genes that promote autonomous cell growth in cancer cells are called oncogenes, and their unmutated cellular counterparts are called proto-oncogenes. Protooncogenes are mutated in a way that makes them continuously active. Oncogenes encode proteins called oncoproteins that have the ability to promote cell growth in the absence of normal growth-promoting signals.

What role does TGF beta play in the cell cycle? What cancer is common with the inactivation of SMAD?

TGF-β is a potent inhibitor of proliferation. It regulates cellular processes by binding to TGF-β receptors I and II. Dimerization of the receptor upon ligand binding initiates intracellular signals that involve proteins of the SMAD family. Under normal circumstances, these signals turn on antiproliferative genes (e.g., genes for cyclin-dependent kinase inhibitors involved in G1 arrest in the cell cycle) and turn off genes that drive cell growth (e.g., MYC, cyclins, and cyclin dependent kinases). These changes result in cell cycle arrest. Mutations affecting the type II TGF-β receptor are common in cancers of the colon, stomach, and endometrium, while mutational inactivation of SMAD4 is common in pancreatic cancers.

What role does p53 play in controlling tumors? What kind of cancers arise when there is a problem in this protein?

TP53: GUARDIAN OF THE GENOME. TP53, a tumor suppressor gene that regulates cell cycle progression, DNA repair and apoptosis, is the most frequently mutated gene in human cancers. Loss-of-function mutations in TP53 are found in more than 50% of cancers. TP53 gene encodes p53 protein which is a transcription factor that binds to DNA and regulates gene expression to prevent mutations of the genome. It can activate DNA repair proteins when DNA has sustained damage. It induces cell cycle arrest at the G1/S checkpoint on DNA damage recognition by activating transcription of p21, a potent cyclin-dependent kinase inhibitor (CKI). Inhibition of cyclin-dependent kinase by p21 leads to dephosphorylation and activation of Rb protein and blocking the progression of cells from G1 phase to S phase. This pause in cell cycling allows DNA repair proteins repair damage. If DNA damage is repaired successfully, p53 levels fall, releasing the cell cycle block. The cells may then revert to a normal state. The p53 can initiate apoptosis if DNA damage proves to be irreparable. p53 directs the transcription of a pro-apoptotic gene such as BAX, which tips the balance in favor of cell death via the intrinsic (mitochondrial) pathway. Protein p53 is tightly regulated at several levels. For example, MDM2 protein (Murine double minute 2) is an important negative regulator of the p53. MDM2 functions as an ubiquitin ligase, an enzyme that ubiquitinylates p53, leading to its degradation by the proteasome. Indeed, the MDM2 gene is amplified in 33 % of human sarcomas, leading to a functional deficiency of p53 in these tumors. DNA tumor viruses target and inhibit p53 and Rb. The human papillomaviruses (types 16 and 18) encode oncogene products E6 and E7 which bind to p53 and Rb respectively. Adenovirus E1A protein interacts with Rb, and a second protein E1B binds the p53. These products are responsible for the ability of these viruses to initiate tumors in humans. In most cases, mutations are present in both TP53 alleles and are acquired in somatic cells (not inherited in the germline). Less commonly, individuals inherit germline mutations in one TP53 allele. Such individuals, considered to have the Li-Fraumeni syndrome, have a 25-fold greater chance of developing a malignant tumor at younger ages than the general population. In contrast to individuals who inherit a mutant RB allele, the spectrum of tumors that develop in individuals with Li-Fraumeni syndrome is quite varied; the most common types of tumors are sarcomas, breast cancer, leukemias, brain tumors, and carcinomas of the adrenal cortex.

What roles do CDDKN2A and CDKN2B play in the cell cycle?

The CDKN2A gene on chromosome 9p21 encodes two proteins: the p16/INK4a and p14/ARF. Both these proteins are involved in cell cycle regulation. The p16/INK4a is an inhibitor of cyclin dependent kinases such as CDK4 and CDK6. These latter kinases phosphorylate and inactivate RB protein which eventually results in progression from G1 to S phase. The p14/ARF, an alternate reading frame protein product of the CDKN2A locus, activates the p53 pathway by inhibiting MDM2 and preventing destruction of p53. Germline mutations in CDKN2A are associated with familial forms of melanoma, and sporadic mutations of this locus have been detected in bladder and liver cancer. The CDKN2B gene lies adjacent to the tumor suppressor gene CDKN2A in 9p21 locus and encodes a cyclin-dependent kinase inhibitor, also known as p15Ink4b protein. The p15Ink4b protein forms a complex with CDK4 or CDK6, and prevents the activation of the CDK kinases by cyclin D. Thus the encoded protein functions as a cell growth regulator that inhibits cell cycle G1 progression.

What are the four categories of cancer inducing genes?

The cancer genes, i.e. genes which mutation can induce cancer, can be grouped into 4 categories: 1. Oncogenes. • Oncogenes are altered versions of protooncogenes (normal versions) that regulate normal cell growth, differentiation and survival. • Gain-of-function mutations activate protooncogenes to become oncogenes. • A gain-of-function mutation causes an excessive increase in one or more normal functions of the encoded gene product. • Mutations of an oncogene can transform cells despite the presence of a normal copy of the same gene. Thus, in genetic parlance, oncogenes are dominant over their normal counterparts. 2. Tumor suppressor genes. • Tumor suppressor genes are normal genes whose products inhibit cellular proliferation. • They code for a protein that is part of the system that regulates cell division; or repressive effect on the regulation of the cell cycle • Proteins coded by tumor-suppressor genes are part of the system that regulates cell division. They have a damping or repressive effect on the regulation of the cell cycle. • However, there are exceptions: sometimes inactivation by mutation of a copy of a gene (a state termed haploinsufficiency) reduces the activity of the single functional copy. • For example, the single functional copy does not produce enough of a gene product (typically a protein) to bring about a wild-type condition. • A loss of function mutation inactivates blocking activities of tumor suppressor genes, thereby permitting unregulated cell growth. 3. Genes that regulate apoptosis. • These genes promote or suppress apoptosis. • Gain-of-function mutations of genes that suppress apoptosis during tumor development enhance tumor cell survival. • Loss-of-function mutations in genes that promote apoptosis also promote tumor progression. • Both these abnormalities result in less death and, therefore, enhanced survival of cancer cells. 4. Genes involved in DNA repair. •These genes normally maintain the fidelity of DNA replication. Genes involved in DNA repair code for proteins that function in pathways that involve the recognition of and removal of DNA lesions, and protection from errors of incorporation made during DNA replication or DNA repair. • Loss-of-function mutations of these genes allow the successive accumulation of further mutations. • These mutations contribute to carcinogenesis indirectly by impairing the ability of the cell to recognize and repair nonlethal genetic damage in other genes. • As a result, affected cells acquire mutations at an accelerated rate, a state referred to as a mutator phenotype that is marked by genomic instability.

What are tumor suppressor genes?

These genes encode proteins that negatively regulate the growth pathways by applying brakes to cell proliferation. Tumor suppressor genes inhibit the same pathways that are activated by proto- oncogenes. Abnormalities in these genes lead to failure of growth inhibition. Mutations in tumor suppressor genes are loss-of-function mutations and so occur in both alleles of a gene. Many tumor suppressors, such as retinoblastoma (RB) and p53, are part of a regulatory network that recognizes DNA damage and responds by shutting down proliferation.

Why transcription factors are involved in human tumors? What type of cancer occurs because of this amplification?

Transcription factors. Ultimate consequence of deregulated growth signaling pathways is inappropriate and continuous stimulation of nuclear transcription factors that drive growth-promoting genes. Thus, autonomous cell growth may also occur as a consequence of mutations affecting the transcription factors that regulate the expression of pro-growth genes and cyclins. MYC is a family of transcription factors and is commonly involved in human tumors. There are three distinct gene family members—C-Myc, N-myc, and L-myc, which function in a similar manner. Gain-of- function mutations of MYC are found in many cancers. In most cases of Burkitt lymphoma, a chromosomal rearrangement [(designated t(8;14)] has moved the C-MYC from its normal position on chromosome 8 to a location close to the enhancers of the antibody heavy chain genes on chromosome 14. In this new location, c-MYC is constitutively (persistently) expressed. Overexpression of the gene N-MYC in neuroblastoma cells can result from gene amplification through the formation of double minutes (i.e., small fragments of extrachromosomal DNA) or intrachromosomal homogeneously staining regions (HSR). Amplification of the N-MYC gene in neuroblastoma is associated with rapid tumor progression and poor outcome.

What type of cancers are associated with mutations of the WT1 gene?

Wilms' tumor gene (WT1), located on chromosome 11p13, codes for Wilms tumor protein. The WT1 protein is a transcriptional activator of genes involved in renal and gonadal differentiation Loss-of-function mutations in the WT1 gene are associated with the development of Wilms tumor, a pediatric kidney cancer.

How does a tumor progress?

A tumor comes to clinical attention when it attains a mass of about 1 g, or about 1 billion cells. A minimum of 30 cell doublings is necessary to reach this size. Early on, all of the cells in a tumor are genetically identical, being the progeny of a single founding transformed cell. Tumors evolve genetically during their outgrowth under the pressure of Darwinian selection (survival of the fittest). Tumor progression refers to the evolutionary process by which tumors become more aggressive over time. During this process, there is competition among tumor cells for access to nutrients and microenvironmental niches. Subclones form with the capacity to overgrow their predecessors tend to "win" this Darwinian contest and dominate the tumor mass. As a result, even though malignant tumors are clonal in origin, by the time they become clinically evident their constituent cells are often extremely heterogeneous genetically, forming multiple clones. One model proposes that there is a dominant tumor cell clone that progressively accumulates genetic and epigenetic alterations and it has growth and survival advantage due to environmental selection pressure. In addition to DNA mutations, epigenetic modifications also contribute to the malignant properties of cancer cells. These include DNA methylation, which tends to silence gene expression, and modifications of histones, which may either enhance or dampen gene expression. Epigenetic modifications dictate which genes are expressed; they are responsible for the silencing of some tumor suppressor genes.

What are the 6 DNA repair pathways?

DNA repair genes code for proteins whose normal function is to correct errors that arise when cells duplicate their DNA prior to cell division. DNA repair genes are active throughout the cell cycle, particularly during G2 after DNA replication and before the chromosomes divide. There are 6 primary DNA repair pathways. Each pathway is composed of a series of biochemical events leading to the sensing, excision, and restoration of normal DNA sequence. These 6 pathways are: (a) Base excision repair; (b) Nucleotide excision repair; (c) Mismatch repair; (d) Homologous recombination repair; (e) Non-homologous end joining; (f) Translesion DNA synthesis. The DNA damage response provides an important "barrier" to the transformation of a normal cell to a malignant cell. Individuals born with germline mutations that disrupt the DNA repair pathways, have cellular hypersensitivity to DNA-damaging agents, genomic instability and an increased risk of cancers.

How are histones involved in malignancies?

Histones are no longer considered to be simple 'DNA-packaging' proteins; they are recognized as being regulators of chromatin dynamics. Histones are subject to a wide variety of post-translational modifications such as acetylation of lysines and methylation of lysines and arginines, as well as phosphorylation of serines and threonines, all of which are carried out by histone-modifying enzyme complexes. Mutations in genes coding for histone-modifying enzymes can affect unwinding of chromatin, which is required for the transcription machinery to physically access DNA. Histone modifications can alter the expression of sets of genes that contribute to the malignant phenotype.

Alterations in nonreceptor tyrosine kinases cause cancer?

Mutations that confer oncogenic activity occur in several nonreceptor tyrosine kinases that normally localize to the cytoplasm or the nucleus. These oncoproteins activate the same signaling pathways as receptor tyrosine kinases. (A) ABL (Abelson murine leukemia viral oncogene homolog). ABL (Abelson murine leukemia viral oncogene homolog) tyrosine kinase is an important example of this oncogenic mechanism. In chronic myelogenous leukemia (CML) the ABL gene is translocated from its normal location on chromosome 9 to chromosome 22, where it fuses with the BCR gene. The resultant chimeric gene encodes a constitutively active, oncogenic BCR-ABL tyrosine kinase. The association of BCR-ABL unleashes tyrosine kinase activity of ABL. (B) JAK2 (Janus Kinase 2). In other instances, nonreceptor tyrosine kinases are activated by point mutations that abrogate the function of negative regulatory domains that normally hold enzyme activity in check. An example of this type of mutation is found in the nonreceptor tyrosine kinase JAK2. This mutation renders hematopoietic cells more sensitive to growth factors such as erythropoietin and thrombopoietin. Mutations in JAK2 have been implicated in myeloproliferative disorders (polycythemia vera, essential thrombocythemia, and myelofibrosis).

What is the two hit hypothesis?

Our current concepts of tumor suppressors evolved from studies of the childhood tumor, retinoblastoma. There are two distinct classes of retinoblastoma, sporadic and familial. Sporadic retinoblastoma is unilateral and is diagnosed at the late age of about two years. Familial retinoblastoma is diagnosed at an earlier age, at 11 months, and is typically bilateral. Yet, tumors from both groups are otherwise identical. Knudson and coll. (1971) found an explanation for the occurrence of retinoblastoma, in two very different ways. One defective RB gene does not affect cell behavior. Two mutations (hits), involving both alleles of RB gene at chromosome locus l3q14, are required to produce retinoblastoma. He developed the "two-hit" hypothesis" that retinoblastoma is a malignancy caused by two mutational events. In familial cases, children inherit one defective copy of the RB gene in the germline (the first hit), and the other copy is normal. Retinoblastoma develops when the normal RB allele is mutated in retinal cells as a result of a spontaneous somatic mutation (the second hit). In sporadic cases both normal RB alleles must undergo somatic mutation in the same retinal cells (two hits).

What type of cancers are associated with PTEN mutations?

PTEN (phosphatase and tensin homologue) is a membrane-associated phosphatase encoded by the PTEN gene on chromosome 10q23. This gene is a tumor suppressor; it inhibits the PI3K/AKT arm of the receptor tyrosine kinase pathway. Loss-of-function PTEN mutations occur in glioblastoma, endometrial, thyroid and prostate cancer. Inherited PTEN gene mutations cause hamartomas in Cowden syndrome.

Mutations in the BRCA1 and BRCA2 genes result in what type of cancer?

The BRCA1 gene (breast cancer 1, early onset), located on chromosome 17q21, encodes a nuclear phosphoprotein that plays a role in repair of DNA damage by homologous recombination repair. BRCA1 gene mutations are responsible for approximately 40% of inherited breast cancers. The BRCA2 gene (breast cancer 2, early onset), located on chromosome 13q12.3 encodes a protein involved in double-strand break repair and/or homologous recombination; it also acts as a tumor suppressor. Carriers of mutations in the BRCA2 gene have a high risk of developing breast and other cancers. Hereditary breast cancer accounts for 5% to 10% of all breast carcinomas.

A mutation in the BCL-2 gene causes what type of cancer?

The Bcl-2 gene (located at 18q21) was first discovered as a target gene in tumors cells of patients with follicular lymphoma (a type of B cell lymphomas). These patients are characterized by a t(14;18) chromosomal translocation which results in the juxtaposition of the Bcl-2 gene with the immunoglobulin heavy chain gene enhancer (IGH) at 14q32. This translocation removes the Bcl-2 gene from its normal controls and places it close to IGH, an element highly transcriptionally active in B lymphoid cells. This fusion gene leads to the transcription of excessively high levels of anti-apoptotic Bcl-2 protein. The overexpressed Bcl-2 in follicular lymphoma suppresses apoptosis. Inhibition of apoptosis provides an efficient mechanism for retaining all transformed B cells.

What is the purpose of the retinoblastoma gene?

The Rb gene encodes the Rb protein, a key negative regulator of the G1/S cell cycle transition. One function of the Rb protein is to prevent excessive cell growth by inhibiting cell cycle progression until a cell is ready to divide. The RB gene is directly or indirectly inactivated in most human cancers. In resting cells, the unphosphorylated form of Rb protein exists in a complex with the E2F transcription factor. The Rb-E2F complex functions as a transcriptional repressor. High levels of CDK4/cyclin D, CDK6/cyclin D and CDK2/cyclin E complexes lead to phosphorylation and inhibition of Rb protein. The phosphorylated form of Rb protein dissociates from E2F and the "free" E2F activates the transcription of genes necessary for progression to the S phase. The function of the Rb protein may be compromised in two different ways: • Loss-of-function mutations involving both Rb alleles • Gain-of-function mutations that upregulate cyclin D or CDK4 activity or loss-of-function mutations that abrogate the activity of CDK inhibitors

What types of cancers are associated with mutations of VHL?

The Von Hippel-Lindau (VHL) gene, on chromosome 3p, is a tumor suppressor. VHL gene codes for VHL protein, which is a component of ubiquitin ligase, a type of protein complex that covalently links ubiquitin chains to specific protein substrates, thereby promoting their degradation by the proteasome. Inherited VHL gene mutations cause Von Hippel-Lindau disease, characterized by hereditary renal cell carcinoma, pheochromocytomas, hemangioblastomas of the central nervous system, and retinal angiomas. Acquired VHL gene mutations cause sporadic renal cell carcinoma. A critical substrate for the VHL ubiquitin ligase is the transcription factor HIF1α (hypoxia-inducible transcription factor 1α). In the presence of oxygen, HIF1α is hydroxylated and binds to VHL, leading to its ubiquitination degradation. In hypoxic environments this reaction does not occur, and HIF1α escapes recognition by VHL. As a result, HIF1α accumulates in the nuclei of hypoxic cells and turns on many target genes, including genes encoding the growth/angiogenic factors such as vascular endothelial growth factor (VEGF) and platelet-derived growth factor (PDGF). Loss-of-function VHL gene mutations also prevent the ubiquitination and degradation of HIF1α, even under normoxic conditions, and are accordingly associated with increased levels of angiogenic growth factors that favor growth.

What is the function of the XPA gene? Mutations of this gene cause what cancer?

The XPA gene (xeroderma pigmentosum, complementation Group A) encodes a protein involved in DNA excision repair. The encoded protein is part of the nucleotide excision repair complex which is responsible for repair of UV radiation-induced photoproducts. Mutations of the XPA gene cause xeroderma pigmentosum (XP), a rare disorder transmitted in an autosomal recessive manner. XP can result from mutations in any one of seven genes involved in nucleotide excision repair (XPA through XPG). XP is characterized by sun sensitivity from early infancy, acquiring severe sunburn with blistering or persistent erythema on minimal sun exposure. Individuals with XP develop multiple cutaneous malignant neoplasms at a young age, such as malignant melanoma and squamous cell carcinoma.

What are the three types of genetic damage that results in somatic mutations in cancer genes?

The growth of cancer cells results from the sequential acquisition of non-lethal somatic mutations in cancer genes. The initial genetic damage may be caused by (a) environmental exposures (such as viruses or environmental chemicals, or endogenous products of cellular metabolism), (b) may be inherited in the germline, or (c) may be spontaneous and random. The clonal expansion of a single precursor cell that has incurred genetic damage forms the tumor. Alterations in DNA are passed to daughter cells, and thus all cells within an individual tumor share the same set of mutations that were present at the moment of transformation. A minimum of 4-7 mutated genes are required for the transformation of a normal cell into a malignant phenotype (malignant transformation). This multistep process takes place over a period of years.

What do the MSH2, MSH6, MLH1 genes code for?

These three genes code for proteins involved in DNA mismatch repair. Individuals with mutations in any one of these genes have about an 80% lifetime risk for a type of colon cancer known as Lynch syndrome or hereditary nonpolyposis colorectal cancer (HNPCC). Also, women with Lynch syndrome have an 80% lifetime risk of endometrial cancer. Lynch syndrome is inherited in an autosomal dominant manner. The hallmark of Lynch syndrome is defective DNA mismatch repair, which leads to characteristic errors of replication, also termed microsatellite instability. These errors are due to the uncorrected mispairing of nucleotides and resultant misalignment of DNA strands. Microsatellites are loci present in DNA that consist of repeating units of 1-6 base pairs in length. The sequence can be repeated 10-100 times. Mutations involving tumor suppressor genes and oncogenes rapidly accumulate, and, allow colon adenomas to progress to colon carcinoma.