From Iusmgenetics

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

Estimated New Cases* Males Females Prostate 218,890 29% Breast 178,480 26% Lung & bronchus 114,760 15% Lung & bronchus 98,620 15% Colon & rectum 79,130 10% Colon & rectum 74,630 11 % Urinary bladder 50,040 7% Uterine corpus 39,080 6% Non-Hodgkin lymphoma 34,200 4% Non-Hodgkin lymphoma 28,990 4% Melanoma of the skin 33,910 4% Melanoma of the skin 26,030 4% Kidney & renal pelvis 31 ,590 4% Thyroid 25,480 4% Leukemia 24,800 3% Ovary 22,430 3% Oral cavity & pharynx 24,180 3% Kidney & renal pelvis 19,600 3% Pancreas 18,830 2% Leukemia 19,440 3% All Sites 766,860 100% All Sites 678,060 100% Estimated Deaths Males Females Lung & bronchus 89,510 31 % Lung & bronchus 70,880 26% Prostate 27,050 9% Breast 40,460 15% Colon & rectum 26,000 9% Colon & rectum 26,180 10% Pancreas 16,840 6% Pancreas 16,530 6% Leukemia 12,320 4% Ovary 15,280 6% Liver & intrahepatic bile duct 11,280 4% Leukemia 9,470 4% Esophagus 10,900 4% Non-Hodgkin lymphoma 9,060 3% Urinary bladder 9,630 3% Uterine corpus 7,400 3% Non-Hodgkin lymphoma 9,600 3% Brain & other nervous system 5,590 2% Kidney & renal pelvis 8,080 3% Liver & intrahepatic bile duct 5,500 2% All Sites 289,550 100% All Sites 270,100 100%

Cancer Genetics

• Why study cancer genetics? 1999-Estimated that a general practioner would see 1-2 pts/month who require genetic services. 2007-The number is doubled and higher for specialty practioners More patients becoming (will be) aware of genetic considerations

Emery et al. (1999) Family Practice 16(4):426-445. MCAN00605_0000[1] Cancer Genetics • In order to study possible hereditary pattern of disease, should take a family history for at least three generations

Is this pedigree compatible with hereditary cancer?

Br ca dx 65 Hereditary predisposition for cancer

Br ca, dx 50

Br ca, dx 42 Pr ca, dx 60 Ov ca,dx 58

Br ca, dx35 Br ca, dx45 Autosomal dominant inheritance high but incomplete penetrance gender specific penetrance variable expression Early-onset diagnosis Multiple cases of a cancer More than 1 primary cancer Familial predisposition for cancer

Br ca, dx60 Co ca,dx60 Clustering of cancer but no clear inheritance pattern Moderate ages at diagnosis Absence of multiple primary cancers Absence of rare 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 is clonal in nature

Hits might be inherited or acquired mutations or environmental factors

Genes involved with controlling cell proliferation and cell death

Categories / classes of genes – Oncogenes

– Tumor suppressor genes

– DNA repair/metabolism genes

– Other

Oncogenes

• Dominantly acting gene(s) involved in upregulating cell growth and prolifieration – Dominant at the cellular level

– Identified because of their ability to cause transformation (promote tumors/cancer)

• Oncogenes are normal genes (proto-oncogenes) that have gone awry (e.g., become activated)

• Proto-oncogenes: Normal genes involved in some aspect of cell division or proliferation

• Growth factors Growth factor receptors

• Signal transduction molecules Nuclear proteins

• Transcriptional regulation Cell cycle related

How is a proto-oncogene “activated” to an oncogene?

“Gain of function” mutations • Change in protein structure

– Point mutation (e.g., Ras)

– Hybrid (fusion) proteins » E.g., Philadelphia chromosome translocation in CML

• Change in expression (levels or site)

– Viral (retroviral) insertion

– Gene Amplification

– Translocation

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Burkitt lymphoma

• B-cell tumor of the jaw (Most common tumor in children in equatorial Africa, rare elsewhere)

• Translocations

– Myc proto-oncogene, 8q24 t(8;14) [Also t(8;22) and t(2;8)]

– Immunoglobulin genes

Chromosomes: 2 (kappa light), 14 (heavychain), 22 (lambda light). Activation of myc as a result of the translocation

Burkitt Lymphoma Enhancer Inherited mutations in oncogenes are not common but can occur

• Multiple endocrine neoplasia (MEN) type 2. – Autosomal Dominant (thyroid carcinoma)

– RET proto-oncogene (tyrosine kinase receptor)

– Mutation leads to constitutive kinase activity

– (Loss of function RET mutations -Hirschsprung disease)

• Hereditary papillary renal carcinoma (HPRC). – Autosomal Dominant

– MET tyrosine kinase receptor gene

– HPRC mutations activate kinase in absence of ligand

Tumor suppressor genes

• Normally block abnormal growth and malignant transformation

• Mutations are recessive at the cellular level

– Two hit theory > Knudson

• Mutations can act as dominants at the organismal level

• Concept of loss of heterozygosity (LOH)

Text fig 16-1

Cancer Genes

• Most gene mutations in cancer occur in somatic cells and are acquired

• However, some mutations do occur in the germline and may be inherited and passed on to future generations.

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• One of the first scientists to explain the phenotypic differences between acquired and inherited gene mutations in cancer was Alfred Knudson in the 1960s.

Knudson’s Hypothesis

.Retinoblastoma observations -Led to “Two-Hit Theory” -Tumor suppressor genes Family history No family history Younger Older Bilateral Unilateral Multifocal Unifocal

Retinoblastoma

(Clinical case #34)

• Retinal tumors

• 1/23,000 live births

• Most common eye tumor in early childhood

• May begin forming prenatally

• Average age of onset 18 months

• Can be inherited as autosomal dominant trait

Text fig C-34

• Treat -removal of orbit

Retinoblastoma (cont.)

• 40% inherited, 60% sporadic – inherited from carrier parent or result of germline mutation • Unilateral vs bilateral – if bilateral, likely inherited

– but, 15% of unilateral have germline mutation

• Unifocal vs multifocal

• Onset age

• Patients have increased risk of other cancers / tumors

– E.g., osteosarcoma

SPORADIC RETINOBLASTOMA FAMILIAL RETINOBLASTOMA RETINAL CELLS

FIRST HIT

SECOND HIT RETINOBLASTOMA

Comparison of Mendelian and sporadic forms of cancers (See text fig 16-6)

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