Molecular Genetics Of Cancer (Bbd Exam Iii)

Front 1

What is the role of RETROVIRUSES in human cancer?

Back 1

1. Simply to identify the ONCOGENES in NON HUMAN MODELS that may be relevant to human cancer... THESE ARE NOT HUMAN VIRUSES!!!
2. Important tools in understanding growth regulation

Front 2

How do RETROVIRUSES aide in identifying ONCOGENES?

Back 2

1. The viral LTR region is a STRONG PROMOTER that has measurable consequences both upstream and downstream of the gene of interest. (placement of the gene during transformation does matter)
2. Integration of viral DNA is part of the retrovirus liffecycle

Front 3

What are the KEY DIFFERENCES between PROMOTER vs. ENHANCER insertion?

Back 3

1. The viral LTR can be inserted into it's host's genome 2 specific ways.
2. PROMOTER INSERTION involves the viral LTR region being inserted between the 1st and 2nd exon with the same orientation having its effect downstream. (ex. LTR promotion of c-myc gene in bursal cell lymphoma.
3. ENHANCER INSERTION involves insertion of the viral LTR downstream of the natural promoter of the gene, however because of the nature of the LTR region... it still increases expression of the gene in question by ENHANCER effects. (usually inserted after the 3rd exon of c-myc)

**these mechanisms involve integration of the virus into it's host's genome, but other mechanisms involve transduction of cellular genes into the viral genome and it's progeny**

Front 4

What types of mutations are involved in mutant oncogenes in human cancer?

Name some key examples:

Back 4

1. SOMATIC MUTATIONS!!
2. RAS, BCR-ABL, MYC

Front 5

Discuss the mutation that causes CML:

Back 5

1. A chromosomal translocation causes the proto-oncogenes BCR and ABL to be placed next to each other. ABL is usually only transiently on (as a tyrosine kinase), but when BCR (which is a strong PROMOTER) is place upstream the ABL exon is mis-spliced into mRNA causing a "hybrid protein" that is ON ALL THE TIME.

**PHILADELPHIA CHROMOSOME**

Front 6

Discuss the mutation that causes Burkitt's Lymphoma:

Back 6

1. C-myc is translocated next to the IgHeavy chain locus (that has an IN TACT ENHANCER REGION). The normal c-myc gene is still in tact, however the IgHeavy chain locus is disrupted with only its enhancer left causing over-expression of c-myc, causing Burkitt's Lymphoma

**c-myc's promoter is still in tact as well**

Front 7

Discuss one of the main mutations involving bladder cancer:

Back 7

1. Caused by somatic mutations in RAS

Front 8

Name the 2 relevant tumor suppressor genes:

Back 8

1. RB
2. p53

***these are mutations you can inherit that affect your predisposition to cancer***

Front 9

What THEORY is relevant to a mutation in the RB gene?

Back 9

1. KNUDSON'S TWO HIT PRINCIPLE

**the RB gene can be DELETED or MUTATED**

Front 10

Name the different types of mutations that could happen to the RB or other inherited genes:

Back 10

1. Nondisjunction (loss)
2. Nondisjunction and reduplication
3. Mitotic recombination
4. Gene conversion
5. Deletion
6. Point mutation

Front 11

What is Li Fraumeni Syndrome?

Back 11

1. Caused by a mutation in the p53 gene where you inherit propensity to get all kinds of tumors (unlike RB where you only inherit likelihood of getting Retinoblastoma)

Front 12

What type of mutations are common in p53 genes? What happens related to the function of the gene?

Back 12

1. POINT MUTATIONS!!
2. Loss of its tumor suppressing capacity
3. Gain of growth promoting function (not well understood)

Front 13

What are the normal functions of p53?

Back 13

1. p53 is a sequence specific transcription factor
2. induces apoptosis in response to DNA damage
3. inhibits the cell cycle in response to DNA damage (increases translation of p21 which directly binds cdks)

Front 14

What gene encodes a protein that regulates APOPTOSIS?

How does it work?

Back 14

1. bcl-2
2. DOES NOT regulate proliferation
3. simply BLOCKS NORMAL APOPTOSIS of lymphocytes (without this function, they accumulate in the blood)

**a balance of pro-survival and pro-apoptotic genes determine the ultimate outcome**

Front 15

Discuss the difference between Angiogenesis and Vasculogenesis:

Back 15

1. Angiogenesis involves the sprouting of CAPILLARIES from pre-existing arteries
2. Vasculogenesis involves LARGE VESSEL development in situ

Front 16

Name 2 angiogenesis activators:

Back 16

1. VEGF
2. bFGF

Front 17

At what sites in the pathway of angiogenesis can drugs be effective?

Back 17

1. Cytokine activation (interferon alpha)
2. Endothelial cell activation at receptor (Anti-VEGF)
3. Inhibit the growth of endothelial cells
4. Inhibition of matrix metalloproteinases (MMPS) - Marmistat
5. Less understood mechanisms - Thalidomide

Front 18

Explain the role of HER2 in Breast Cancer:

Back 18

1. HER2 is a TK which is usually active in the dimerized form with the presence of a ligand. If HER2 is overexpressed, the TK no longer needs a ligand to dimerize and autophosphorylates much more easily causing an ON signal.

Front 19

Discuss how the RAS Gene works:

Back 19

1. RAS is a molecular switch (RAS-GTP = ON, RAS GDP = off)
**concentration of GTP is much higher in cell**
2. GAP increases RAS GTAase activity (making it GDP - turning RAS off)
3. Mutations in RAS block interaction with GAP, thus allowing GTP to stay bound... ON SIGNAL and unrestrained growth of cell

**this is true in 20-30% of all human tumors**

Front 20

Discuss how the RB gene works:

Back 20

1. RB is active in the G1 phase of the Cell Cycle (dephosphorylated RB inhibits E2F)
2. E2F is a transcription factor that works when RB is phosphorylated (off)
3. RB is phosphorylated by CDK4/Cyclin D in G1 (regulated by p16)

**RB-P-P cannot bind E2F, therefore uncontrolled growth, RB-dephosphorylated binds E2F therefore little growth**

Front 21

We must know where the lesion is in the pathway for effective treatment... Discuss some examples of this.

Back 21

1. Loss of RB gene - Retinoblastoma
2. Increased CDK4/Cyclin D - many tumors
3. loss of p16 - Melanoma

**unregulated E2F is final outcome**

**OVER 90% OF HUMAN TUMORS HAVE A DISRUPTION IN RB/CDK4/P16 PATHWAY**

Front 22

Which part(s) of the Cell Cycle does p53 effect?

Back 22

1. ALL PARTS OF THE CELL CYCLE
- Binds CDK/cyclin complexes throughout the cell cycle (G1, S, G2) M?

Front 23

If APOPTOSIS dysregulation is the suspected etiology of a cancer, what would you expect to observe on the molecular level?

Back 23

1. Chromatin condensation
2. Enlarged nucleolus
3. DNA degredation
4. Cell shrinkage
5. Membrane protuberances (blebs)
6. Appearance of phosphatidylserine on external surface of plasma membrane

Front 24

How does APOPTOSIS ultimately occur?

Back 24

1. by activation of proteases known as CASPASES or executioner proteins
2. Caspases are normally found in the cell as zymogens taht need to be cleaved to be activated - loss of fas ligand causes inability to cleave zymogenic form of caspase

**damage to cell, leakage of cyt-c, cyt-c binds protein, protein cleaves zymogen to activate caspases**

Front 25

Which gene has anti-apoptotic capacity?

Back 25

1. BCL-2 (which is overexpressed in 80% of follicular B-cell lymphomas
2. mechanism unclear, but inhibits caspases somewhere in apoptosis pathway

Front 26

What are the most common p53 mutations and what agents are likely to cause the mutation?

Back 26

1. G --> T = Aflotoxin B (HCC), Cigarette Smoke (SCCL)
2. CC --> TT = UV light (SCCS)

Front 27

What types of Cancer is EBV associated with?

What is its Mechanism?

Back 27

1. Burkitt's Lymphoma
2. Nasopharyngeal Cancer
3. B-lymphomas (in immunocompromised patients)
4. mechanism - chronic proliferation

**Don't dirrectly cause cancer… just force cells to divide more than they normally would (not malignant, but more than normal… induce constant proliferation in target tissues
- DNA is copied over and over again (more than normal) thus higher chance of mutation… could mutate Ras and result in cancer**

Front 28

What types of Cancer is HBV associated with?

Back 28

1. Hepatocellular Carcinoma (HCC)
2. mechanism - chronic proliferation

**Don't dirrectly cause cancer… just force cells to divide more than they normally would (not malignant, but more than normal… induce constant proliferation in target tissues
- DNA is copied over and over again (more than normal) thus higher chance of mutation… could mutate Ras and result in cancer**

Front 29

What types of Cancer is HPV (excluding 16, 18) associated with?

Back 29

1. Skin carcinomas (in sun-exposed areas)

Front 30

What types of Cancer are HPV types 16, 18 associated with?

Back 30

1. Cervical, vulvar, penile, and perianal cancer
2. Mechanism - inactivates tumor supressor genes (p53)

**cervical tumors that are HPV positive DO NOT HAVE p53 mutations... the virus encodes a protein that inhibits it! Cervical tumors that are HPV negative DO HAVE p53 mutations.**

**HPV oncogenes E6 and E7 bind p53 and RB respectively**

Front 31

What types of cancer is HTLV-1 associated with?

Back 31

1. Adult T-cell
2. mechanism - chronic proliferation

**Don't dirrectly cause cancer… just force cells to divide more than they normally would (not malignant, but more than normal… induce constant proliferation in target tissues
- DNA is copied over and over again (more than normal) thus higher chance of mutation… could mutate Ras and result in cancer**


**HTLV-1 does not carry an oncogene or insert itself into our genome however**

Front 32

What type of cancer is HSV8 associated with?

H. pylori?

Back 32

1. Kaposi's Sarcoma
2. Gastric Cancer
3. mechanism - DIRECT STIMULATION of the cell - only one with this mechanism that's not a somatic mutation!

Front 33

Name the 10 steps in the pathogenesis of metastasis:

Back 33

1. Growth of tumor
2. Vascularization
3. Invasion
4. Transport (Interactions with Vascular Components)
5. Attachment to Endothelium
6. Retraction into Endothelium
7. Underlapping into Endothelium
8. Overlapping Epithelium
9. Invasion through Basement Membrane at distant Site
10. Establishment of Micrometastases

Front 34

Name 5 mutations that commonly lead to metastatic disease:

Back 34

1. Mutation/loss of FAP
2. DNA Methylation (leads to rapid transcription)
3. Mutation/loss of RAS
4. Loss of DCC
5. Loss of p53

Front 35

Mutations vs. Epigenetic changes that lead to cancer:

Back 35

1. Mutations involve most of what we have discussed in lecture other than the METHYLATION of DNA that leads to faster transcription. Less METHYLATION slows transcription. Alterations in METHYLATION are considered EPIGENETIC changes

Front 36

Copy Number Polymorphism (CNP or CNV)

Back 36

A copy number variant (CNV) is a segment of DNA in which copy-number differences have been found by comparison of two or more genomes. The segment may range from one kilobase to several megabases in size. Humans (being diploid) ordinarily have two copies of each autosomal region, one per chromosome. This may vary for particular genetic regions due to deletion or duplication.

CNP - polymorphism is where each chromosome can be different… variation in two chromosomes or ina a population. CNP vs SNP.

Front 37

Synteny

Back 37

"teny" means thread in Latin. Syntenic sequences are in the same order in humans and in other species such as "syntenic" genes shared by zebrafish and humans.

Front 38

Hypomorph

Back 38

"hypo" - less
"morph" - shape or form
Alcohol dehydrogenase in Asians is in a hypomorphic form due to its "underfunction" in the fact that they cannot metabolize alcohol as effeciently

Front 39

What does LOH refer to?

Back 39

1. Loss of Heterozygosity
2. Can occur by Chromosome loss, recombination, independent mutation, or epigenetic gene inactivation

Front 40

Microsatellite

Back 40

1. A short repeat that gets longer and shorter over and over again. Microsatellites were critical in mapping the human genome

Front 41

Forward vs. Reverse genetics

Back 41

1. Forward Genetics - asks what genes are involved with the phenotype of interest

analogy - If aliens wanted to find out what made cars stop.. throw cosmic rays that randomly deactivated parts of the cars... take the cars that no longer stop and analyze them to see what caused the problem (find the genes)

2. Reverse Genetics - Start with the gene, see what it does, make the gene defective and see what the lack of function is

analogy - Aliens see cars, take some and cut brake lines, see if it can stop

Front 42

What are MUTANT SCREENS and what "type" of genetics is it using?

Back 42

1. A mutant screen is a procedure or test to identify and select individuals who possess a phenotype of interest. A genetic screen for new genes is often referred to as forward genetics as opposed to reverse genetics, the term for identifying mutant alleles in genes that are already known. Mutant alleles that are not tagged for rapid cloning are mapped and cloned by positional cloning.
2. Forward (Classical) Genetics

Front 43

What are KNOCK-OUT SCREENS and what "type" of genetics is it using?

Back 43

1. Knock-out the gene of interest to observe they phenotype
2. Reverse genetics

Front 44

SKY

Back 44

1. Spectral Karyotyping
2. Color probes generated for each chromosome
3. Gain ability to detect translocation or insertion in chromosomes
4. Good for detecting large scale changes in cancer (Ph+ ?)

Front 45

Microarrays

Back 45

1. Genomic toos where sequence specific hybridization can anneal to a gene sequence of interest using color labeled RNA probes

Front 46

When testing for predisposition for breast cancer, what genes would you examine for mutations?

What comprehensive method could you use to detect a mutation?

What analysis would you use to test for foundation mutations of a given group of people (and what group is that?)

Back 46

1. BRCA1 and BCRA2
2. MultiSite 3 BRCA Analysis (Ashkenazi Jewish population)

Front 47

What "chemoprevention" agents are used in breast cancer prophylaxis?

Back 47

1. Tamoxifen
1. Avista/roloxaphine

**Risk lowered by 50%**

Front 48

What are some of the major benefits of genetic testing?

Back 48

1. Prevents unnecessary surgery
2. Encourages surgery when necessary (as found in the case where cancer was discovered during prophylactic surgery)

Front 49

What are some of the negative aspects of genetic testing?

Back 49

1. could open "pandora's box" (switched at birth example)
2. EXPENSIVE

Front 50

Mutations of p53 are associated with what syndrome?

Back 50

1. Li-Fraumeni Syndrome

**increases susceptibility to all types of cancer**

Front 51

Mutations in p10 are associated with what syndrome?

Back 51

1. Cowden Syndrome

**pathogenic mucocutaneus lesions, 1:200,000)

Front 52

A mutation in STK11 leads to what syndrome?

What cancers are those affected at increased risk for?

Back 52

1. Peutz-Jeghers Syndrome
2. Colon, breast, pancreas, stomach, ovaries, and others

Front 53

Those people that mutations in HNPCC and FAP are at high risk for what type of cancer?

Back 53

1. CRC (colorectal cancer) - HNPCC or Lynch Syndrome


**only 5-10% is hereditary, lesions occur in proximal colon in HNPCC**

Front 54

If you're diagnosed with CRC under 50, what should you do?

Back 54

1. Genetic Testing

Front 55

Lynch Syndrome
(defect in what cellular mechanism, diagnosis)

Back 55

1. Defect in DNA mismatch repair (MMR) leading to MICROSATELLITE instability
2. Diagnosed by extra lines on electrophoresis gel (MSI assay)

Front 56

What are "variants" in genetic testing?

Back 56

1. positive, but un-understood results that may be determined in the future

Front 57

What is FAP? What mutation?

Back 57

1. Familial Adonematous Polyposis
2. APC mutation (tumor suprressor)
3. 100% Penetrance

**Gardner's Syndrome is a variant of FAP**

Front 58

Attenuated FAP
(general characteristics)

Back 58

1. later onset
2. few colonic adenomas

**same, but milder form of mutation**

Front 59

What is the ONLY AUTOSOMAL RECESSIVE gene mutation in COLON cancer genetics?

Back 59

1. MYH!!
2. Present in 30% of patients with moderate number of adenomas
3. Recessive disorder, so it requires 2 mutations (like RB)

Front 60

Hereditary Diffuse Gastric Cancer (HDGC)
(mutation)

Back 60

1. due to mutations in e-Cadherin gene (cell adhesion molecule)