Lecture 1: Pharmacogenomics CB

Question 1

DNA

Answer 1

4 nucleotide bases 
◦ Adenine - Thymine 
◦ Guanine - Cytosine
Deoxyribose sugar phosphate backbone
Double-stranded

Question 2

RNA

Answer 2

4 nucleotide bases 
◦ Adenine - Uracil 
◦ Guanine - Cytosine
Ribose sugar phosphate backbone
Single-stranded

Question 3

Protein

Answer 3

3 nucleotides = 1 codon → 1 amino acid

Sequences start with methionine (AUG) and end with stop codon

Question 4

SNP (Single nucleotide polymorphism)

Answer 4

Single nucleotide polymorphism is a DNA sequence variation that occurs when a single nucleotide
(A/C/T/G) in the genome is altered:
o Frequency: must occur in at least 1% of the population
o Accounts for 90% of human genetic variation
o Can occur in coding or non-coding regions

Question 5

Not the same as disease-causing mutations, the majority of SNPs are in the coding or non-coding region?

Answer 5

non-coding

Question 6

What would happen if a SNP is in a coding region vs noncoding region?

Answer 6

?

Question 7

Do all SNPs lead to changes in amino acids?

Answer 7

Not all SNPs in the coding region will cause change in amino acid

Question 8

G6PD (glucose-6-phosphate dehydrogenase)

Answer 8

Part of pentose phosphate pathway

- Provides reducing energy (NADPH) to cells to protect them from ROS

Question 9

G6PD deficiency

Answer 9

-> hemolysis, RBC breakdown

Hemolytic anemia

• RBC broken down faster than body can produce them
• Usually goes unnoticed until…

Question 10

G6PD deficiency (External factors):
Example 1: During WW2, more \_\_\_\_\_\_\_\_\_\_\_\_\_\_ soldiers than Caucasian developed acute hemolytic crises when given antimalarial drugs.

Answer 10

African-American

Question 11

G6PD deficiency (External factors):
Example 2: Favism – hemolysis after eating fava beans. More common in people of \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ descent.

Answer 11

Middle Eastern

Question 12

G6PD deficiency - Locus:

Answer 12

X chromosomes

Question 13

G6PD deficiency - Heredity:

X or Y-linked recessive pattern?

Are males or females more likely to have G6PD deficiency? Why?

Answer 13

X-linked recessive pattern

Males are more likely to have it, but depends on your mother’s gene. Males only have 1 X, where females have 2 Xs and would require both to represent the predisposition.

Question 14

BChE =

Answer 14

Plasma cholinesterase (also known as butyrylcholinesterase (BChE) or pseudocholinesterase)

Question 15

BChE Deficiency

Answer 15

Butyrylcholinesterase is structurally and functionally related to ACh-ase, the enzyme that catalyzes the
hydrolysis of ACh.

Question 16

BChE breaks down……

Answer 16

succinylcholine (muscle relaxant)
o BChE deficiency will caused prolonged apnea
Mivacurium (muscle relaxant)
Cocaine (local anesthetic)
Procaine (local anesthetic)
Chloroprocaine (local anesthetic)
Tetracaine (local anesthetic)

Question 17

BChE Deficiency - Locus:

Answer 17

Chromosome 3

Question 18

BChE Deficiency - Heredity: ___________ recessive
- Highest prevalence in _________? What percentage?
- Partial deficiency = ____ min of apnea
o _/____ have 1+ hour of apnea

Answer 18

Autosomal recessive
- Highest prevalence in Caucasians (~4%)
o Have partial deficiency= 5-60 min of apnea
o 1/3000 have 1+ hour of apnea

Question 19

Acute Intermittent Porphyria

REVIEW CHART Slide 19

Answer 19

o Autosomal dominant
o One of several mutations in the biosynthetic pathway of heme (slide 18).
o Clinical symptoms result from buildup of pre-cursors (porphyrins)
o Exacerbation can be spontaneous or result from exposure to drugs,
hormones, other compounds
o Exacerbations more common in women (hormonal enzyme induction)
o Drugs that induce CYP system often also induce ALA synthase and can cause exacerbation (barbiturates, estrogens, many anesthetic/sedative drugs)

Question 20

Drug Acetylation or NAT2 deficiency N-acetyltransferase (NAT2)

Isoniazid (1st effective drug for ___________)
◦ Observation: Concentration of unchanged isoniazid in urine depends on individual’s ability to convert isoniazid to ____________

Answer 20

tuberculosis

acetylisoniazid

Question 21

Drug Acetylation or NAT2 deficiency N-acetyltransferase (NAT2)

Fast or Slow acetylators: more prone to suffer from isoniazid toxicity (peripheral neuropathy)?

Answer 21

Slow acetylators: more prone to suffer from isoniazid toxicity (peripheral neuropathy)

Question 22

Drug Acetylation or NAT2 deficiency N-acetyltransferase (NAT2)

Fast or slow acetylators: more prone to suffer from hepatotoxicity?

Answer 22

Fast acetylators: more prone to suffer from hepatotoxicity

Question 23

Drug Acetylation or NAT2 deficiency N-acetyltransferase (NAT2)

Acetyltransferase is also important in metabolism of?

Answer 23

hydralazine, procainamide, dapsone and sulfonamides: deficiency can result in a lupus type syndrome (autoimmune disease skin, joints, kidneys, etc.)

Question 24

NAT2 deficiency

Locus:

Answer 24

Chromosome 8 Single recessive gene

Question 25

NAT2 deficiency
Heredity: How many 27 reported NAT2 alleles?
◦ 2 common alleles (NAT2 #?, NAT2 #?) account for 90+% of fast or slow-acetylators?
◦ NAT2 has no ______ (just protein-coding regions)
◦ Most variant alleles involve how many point mutations?

Answer 25

27 reported NAT2 alleles
5 & 6
slow
introns
2-3 point mutations

Question 26

NAT2 deficiency
Incidence of NAT2 variations = ? 
◦ 40-70% of ? 
◦ 10-20% of ? 
◦ 80+% of ?

Answer 26

5-95%
Caucasians and African-Americans
Japanese and Canadian Eskimo
Egyptians

Question 27

Drug Metabolism (see slide 25)
Phase I: \_\_\_\_\_\_\_\_\_\_\_\_\_\_ reaction 
◦ ~?% of drug metabolized this way! 
◦ Exposes a ? 
◦ Small increase in ?
◦ Ex = ?

Answer 27

Phase I: Functionalization reaction 
◦ ~80% of drug metabolized this way! 
◦ Exposes a functional group 
◦ Small increase in polarity 
◦ Ex. oxidation, reduction, hydrolysis

Question 28

Drug Metabolism (see slide 25)
Phase II: \_\_\_\_\_\_\_\_\_\_\_\_\_ reaction 
◦ \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ attached to functional group 
◦ Large increase in ? 
◦ Ex = ?

Answer 28

Phase II: Conjugation reaction
◦ Large polar compound attached to functional group (covalent bond)
◦ Large increase in polarity
◦ Ex: acetylation, glucuronidation

Question 29

Enzyme most commonly used for phase 1 of metabolism is ?

Answer 29

CYP3A4/5/7

Question 30

Human Genome Project:
Coordinated by ?
Goals = ?

Answer 30

Coordinated by U.S. Dept of Energy and NIH, 1993-2003

Goals
▫ Identify all the genes
▫ Determine sequences of base pairs that make up human DNA
▫ Store this information
▫ Improve data analysis tools
▫ Transfer related technologies to private sector
▫ Address ethical, legal, and social issues (ELSI) that may arise from the project

Question 31

Human Genome Project:
Findings include… 
◦ Genome contains ~_ billion bases 
◦ Average gene has \_\_\_\_ bases 
◦ Total # of protein coding genes = ? 
◦ >\_\_% of nucleotide bases are the same in all people

Answer 31

◦ Genome contains ~3 billion bases
◦ Average gene has 3,000 bases
◦ Total # of protein coding genes: ~22,300
◦ >99% of nucleotide bases are the same in all people

Question 32

GINA stands for ?

Projects Americans from ?

Answer 32

Genetic information nondiscrimination act (2008)

Projects Americans from discrimination based on genetic information in health insurance and employment

Question 33

Warfarin:
Class?
Anticoagulant Used to prevent and treat _________ in patients with ?

Answer 33

Anticoagulant

Used to prevent and treat blood clots in patients with
▫ Pulmonary embolism
▫ Atrial fibrillation
▫ Artificial heart valves
▫ Post-orthopedic surgery (ex: knee/hip replacement)

Question 34

Warfarin:
Inhibits ?
o \_\_\_\_\_\_\_\_\_\_\_ is a cofactor for GGCX which catalyzes the formation of functional clotting
factors
o Decreased clotting factors = ?

Answer 34

vitamin K epoxide reductase
o Reduced vitamin K is a cofactor for GGCX which catalyzes the formation of functional clotting
factors
o Decreased clotting factors -> decreased coagulation

Question 35

Warfarin mixture (slide 31 diagram): 
R-warfarin metabolized by ?

Answer 35

CYP3A4, 1A2, 1A1

Question 36

Warfarin mixture (slide 31 diagram): 
S-warfarin metabolized by ?

Answer 36

CYP2C9

Question 37

Warfarin mixture (slide 31 diagram): 
_-warfarin is _X more potent than _-warfarin

Answer 37

S- is 5X more potent than R-warfarin

Question 38

How Warfarin Affects blood clotting:
o Vitamin K can’t form ?
o So, there’s a balance between ?
o Factors that affect the balance ?

Answer 38

o Vitamin K can’t form clotting complex
o So, there’s a balance between preventing clots and preventing coagulation/warfarin toxicity
o Factors that affect the balance: age, BMI, and genetics

Question 39

Contributions to variable warfarin metabolism:
CYP2C9 = _%
VKORC1 = _%
Sex, BMI, Age, Diet, Drugs = _%
Unknown = _%

Answer 39

CYP2C9 = 10%
VKORC1 = 25%
Sex, BMI, Age, Diet, Drugs = 20%
Unknown = 45%

Question 40

WARFARIN METABOLIZED BY ________ SNPs

o Wild type variant *1:

Answer 40

CYP2C9

Metabolizes warfarin normally

Question 41

CYP2C9 SNPs (slide 33 diagram):
Two polymorphic variants:
▫ _ reduced warfarin metabolism by X%
▫ _ reduced warfarin metabolism by X%

Answer 41

2, 30

3, 90

Question 42

Target enzyme for warfarin ?
◦ Many common polymorphisms
▫ Ex = ?
◦ Individuals with ? variant have lower levels of the ? enzyme

Answer 42

VKORC1 (slide 34 diagram)
◦ Many common polymorphisms
▫ Ex: G1639A
◦ Individuals with G1639A (G/A and A/A) variant have lower levels of the VKOR enzyme

Question 43

Clopidogrel: 
o Class = ? 
o Prevents ?
o Given to patients with ?
o Is a \_\_\_\_\_\_\_\_\_\_: absorbed in the liver, but not active until the liver

Answer 43

o Antiplatelet
o Prevents formation of harmful blood clots
o Given to patients with recent MI, stroke etc.
o Is a PRODRUG: absorbed in the liver, but not active until the liver

Question 44

Clopidogrel:
MOA = ?
Absorbed in _______, activated in the ______.
Active metabolite binds to the _______ receptor, irreversibly blocks ___ binding and receptor
activation, inhibiting blood clotting

Answer 44

MOA: binds to ADP receptors on platelets, prevents aggregation/thrombosis
Absorbed in intestine, activated in the liver.
Active metabolite binds to the P2RY12 receptor, irreversibly blocks ADP binding and receptor
activation, inhibiting blood clotting

Question 45

Clopidogrel:
Metabolized by ?
o Most prevalent variant =? (but causes no alteration)
o *, *, *_ – not very prevalent across the races, but also no alterations
o *_ – 40% of ? & INCREASED activity

Answer 45

Metabolized by CYP2C19 – variants lead to altered metabolism
o 2** – most prevalent variant – but causes no alteration
o *3, *4, *5 – not very prevalent across the races, but also no alterations
o 17** – 40% of Caucasians, Blacks, Asians – INCREASED activity

Question 46

Clopidogrel:

Black-box warning added to label (slide 38)

Answer 46

About the patients CYP2C19 genotype

o Testing exists focusing on *2 variant

Question 47

Clopidogrel:

Genetic testing exists for CYP2C19 variants, mostly focusing on *_ variant ← why do you think this may be?

Alternative = ?
◦ Ex = ?

Answer 47

2, higher prevalence

Alternative: Other drugs that do the same thing but don’t require CYP2C19 activity ◦ Ex: Prasugrel (Effient)

Question 48

Codeine: Opiate for ?

Answer 48

pain, cough suppression, and diarrhea

Question 49

Codeine: Low affinity for ____________, considered a _________.

Answer 49

Low affinity for opioid receptors, considered a PRODRUG

Question 50

Codeine: Metabolized and ACTIVATED INTO _________ by __________.

Answer 50

Metabolized and ACTIVATED INTO MORPHINE by CYP2D6

◦ ~10% is converted to morphine, partially by CYP2D6

Question 51

Codeine (see slide 41 chart):
o Poor metabolizers …………
o Ultra-rapid metabolizers …………..

Answer 51

o Poor metabolizers can’t convert codeine into morphine so have no pain relief
o Ultra-rapid metabolizers convert codeine to morphine too quickly and cause intoxication (ex: severe respiratory depression)

Question 52

Tamoxifen:

_______________ antagonist, used to treat ?

_________, metabolized by _______, the rate-limiting enzyme in the catalysis of tamoxifen to metabolites with greater affinity for the ________ receptor.

Answer 52

Estrogen receptor (ER) antagonist, used to treat ER+ breast cancer.

PRODRUG, metabolized by CYP2D6, the rate-limiting enzyme in the catalysis of tamoxifen to metabolites with greater affinity for the estrogen receptor.

*same concept at Codeine…..?

Question 53

Vemurafenib (see chart on slide 45 & 46):

__________ drug for ___________ mutations only!

Answer 53

Melanoma drug for BRAF V600E mutations only!
B-Raf mutated in ~80% of melanomas (commonly BRAF V600E, >60% of melanomas → constitutive activation of B-Raf). BRAF testing is offered :)

RESISTANCE!!!!

Question 54

Research Challenges (slides 47-53):

Answer 54

• False positives: disconnect between research and clinical practice
• Cost
• Mutations are rare, tests would benefit minority of people
• Pharmacoeconomic model: used to determining whether tests are worthwhile to implement
  o Compare cost of genetic test to cost of monitoring the patient for adverse drug reactions
• But it is still worth it
  o Increase efficacy, reduce toxicity [reduce ADRs],

Objective – what SNP is, how to identify one.

Question 55

Drug Enzyme & Target:

Warfarin

Answer 55

Warfarin -> CYP2C9 & VKORC1

Question 56

Drug Enzyme & Target:

Codeine

Answer 56

Codeine -> CYP2D6 & Prodrug (liver

Question 57

Drug Enzyme & Target:

Tamoxifen

Answer 57

Tamoxifen -> CYP2D6 & Prodrug (liver)

Question 58

PRODRUG = ?

Answer 58

a biologically inactive compound which can be metabolized in the body to produce a drug!