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 1.6.5 Loss of heterozygosity

Cancer Genetics

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.

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.

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

Features suggesting an inherited predisposition to cancer

• Two or more close relatives affected.
• Early age of onset.
• Cancers of a specific type occurring together (e.g., breast and ovary).
• Multiple or bilateral cancers occurring in one person.

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 clonal
• 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.

Cell Proliferation and Cell Death Genes

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

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.
    • 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)

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
  • 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

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).

Tumor suppressor genes

• Tumor suppressor genes are those that normally serve to discourage growth and replication.
• Tumor suppressor gene mutations act in a recessive manner because though one copy of the gene may become defective, the other copy can usually maintain the proper cell cycle.
• 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.

• 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: antiapoptotic

Text fig 16-1

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.

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

Loss of heterozygosity

Loss of Heterozygosity

• (Definition from text) 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.

• Represents the mutation, inactivation or loss of the remaining wild-type allele tumor suppressor gene.

• Also used to refer to a laboratory analysis of the mechanism of the “second hit”.

• Loss of heterozygosity (or reduction to homozygosity) results in loss of a flanking or intragenic marker.

• A way to identify the existence of tumor-suppressor genes.

Types of Second Hits Modified text fig 16-7

Not LOH for distal Loss of Heterozygosity (LOH) for rb and also for marker(s) distal marker(s) Breast Cancer • Breast cancer is a common disorder

• Lifetime risk is ~ 1 in 8.

• 180,000 new case each year

How Much Breast and Ovarian Cancer Is Hereditary?

15%-20% -10%

Breast cancer Ovarian cancer • Sporadic

• Family clusters

• Hereditary

ASC®"

Breast Cancer

• Two major susceptibility genes, BRCA1 and BRCA2 have been identified.

• Mutations in these genes account for 3-5% of all breast cancers.

BRCA 1 and BRCA2: An Overview

BRCAl BRCA2 Year cloned 1994 1995 Chromosome location 17q21 13q12 Genomic DNA I coding exons 5.6 kb I 22 exons 10.2 kb I 26 exons Number of amino acids 1,863 3,418 Number of mutations > 1,230 > 1,380 reported Inheritance pattern Autosomal dominant Autosomal dominant

Breast Information Core. Available at: http://research.nhgri.nih.gov/bic/. Accessed October 17, 2003. ASC®~

BRCA1-Associated Cancers: Lifetime Risk

BRCA2-Associated Cancers: Lifetime Risk

Breast ca. risk by age 70 (Pop risk 10-12%) Ovarian ca. risk by age 70 (Pop risk 1-2%) BRCA1 In AD families 50-85% Not . male risk In AD families 15-45% BRCA2 In families 50-85% In families 10-20%

Male carriers, 6% risk BRCA2 – ca. 10-20% of all male breast ca.

In population screen for BRCA1 or BRCA2 carriers, the risk for breast cancer by age 70 is 45-60%. Ashkenazi Jews (1/40 carriers): BRCA1: 185del AG, 5382insC -BRCA2: 6174delT

COLON CANCER

• 150,000 new cases a year.

• 57,000 deaths a year.

• All Americans have a 2-5% life-time risk for Colorectal Cancer (CRC).

Etiology of Colorectal Cancer

Familial

A small proportion of colorectal cancer is due to Familial adenomatous polyposis (FAP) and a subvariant Gardner syndrome. Familial adenomatous polyposis (FAP) (Clincal case # 13)

– Also known as Adenomatous polyposis coli (APC).

– Gene is named APC

– Autosomal dominant.

– Heterozygotes develop numerous adenomatous (benign)polyps in the first two decades of life.

– In almost all cases, one or more polyps becomes malignant.

– Treat by surgical removal of colon.

– Relatives/carriers examined by periodic colonoscopy.

Text Clinical Case Study

APC gene Tumor suppressor

Individuals without FAP but with adenomatous polyps (sporadic) Nearly 70% have loss of both APC genes in tumor

See text fig 16-13

HNPCC

Hereditary Non-polyposis Colon Cancer

• First describe in 1913 by Alfred Warthin, who identified a clustering of predominantly stomach and endometrial cancers in the family of his seamstress (family G).

• Fifty years later, HNPCC was characterized further by Henry Lynch, as Lynch syndrome.

HNPCC

• Autosomal dominant

• Colon Cancer (proximal location)

• Endometrial Cancer

• Ovarian Cancer

• Urinary Tract (Kidney/Ureter)

• Stomach

• Biliary Tract

• Brain

• Small Intestine

• Average age of CRC in HNPCC:

• 44 years old

• Average age of CRC in general population:

HNPCC

• 64 years old

Amsterdam Criteria For identifying HNPCC families (high-risk candidates for molecular genetic testing)

• 3 relatives with CRC.

– 2 of the relatives are first degree

• Two successive generations

• 1 case of CRC before 50 years of age.

Mismatch Repair Defect (MMR) Genes

• Mutations in 5 genes lead to a MMR phenotype in HNPCC.

• hMLH1

• hMSH2

• hMSH6

• hPMS1

• hPMS2

• Mutations lead to ineffective DNA repair and microsatellite instability (MSI).

Microsatellite Instability (MSI)

• Found in tumors, not normal tissue.

• Characterized by expansion or contraction of short, repeated DNA sequences.

• Found in >90% of tumors of patients with HNPCC.

• Found in approximately 15% of sporadiccolorectal cancers.

BAT-25 BAT-26 D2S123 D5S346

HNPCC Key Points

• Mutations in the MLH1 and MSH2 genes increase the risk of CRC to 70-82% before the age of 70, as compared to the general population risk of 2-5%.

• Mutations in the MLH1 and MSH2 genes are associated with an approximately 42­60% risk of endometrial cancer before the age of 70.

Cancer cells show changes of epigenetic

marks in their genome

• Global DNA hypomethylation

– In both benign and malignant neoplasms

– Typically at repetitive sequences (satellite or pericentromeric)

• May add to genomic instability

• May lead to activation of oncogenes or retrotransposons

• May lead to loss of imprinting (LOI)

– E.g., LOI of the IGF2/H19 region seen in about 40% ofcolorectal cancer

• Hypermethylation

– Tends to be focal at CpG islands

– E.g., Promoter silencing of tumor suppressor genes byhypermethylation

DNA and epigenetic changes that inactivate tumor-suppressor genes Norma

Indiana Familial Cancer Clinic • Genetic Services for Familial Cancer

• Referral

• Intake Information

• Family History Questionnaire

END