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CANCER GENETICS

 

M.Tevfik Dorak, M.D., Ph.D.

See also: R&D Systems mini-reviews: Genomic Instability Syndromes and DNA Damage Response

Reviews on Genetic Predisposition to Cancer: Dong et al, 2008; Turnbull et al, 2005; Frank SA, 2004; Mohandas KM, 2001 (Book: Eeeles et al, 2004)

Reviews on GWAS and Cancer Susceptibility: Easton & Eeles, 2008; Stadler et al, 2010; Ioannidis et al, 2010; Varghese & Easton, 2010

Taby & Issa, 2010: Cancer Epigenetics   Dorak MT: Cancer Immune Surveillance Presentation

WHO Report: Genetics in Prevention and Treatment of Cancer

Cancer has a genetic component in its etiology. This is evident from increased risk in family members of cancer patients, twin studies, the presence of familial forms of cancer, experimental studies and classical/molecular genetic studies. In the majority of human cancers, there is no clear-cut mode of inheritance. This and other evidence suggest that cancer is a multigenic (oncogenes, tumor suppressor genes, MHC genes), multifactorial (radiation, chemicals, hormones, viruses, ultraviolet, diet, etc) and multistep (transformation, promotion, overt cancer) process. In sporadic tumors, there is no inherited genetic abnormality predisposing to tumor. Genetic predisposition, however, occurs when a mutation is present in the heritable genetic material (germ-line). About 5-10% of cancers result from germ-line mutations and most are evident as cancer family syndromes.

Knudson proposed a two-hit model for the development of cancer in 1971 from the evidence in familial retinoblastoma cases. This simplified model suggests two separate genetic events in the development of retinoblastoma. The first one is inherited in the familial form and the time required for the second hit to occur is shorter than two hits to occur in a normal person. This is why the familial form occurs at an earlier age and is usually bilateral. In general, inherited cancer occurs earlier and is more severe, whereas, sporadic cancer has later onset. (The original Knudson's two-hit hypothesis based on bi-allelic gene inactivation has now been extended to include transcriptional silencing by epigenetic changes (such as DNA methylation of promoters) that can disable tumor-suppressor genes (Jones & Laird, 2000), and haploinsufficiency that can disable the whole gene function. See Yu & Shen, 2002; Balmain, 2003; Paige, 2003; Taby & Issa, 2010)

The immune system is one of the factors influencing susceptibility to cancer. The evidence for this is that in immune deficiencies, there is an increased risk for cancer. These tend to be lymphoid tumors. Immunogenicity of cancer is suggested by the presence of tumor-specific cytotoxic T lymphocytes (CTL) and tumor infiltrating lymphocytes (TIL). Immunogenicity is impaired by the loss of MHC expression. The immune surveillance theory proposes that oncogenic transformation of normal cells is a frequent occurrence but the immune system clears them as they emerge. The cell surface expression of MHC molecules is a major regulator of this function (Meruelo 1979, 1980; Tanaka, 1985, 1986). Recent studies have provided further support to the immune surveillance idea (Dunn, 2002; 2003; 2004; Nakachi, 2004; Zitvogel, 2006) and particularly to the role played by natural killer (NK) cells (Nakachi, 2004; Hayashi, 2006; Hoglund, 2006). A recent study in Japan (the Saitama prospective cohort study) has reported the correlation between NKG2D haplotype variants and natural killer cell cytotoxic activity (Hayashi, 2006). This activity that appears to be linked to NKG2D genetic variation is inversely correlated with cancer development risk (Imai, 2000). The immune surveillance theory implies that homozygosity for the MHC molecules would be deleterious. Several modes of cancer treatment are based on the role played by the immune system (in vitro activation of CTLs and TILs, vaccination with tumor-derived peptides and even gene therapy using TILs).

Cancer is a combination of uncontrolled cellular proliferation and immortality (lack of apoptosis, which is a mechanism of the organism that regulates embryogenesis and development, maintains homeostasis of the immune system and removes potentially hazardous cells. A dysregulation of apoptosis signaling may disturb the balance of cell survival and cell death). Cell division is regulated by growth factors, their cell surface receptors, membrane tyrosine kinase, signaling molecules (GTP-binding proteins), nuclear/transcription factors (the signal transduction system) and growth regulatory (inhibiting) factors. The genes with growth promoting activity are generally called oncogenes (dominant) and those with growth inhibitory activities are tumor suppressor genes (recessive). Proto-oncogenes may encode surface membrane proteins (HER2/neu/erbb2), signal transduction pathway molecules (ras) or transcription factors. Tumor suppressor genes encode cell cycle regulators, adhesion molecules (APC), DNA repair enzymes (MSH2, MLH1) or signal transduction pathway molecules. The cancer causing genes are activated during carcinogenesis due to an extremely increased rate of somatic mutation which results from combined effect of genetic and environmental factors (Bielas, 2006).

Genes involved in oncogenesis

The human genome contains more than 50 genes (cellular oncogenes, c-onc) that are similar to the genes carried by carcinogenic retroviruses (viral oncogenes, v-onc). The cellular counterparts of v-onc are normal cellular genes coding for proteins playing roles in normal cell growth and division. They are normally called proto-oncogenes but when activated they show their oncogenic effects (oncogenes). Examples of oncogenes include sis which encodes a chain of platelet derived growth factor (PDGF); int-2 have similarities to fibroblast growth factor (FGF); c-erb-B (on chromosome 7p) which encodes a truncated form of the receptor for epidermal growth factor (EGFR); mutant ras genes have a reduced capacity to terminate a growth stimulating signal; abl and src have tyrosine kinase activity; c-myb and c-myc are stimulators of cell cycle; and bcl-2 blocks apoptosis and promotes cell survival. One of the earliest phenomena in tumor formation is genomic instability. It is due to defects in DNA repair and cell cycle controls. This can happen by gain-of-function mutations in proto-oncogenes or loss-of-function mutations in tumor suppressor genes.

a. Proto-oncogenes may be activated to act like oncogenes by the following events:

1. Amplification: Int-2 and c-erb-B2 in breast cancer; N-myc in neuroblastoma.

2. Insertional mutagenesis: c-myc (nuclear DNA-binding phosphoproteins) activation by EBV in Burkitt lymphoma (Int3 activation by MMTV in mouse mammary tumors). c-myc may be activated by rearrangement, amplification or overexpression.

3. Chromosomal translocations: In Burkitt lymphoma, c-myc (8q24), in 85% of follicular lymphoma, bcl‑2 (18q21), and in mantle-cell lymphoma bcl-1 (11q13) translocate to the immunoglobulin heavy chain gene region on chromosome 14q32 (subsequently these oncogenes are over expressed); in chronic myeloid leukemia, the bcr gene moves next to c-abl [t (9;22) (q34; q11)] resulting in the expression of a fusion protein. In M3 AML (acute promyelocytic leukemia) RARa / PML genes are rearranged by translocation t(15,17).

4. Mutations in coding sequences: Activating point mutations occur in the ras genes in about 30% of human cancers. ras gene family consists of N-ras, H-ras and K-ras whose products are involved in intracellular transduction of external stimulation of growth factor receptors. Mutated RAS proteins are expressed but functionally appear to have lost the ability to be inactivated. In general, mutations changing the activity of a gene may be missense, nonsense or frameshift type.

Gene expression and function can also be affected by non-DNA base pair changes, namely epigenetic effects:

5. Demethylation or hypomethylation: bcl-2 overexpression in chronic lymphoid leukemia, c-erb-B1 (epidermal growth factor receptor) overexpression in breast cancer.

A number of genes involved in regulation of the cell cycle, cyclins, may also act as oncogenes when mutated (for example, cyclin D2 in mantle cell lymphoma and cyclin D1 and E in breast cancer). On the other hand, germ-line mutation of a cyclin-dependent kinase inhibitor CDKN2/p16 has been implicated as a tumor suppressor gene in hereditary melanoma.

b. Tumor suppressor genes (TSGs) act like recessive anti-oncogenes. Theoretically, both copies of a TSG must be lost or inactivated for oncogenesis through loss-of-heterozygosity events (unlike a single mutation in proto-oncogenes). There are, however, exceptions to this expectation. The best-known TSG is p53 (on chromosome 17p) and mutation of a single copy of the two copies is enough for the deleterious effect. This is because mutant p53 protein monomers are more stable than the normal p53 proteins and can form complexes with the normal wild type p53 acting in a dominant-negative manner to inactivate it. Therefore, one mutated copy is enough for the loss of whole p53 function. The tumor suppressor gene p53 is the guardian of the genome because it prevents progress through the cell cycle when there is something wrong to allow the damage or fault to be repaired. Because mutation of a single allele (single hit) is enough for neoplastic transformation, p53 mutations are the most frequent genetic abnormalities found in human cancers (over 50% in bladder, breast, colon and lung cancers). Different mutations differentially occur in specific cancers (like the codon 249 mutation in aflatoxin-related liver cancer). Inherited (germ-line) p53 mutation is the cause of a well-known inherited cancer syndrome (Li-Fraumeni syndrome; childhood sarcomas, early-onset familial breast cancer and other neoplasms). Most familial cancers are related to defects in TSGs.

Other TSGs are the retinoblastoma (RB1) gene on chromosome 13q, the deleted in colorectal cancer (DCC) gene on chromosome 18q, and the Wilms tumor gene (WT1) on chromosome 11p13. In these cases, the loss of both alleles is required for neoplastic transformation (via mutation or deletion). The RB1 gene encodes a nuclear protein that is involved in the regulation of the cell cycle (it suppresses growth). Various viral proteins interact with the RB protein and inhibit its action (adenoviral E1A, HPV-E7 protein and SV40 large T antigen). The DCC gene is involved in cell adhesion and is deleted in over 70% of colorectal cancer cases. WT1 is a transcription factor for normal kidney and gonadal development. Like most TSGs, p53 and RB1 are also transcription factors.

Alterations in the patterns of DNA methylation are a common genomic alteration in human cancer. Abnormal methylation of CpG islands in the promoters of TSGs (such as RB, von-Hippel Lindau gene and p16) can contribute to their functional inactivation as one of the two hits. For a recent review of DNA methylation in neoplasia, see (Rountree, 2001). The more conventional way of TSG inactivation is its loss due to deletion or mutation. The loss-of-heterozygosity events are genomic deletions that discard the normal copies of TSGs, or uncover the existing TSG mutations. Inherited abnormalities of TSGs are associated with familial cancer syndromes that cause a variety of cancers at an early age.

c. DNA repair genes: DNA repair involves base-excision repair (BER), nucleotide excision repair (NER) and mismatch repair (MSH) (see Table). While oncogenes act as accelerators of growth during G1 phase of cell cycle, and suppressor genes act as stop signals during S phase, DNA repairs gene are not directly involved in cell growth. Their role is repairing DNA mismatches during replication of DNA just before the chromosomes condense in G2 phase for mitosis. These are DNA damage response genes and their defects result in predisposition to a range of tumor types (usually skin or colon cancer and hematological malignancies). Mutations in DNA mismatch repair genes represent more of a predisposition state than a transforming event. BRCA1 and BRCA2 are two of the DNA repair genes. Mutations in critical oncogenes and TSGs are more likely to occur in the repair-deficient cells. One mechanism for inactivation of one of the DNA repair genes (MLH1) is silencing via promoter methylation (as in sporadic colon cancer). The best-known DNA repair genes MSH2 and MLH1 are involved in hereditary non-polyposis colon cancer (HNPCC1 and HNPCC2, respectively) when mutated. PMS1 is mutated in HNPCC3, PMS2 in HNPCC4, MSH6 (mutS homolog 6) in HNPCC5 (HNPCC6 is due to mutations in TGFBR2). DNA repair genes are referred to as 'caretakers' while the genes involved in cell cycle control are called 'gatekeepers' (See Kinzler & Vogelstein, 1997). Microsatellite instability (MSI) is a hallmark of DNA mismatch repair defect (Duval & Hamelin, 2002). For a review of polymorphisms of DNA repair genes and associations with cancer risk see Wood et al, 2001 and Goode et al, 2002. See also DNA Repair Interest Group Website and DNA Repair Mechanisms in the Molecular Biology Web Book, and DNA Damage and Repair and Their Roles in Carcinogenesis in Molecular Cell Biology. For a review, see Jefford, 2006.

d. Growth factors: They regulate cellular proliferation through receptor mediated autocrine or paracrine mechanisms. Transforming Growth Factor-a (TGFa) is one of them (ligand for epidermal growth factor receptor-EGFR). It is over expressed in 50% of invasive breast cancer cases. Insulin-like Growth Factor-1 (IGF1) is a physiologic mediator and stimulator of normal cell growth. Most breast cancers express receptors for it.

e. Other genes: Ataxia-telangiectasia (ATM) gene confers increased risk for leukemia and lymphoma in homozygous subjects for its mutations. BRCA1 (probably a transcription factor) and BRCA2 are involved in familial breast cancer predisposition (hereditary form is no more than 5% of all breast cancers). Most recently, microRNAs have gained importance in cancer genetics and their (or their binding site) polymorphisms are becoming useful markers of cancer genetic risk in molecular epidemiology (Chen, 2008; see also the microRNA database miRBase that lists known human miRNAs).

Genetic prediction

Having a gene mutation/variant may be necessary but most of the time is not sufficient for developing a disease. Penetrance is defined as the proportion of individuals with a specific genetic alteration who will express the associated trait. Thus, genetic tests are not always perfect predictors of health risks. The BRCA1 mutations, for example, cause familial breast cancer in 60% of women by the age of 60 (45-90% risk for life-time). The detection of a mutation in this gene (>100kb) does not necessarily indicate an absolute risk. Examples of high penetrance are polyposis-associated colon cancer and MEN2a-associated medullary thyroid cancer (penetrance close to 100%). Pharmacogenetic studies deal with the polymorphisms in xenobiotic enzyme genes. One of them, CYP1A1 is involved in the activation of polycyclic aromatic hydrocarbons (PAH). The susceptibility allele of CYP1A1 increases the risk of lung cancer in smokers, whereas, those lacking the PAH activating allele are relatively protected from the carcinogenic effects of smoking. A striking example of gene and environment interaction has been shown in mesothelioma cases in central Turkey (Carbone, 2007). There is also parental imprinting effect in inherited cancer predisposition. Paraganglionoma occurs only if the mutation on chromosome 11 is inherited from the father. In neurofibromatosis type 2, however, children of affected females show earlier and more severe symptoms than children of affected males.

Genetic anticipation refers to the younger age or increased severity of a disease in successive generations. This phenomenon is better known in some non-malignant diseases caused by unstable triplet repeats (as in Huntington disease and congenital myotonic dystrophy) but is also rarely seen in familial leukemia and ovarian cancer. Like anticipation and imprinting, sex influence and mosaicism also cause a non-Mendelian inheritance pattern in familial cancers. Mosaicism refers to the presence of the normal (wild type) genotype as well as the abnormal (mutant) genotype in the germ-line of an individual. In this case, the parent will not have the phenotype but the offspring will. Germ-line mosaicism has been observed in retinoblastoma.

One important issue about genetic prediction of cancer is genetic heterogeneity. There may be a number of distinct genotypes associated with the same phenotype. Absence of a known genotype causing a particular cancer may not mean the lack of genetic predisposition to that cancer. Similar to the effect of genetic heterogeneity, phenocopies also confound pedigree analysis in cancer families. Phenocopy is a trait that appears to be identical to a genetic trait but that does not have a genetic basis. Sporadic form of a tumor in a cancer family may make the interpretation of the pedigree difficult.

Genetic therapy in cancer

Antisense therapy (for HPV in cervical cancer); targeted cytotoxic treatment against fusion proteins, somatic gene therapy (using carrier vectors incorporated with a toxin, an enzyme activating the cytotoxic agents; using DNA/liposome complex containing a foreign MHC antigen; or TILs infected with retroviruses carrying TNF or IL-2); immunization with tumor-specific proteins (p53, fusion proteins) or idiotypic antibodies in B-cell malignancies.

 

BOOK: Lynch HT & Hirayama T: Genetic Epidemiology of Cancer, CRC, 1989

NCI Cancer Genome Anatomy Project   NCI Cancer Genetics Overview  (another version)

 NCI Cancer Dictionary   Cancer Research UK: Glossary

 

HuGE Navigator > Cancer GAMAdb    GWAS Catalogue

NCI Division of Cancer Epidemiology and Genetics   Cancer Genetic Markers of Susceptibility (CGEMS)

Breast and Prostate Cancer and Hormone-Related Gene Variant Study by BPC3

ACS Cancer Facts and Figures 2007

The Wellcome Trust: Cancer Genome Project

NCBI Bookshelf: Cancer Medicine 6th Edition  NCI: Understanding Cancer Series

Concise Handbook of Familial Cancer Susceptibility Syndromes  

What Makes a Cancer Cell a Cancer Cell? in Cancer Medicine

Oncogenes, Tumor-Suppressor Genes & Genetic Basis for Tumor Development in Cancer Medicine

Genetic Predisposition to Cancer in Cancer Medicine

Proto-oncogenes and Cancer & Tumor Suppressor Genes in the Medical Biochemistry Page

Cancer Genetics WebGenes - Chromosomes - Diseases  (last updated in 2003)

Atlas: Chromosomes in Cancer

Cancer in Molecular Cell Biology

Breast Cancer Epidemiology   Cancer Research UK: Cancer Stats

Overview of Cancer in Merck Manual

New Scientist Special Reports: Cancer

AICR: Brochures for Cancer Prevention

Childhood Cancer Epidemiology

 

Address for bookmark: http://www.dorak.info/genetics/notes06.html

M.Tevfik Dorak, M.D., Ph.D.

Last updated on 28 August 2012

Genetics      Evolution     HLA     MHC     Epidemiology     Genetic Epidemiology     Population Genetics    Glossary     Homepage