From Iusmgenetics

Contents 1 Cancer Genetics 1.1 Objectives 1.2 Cancer 1.3 Hereditary Predisposition for Cancer 1.4 Features suggesting an inherited predisposition to cancer 1.5 Cancer is a genetic disease 1.6 Cell Proliferation and Cell Death Genes 1.6.1 Oncogenes 1.6.1.1 Burkitt lymphoma 1.6.2 Inherited mutations in oncogenes 1.6.3 Tumor suppressor genes 1.6.4 Cancer genes 1.6.4.1 Retinoblastoma 1.6.4.2 Loss of heterozygosity 1.6.5 Breast cancer 1.6.6 Colorectal Cancer (CRC) 1.6.6.1 Familial adenomatous polyposis (FAP) 1.6.6.2 HNPCC: Hereditary non-polyposis colon cancer (Lynch Syndrome) 1.6.6.2.1 Amsterdam criteria 1.6.6.2.2 MMR Defects in HNPCC and MSI 1.6.6.3 HNPCC Take-home Points 1.6.7 Cancer cells and Epigenetics 1.7 Indiana Familial Cancer Clinic

[edit] Cancer Genetics

[edit] Objectives

• Understand that cancer is a genetic disease and a multistep process.
• Know the types of genes associated with cancer.
• Know fundamentals about cancer pathogenesis, including the concepts of:
  • oncogene action / activation;
  • modes of disease pathogenesis associated with tumor suppressor genes (e.g., two hit);
  • microsatellite instability
  • potential role of epigenetics in cancer
• Know features of the specific disorders discussed in class.

[edit] Cancer

• Cancer is a heterogeneous disease that will claim more than 560,000 lives in our country this year.

• Cancer INCIDENCE

Cancer	% of all cancers cases	Gender	Gender	% of all cancer cases	Cancer
Prostate	29%	Male	Female	26%	Breast
Lung / Bronchus	15%	Male	Female	15%	Lung / Bronchus
Colon / Rectum	10%	Male	Female	11%	Colon / Rectum
Bladder	7%	Male	Female	6%	Uterine

• Cancer DEATHS

Cancer	% of all cancers cases	Male	Female	% of all cancer cases	Cancer
Lung / Bronchus	31%	Male	Female	26%	Lung / Bronchus
Prostate	9%	Male	Female	15%	Breast
Colon / Rectum	9%	Male	Female	10%	Colon / Rectum
Pancreas	6%	Male	Female	6%	Pancreas

• 1999: estimated that a general practioner would see 1-2 pts / month who require genetic services.
• 2007: estimated 2-4 pts / month require genetic services.
• More patients becoming (will be) aware of genetic considerations.
• In order to study possible hereditary pattern of disease.
  • Take at least three generations of family history into account.

[edit] Hereditary Predisposition for Cancer

• Cancer inheritance is not necessarily straight forward.
  • Autosomal or sex chromosomes inheritance
  • Incomplete penetrance
  • Gender specific penetrance
  • Variable expressivity
  • Early-onset diagnosis
  • Multiple primary cancers manifested
  • Multiple cases of cancer
  • Unclear ages of onset
  • Commonality of cancers

[edit] Features suggesting an inherited predisposition to cancer

• Factors suggesting an inherited predisposition for cancer include (as in a single gene causing high susceptibility to cancer):
  • Two or more close relatives affected.
  • Early age of onset.
    • Or earlier onset in each generation
  • Cancers of a specific type occurring together (e.g., breast and ovary).
  • Multiple or bilateral cancers occurring in one person.
  • Rare cancers

• Factors suggesting familial clustering of cancer:
  • A clear increase in cancer compared to expected, though no clear inheritance pattern
  • Moderate age at diagnosis
  • Absence of multiple primary cancers (as seen in hereditary predisposition)
  • Absence of rare cancers

[edit] Cancer is a genetic disease

• All cancers involve genetic changes in somatic cells, the germ line, or both.
• In addition to genes, there are other predisposing factors such as:
  • Infection (virus)
  • Radiation
  • Carcinogens
  • Immunological defects

• Cancer is a multistep process and is clonal in nature.
• "Hits" might be inherited or acquired mutations or environmental factors.
• "Hits" (mutations in a cell's genome) accumulate over time, potentially lending it neoplastic features like auto-regulation.
• There is increasing aneuploidy as the cell accumulates lesions.
• Recall that lesions to DNA repair genes can accelerate the rate of lesion accumulation.

• Genes controlling cell proliferation and death are important in the natural history of cancer development.

[edit] Cell Proliferation and Cell Death Genes

• Genes involved in proliferation and death (apoptosis) are important regulators of cancer.
• There are several categories of these genes:
  • Oncogenes
  • Tumor suppressor genes
  • DNA repair/metabolism genes
  • Other

[edit] Oncogenes

• To understand oncogenes, first understand that proto-oncogenes are normal genes that have something to do with the cell cycle or proliferation.
  • Proto-oncogenes are found in the normal genome and are an important part of cellular function and organism development.
  • Proto-oncogenes have many regulations upon them that cause them to function at the right time and place in the organism and in development.
  • Examples of proto-oncogenes include:
    • Growth factors / receptors
    • Signal transduction molecules (nuclear proteins)
    • Transcriptional regulators (which affect the cell cycle)

• An oncogene, then, is a proto-oncogene that is out of control--acting aberrantly in time or space.
• Oncogenes are "dominantly acting" because only one copy of the gene need be turned on to induce it's pro-growth, pro-proliferation effect.

*Oncogenes are "dominant at the cellular level"

• Oncogenes have been identified by their ability to convert non-neoplastic cells into neoplastic cells--that is they promote tumors / cancers.

• Activation of a proto-oncogene (into an oncogene):
  • Activation of a proto-oncogene generally requires a gain of function mutation.
  • A gain of function occurs either through a change in protein structure or a change in expression.
  • Proteins structure changes can occur in many ways, including point mutations and hybrid proteins:
    • Ras is commonly point mutated to gain function.
    • CML has the t9:22 to generate the function-gained bcr-abl gene.
  • Protein expression changes can manifest as a change in expression level or a change in expression location (as in tissue):
    • Viral insertion can cause expression in a new location or a new level.
      • From gene therapy, think about the virus donating a novel promotor that upregulates downstream genes.
    • Gene amplification causes increased expression.
    • Translocation can cause increased or decreased expression depending on the promotor relavant to the translocation.

• Common oncogenes incluede:
  • ret, met, and ras: kinases and signaling genes
  • fas: pro-apoptotic (in wildtype form)

[edit] Burkitt lymphoma

• Burkitt lymphoma is the most common tumor in children of equatorial Africa (but is rare, elsewhere).
• Burkitt lymphoma is a B-cell tumor of the jaw.
• Burkitt lymphoma is characterized by translocations that convert proto-oncogenes to oncogenes.
• myc conversion
  • t(8;14) is the primary translocation associated with Burkitt lymphoma and the c-myc gene.
  • Converts myc to an oncogene.
  • t(8;22) and t(2;8) are also common translocations that convert myc to an oncogene.
• Immunoglobulin genes
  • Chromosomes 2, 15, and 22 carry genes required for immunoglobulin formation.
  • Ch 2: kappa light chain
  • Ch 14: heavy chain
  • Ch 22: lambda light chain
• c-myc is a proto-oncogene
  • When translocation occurs, it brings c-myc from 8 to elements important for Ig expression and thus c-myc is upregulated in cells that function to make Ig (B cells).
  • Elevated c-myc results in excessive proliferation and thus t(8;22) generates Burkitt lymphoma.

[edit] Inherited mutations in oncogenes

• It is rare to inherit a mutation in an oncogene, but it does happen; MEN2 and HPRC are two examples.

• MEN2 is associated with an inherited RET mutation
  • MEN2 presents as an autosomal dominant cancer predilection syndrome.
    • This makes sense as we previously mentioned the dominant activity of oncogenes (only one has to be mutated to cause cancer).
  • Thyroid carcinoma is usually the primary tumor culprit.
  • RET is a tyrosine kinase receptor
  • Gain-of-function mutations in RET (inherited, remember) lead to constitutive kinase activity.
  • NB: loss-of-function mutations in RET lead to Hirschsprung disease

• Hereditary papillary renal carcinoma (HPRC):
  • HPRC, like MEN2, is inherited in an autosomal dominant fashion.
  • HPRC is associated with gain-of-function mutations in MET.
  • MET is a tyrosine kinase receptor.
  • Gain-of-function mutation in MET lead to constitutive activation of the kinases to which MET is bound (even when the proper ligand isn't present).

[edit] Tumor suppressor genes

• Tumor suppressor genes are those that normally serve to discourage growth and replication.
• Tumor suppressor gene mutations act in a cellular recessive manner because though one copy of the gene may become defective, the other copy can usually maintain the proper cell cycle, and therefore cellular function is not usually affected by this first hit.
• Because tumor suppressor gene mutations act in a recessive mannner, the two hit hypothesis suggests that at least two hits (genetic lesions) are required to "knock-out" the function of a tumor suppressor gene.
  • The two hit hypothesis was developed by Knudson.
• Loss-of-function lesions on tumor suppressor genes can act dominantly at the organismal level.
  • Recall that something of a "dominant" nature always--or close to always--occurs; like brown eyes.
  • Recall that a second "hit" that would cause cancer is unlikely.
  • However, note that there are many, many cells in the body.
  • Therefore, development of cancer always--or nearly always--occurs when all cells of the body start out with a single hit (and therefore, development of a tumor is considered "dominant" at the organism level).
    • This makes sense because even though the odds of a second hit are very low, there are trillions of cells that only need 1 more hit to develop cancer.
• Mutation of only one copy of a tumor suppressor gene leads to loss of heterozygosity: the state of having two of the same allele for a gene (or having only one functional copy of the allele and therefore no hetergeneity in gene product).

• Common tumor suppressor genes are:
  • rb, p53: cell cycle regulators
  • msh2, mlh1: DNA repair / inspection regulators
  • bcl2, telomerase: anti-apoptotic

[edit] Cancer genes

• Most mutations related to cancer occur in somatic cells that are not passed on to off-spring.
• However, some mutations do occur in the germ line and can be passed to off-spring.
• Inherited mutations can come from the egg, the sperm, or the zygote.
• Inherited mutations are usually / often found in the genome of every cell of the body.

• Alfred Knudson was the first to describe the phenotypic difference between somatic and inherited mutations in cancer.
• Knudson observed that cases of retinoblastoma had distinct characteristics when there was a family history of retinoblastoma:
  • tumors occurred earlier in life,
  • tumors were more likely to be bilateral, and
  • tumors were mutlifocal (have more than one site of origin).
• So he reasoned that a family history suggests that the germline contains a "hit" or lesion against the rb gene and that offspring had earlier tumors that were more likely to be bilateral and multifocal because they had only to receive one more "hit" to develop retinoblastoma.
• In comparison, with no family history, two independent "hits" had to occur to develop retinoblastoma and therefore the tumors occurred later in life and were less likely to be bilateral or multifocal.

[edit] Retinoblastoma

• Rb is the most common eye tumor in early childhood.
• Retinoblastoma is a tumor of the retina.
• Retinoblastomas may actually begin forming in utero.
• Average age of Rb onset is 18 months.
• Treatment for retinoblastoma is to remove the entire orbit.

• 1/23k live births have retinoblastomas.
• Retinoblastoma can be inherited as an autosomal dominant trait.
• 40% of retinoblastomas are inherited.
  • Parent may be a carrier or there may have been a germline mutation.
  • Bilateral state suggests inheritance.
  • 15% of inherited retinoblastomas are unilateral.
• 60% of retinoblastomas are sporadic.

• Retinoblastoma pts have elevated risk for other cancers, too.
  • Including osteosarcoma

• So, we say that rb is recessive at the cellular level because one loss makes no difference in cellular function but rb is dominant at the organismal level because it nearly always results in tumor development because of the large number of cells of the organims--all of which are at risk to develop cancer because they are starting with a single hit.

[edit] Loss of heterozygosity

• Loss of heterozygosity: "loss of a normal allele from a region of one chromosome of a pair, allowing a defective allele on the homologous chromosome to be clinically manifest. A feature of many cases of retinoblastoma, breast cancer, and other tumors due to mutation in a tumor-suppressor gene."
• That is, when a tumor suppressor gene is mutated, the organism is then relying on the second copy of the gene to maintain proper function; when a second loss occurs ("loss of heterozygosity") the deficiency is finally manifested since, now, neither copy works sufficiently well to maintain normal cellular function.
• LOH occurs when the second, functional allele (that is allowing for proper function) is overwritten by the non-functional copy (perhaps because of complexity of DNA replication or because of repair at the allele that used the other allele as a template).
• LOH can result from several mechanisms: somatic recombination, loss / duplication, chromosomal atresia.
  • Note that a very small lesion directly at the site of the (second, still functional) allele will not change flanking / intragenic markers and is therefore not considered a loss of heterogeneity
  • Linked markers are genetic markers that tend to be inherited with the locus of origin (that is, they are nearby the locus).

• LOH (loss of heterozygosity) can also refer to a laboratory analysis technique that identifies the mechanism of the second hit.
• LOH is a way to identify the existence of tumor suppressor genes.

[edit] Breast cancer

• Breast cancer is common (#1 in incidence for women, #2 in deaths for women).
• Lifetime risk of breast cancer is 1/8.
• 180k new cases each year.

• Most breast cancer is sporadic.
• 5% of breast cancer is considered hereditary
• 15-20% of breast cancer is considered family-clustered
• 10% of ovarian cancer is considered hereditary

• Susceptibility genes for breast cancer include brca1 and brca2.
• Mutations in these genes account for 3-5% of all breast cancers
• brca1 and brca2 were cloned in 1994 / 5.
• brca1 and brca2 have autosomal dominant effects
• brca1 and brca2 are on different chromosomes.

• Inheriting a mutated brca1 gene allele increases one's lifetime risk of developing cancer:
  • One primary breast cancer risk: 50-85% (compared to 12% population risk)
  • Second primary breast cancer risk: 40-60% (compared to 2% population risk)
  • Ovarian cancer risk: 15-45%
  • Potentially elevated risk for other cancers like prostate and colon, too.

• Inheriting a mutated brca2 gene allele increases one's lifetime risk of developing cancer:
  • Breast cancer risk (female): 50-85% (same as brca1 mutation risk)
  • Breast cancer risk (male): 6% (no increased risk with brca1 mutation)
  • Ovarian cancer risk: 10-20% (compared to 15-45% with brca1 mutation)
  • 'Increased risk of prostate, laryngeal, and pancreatic cancers, too.
    • Magnitude unknown.

• 45-60% of brca1 or brca2 mutant carriers develop breast cancer by the age of 70.

• Ashkenazi Jews are more likely to be carriers of brca1 and brca2 mutant alleles than other populations: 1/40.

[edit] Colorectal Cancer (CRC)

• 150k new cases each year
• 57k deaths each year (#3 cancer killer in both men and women)
• 2-5% lifetime risk
• The vast majority of colorectal cancer is sporadic in etiology.
• About 25% of colorectal cancer is familial or HNPCC in etiology.
• A small proportion of colorectal cancer is due to Familial adenomatous polyposis (FAP) and a subvariant called Gardner syndrome.

[edit] Familial adenomatous polyposis (FAP)

• Familial adenomatous polyposis is also known as adenomatous polyposis coli.
  • Hence the causative gene is called APC.
• Inheritance of FAP is autosomal dominant.
• Offspring with FAP are heterozygous at the APC locus for function.
• Heterozygotes develop many polyps within the first two decades of life.
  • These polyps are benign.
• Because there are so many polyps (hundreds, thousands), there is always transformation to malignancy.
• Treatment is by surgical removal of the colon.
• Carriers and relatives of pts should be screened with regular colonoscopy.
• 70% of sporadic colon cancer cases have loss of APC at both alleles despite not having inherited a defunct copy as with FAP cases.

• APC is a tumor suppressor gene.
• Beta-catenin is a pro-proliferation transcription factor.
• APC acts to inhibit cell proliferation by maintaining low beta-catenin levels.
  • APC is a kinase that phosphorylates beta-catenin, thus targeting it for destruction.
• When APC becomes non-functional, beta-catenin accumulates, migrates to the nucleus, and induces transcription of myc and other pro-proliferation genes.

• As colon cancer develops, mutations accumulate in common sites:
  • APC
  • Mismatch repair genes
  • RAS
  • DCC (a tumor suppressor gene)
  • SMAD4
  • p53 (a tumor suppressor gene)
  • TGF-beta receptor 2

[edit] HNPCC: Hereditary non-polyposis colon cancer (Lynch Syndrome)

• HNPCC was first describe in 1913 by Alfred Warthin.
• Warthin noticed that his seemstress's family had a string of stomach and endometrial cancers
• Lynch (Henry) then characterized hereditary non-polyposis colorectal cancer
  • HNPCC = Lynch Syndrome

• HNPCC is autosomal dominant
• HNPCC usually results in a proximal colon cancers.
• HNPCC increases risk for endometrial cancer and ovarian cancer in women.
• HNPCC increases urinary tract cancers (in the kidneys and ureter).
• HNPCC also gives rise to cancers in non-colon areas of the GI tract: stomach, biliary tract, small intestine.
• Finally, HNPCC is associated with increased brain cancer.

• Average age of colorectal onset in HNPCC is 44 years old (as compared to the general population average age of 64).

[edit] Amsterdam criteria

• The Amsterdam criteria identifies HNPCC families
  • These are high risk individuals who are candidates for confirmatory molecular testing for APC mutations.
• The criteria has a series of 3-2-1 requirements:
  • 3 relatives with CRC (2 of them must be first degree relatives to the proband)
  • 2 successive generations with CRC
  • 1 case of CRC before 50 yo

[edit] MMR Defects in HNPCC and MSI

• HNPCC is caused by a defect in mismatch repair.
• There are 5 genes related to mismatch repair, each of which can cause HNPCC if mutated:
  • hMLH 1/2/6
  • hPMS 1/2
• Mutations in these genes cause ineffective DNA repair and therefore microsatellite instability (MSI) and therefore HNPCC.

• MSI (microsatellite instability) is the expansion or contraction of short, repeated segments of DNA secondary to MMR defects.
• MSI is not normally found in properly functioning cells.
• MSI is found in 90% of HNPCC tumors.
• MSI is found in only 15% of sporadic colorectal cancers.

*What is the significance of MSI?  Diagnosis?

[edit] HNPCC Take-home Points

• Mutations in MLH1 and MSH2 result in defective mismatch repair and thus cause HNPCC.
• Mutations in MLH1 and MSH2 raise the risk of CRC (colorectal cancer) by the age of 70 to 70-85%.
  • The general population risk is 2-5%.
• Mutations in MLH1 and MSH2 raise the risk of endometrial cancer by the age of 70 to 42-60%.
  • The general population is much lower.

[edit] Cancer cells and Epigenetics

• Cancer cells demonstrate several epigenetic changes: hypo / hyper methylation.
• Recall that methylation closes DNA off from expression.
• Improper methylation (or improper epigenetics of any form, really) should be considered one way to implment a "hit".

• Hypomethylation:
  • Recall that hypomethylation will generally allow more expression of the DNA.
  • Hypomethylation can be seen in both benign and malignant neoplasms.
  • Hypomethylation usually occurs at repetitive sequences.
  • Hypomethylation may have several effects:
    • genomic instability
    • activation of oncogenes
    • activation of retrotransposons
    • loss of imprinting
  • For example, loss of imprinting on the IGF2 gene is seen in 40% of colorectal cancers.

• Hypermethylation:
  • Recall that hypermethylation will generally inhibit expression of the DNA.
  • Hypermethylation is usually at CpG islands.
  • Hypermethylation may contribute to cancer via promotor silencing of tumor suppressor genes.

[edit] Indiana Familial Cancer Clinic

• Genetic Services for Familial Cancer
• Referral
• Intake Information
• Family History Questionnaire