Lecture 1: Pharmacogenomics CB Flashcards
DNA
4 nucleotide bases ◦ Adenine - Thymine ◦ Guanine - Cytosine Deoxyribose sugar phosphate backbone Double-stranded
RNA
4 nucleotide bases ◦ Adenine - Uracil ◦ Guanine - Cytosine Ribose sugar phosphate backbone Single-stranded
Protein
3 nucleotides = 1 codon → 1 amino acid
Sequences start with methionine (AUG) and end with stop codon
SNP (Single nucleotide polymorphism)
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
Not the same as disease-causing mutations, the majority of SNPs are in the coding or non-coding region?
non-coding
What would happen if a SNP is in a coding region vs noncoding region?
?
Do all SNPs lead to changes in amino acids?
Not all SNPs in the coding region will cause change in amino acid
G6PD (glucose-6-phosphate dehydrogenase)
Part of pentose phosphate pathway
- Provides reducing energy (NADPH) to cells to protect them from ROS
G6PD deficiency
-> hemolysis, RBC breakdown
Hemolytic anemia
- RBC broken down faster than body can produce them
- Usually goes unnoticed until…
G6PD deficiency (External factors): Example 1: During WW2, more \_\_\_\_\_\_\_\_\_\_\_\_\_\_ soldiers than Caucasian developed acute hemolytic crises when given antimalarial drugs.
African-American
G6PD deficiency (External factors): Example 2: Favism – hemolysis after eating fava beans. More common in people of \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ descent.
Middle Eastern
G6PD deficiency - Locus:
X chromosomes
G6PD deficiency - Heredity:
X or Y-linked recessive pattern?
Are males or females more likely to have G6PD deficiency? Why?
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.
BChE =
Plasma cholinesterase (also known as butyrylcholinesterase (BChE) or pseudocholinesterase)
BChE Deficiency
Butyrylcholinesterase is structurally and functionally related to ACh-ase, the enzyme that catalyzes the
hydrolysis of ACh.
BChE breaks down……
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)
BChE Deficiency - Locus:
Chromosome 3
BChE Deficiency - Heredity: ___________ recessive
- Highest prevalence in _________? What percentage?
- Partial deficiency = ____ min of apnea
o _/____ have 1+ hour of apnea
Autosomal recessive
- Highest prevalence in Caucasians (~4%)
o Have partial deficiency= 5-60 min of apnea
o 1/3000 have 1+ hour of apnea
Acute Intermittent Porphyria
REVIEW CHART Slide 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)
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 ____________
tuberculosis
acetylisoniazid
Drug Acetylation or NAT2 deficiency N-acetyltransferase (NAT2)
Fast or Slow acetylators: more prone to suffer from isoniazid toxicity (peripheral neuropathy)?
Slow acetylators: more prone to suffer from isoniazid toxicity (peripheral neuropathy)
Drug Acetylation or NAT2 deficiency N-acetyltransferase (NAT2)
Fast or slow acetylators: more prone to suffer from hepatotoxicity?
Fast acetylators: more prone to suffer from hepatotoxicity
Drug Acetylation or NAT2 deficiency N-acetyltransferase (NAT2)
Acetyltransferase is also important in metabolism of?
hydralazine, procainamide, dapsone and sulfonamides: deficiency can result in a lupus type syndrome (autoimmune disease skin, joints, kidneys, etc.)
NAT2 deficiency
Locus:
Chromosome 8 Single recessive gene
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?
27 reported NAT2 alleles 5 & 6 slow introns 2-3 point mutations
NAT2 deficiency Incidence of NAT2 variations = ? ◦ 40-70% of ? ◦ 10-20% of ? ◦ 80+% of ?
5-95%
Caucasians and African-Americans
Japanese and Canadian Eskimo
Egyptians
Drug Metabolism (see slide 25) Phase I: \_\_\_\_\_\_\_\_\_\_\_\_\_\_ reaction ◦ ~?% of drug metabolized this way! ◦ Exposes a ? ◦ Small increase in ? ◦ Ex = ?
Phase I: Functionalization reaction ◦ ~80% of drug metabolized this way! ◦ Exposes a functional group ◦ Small increase in polarity ◦ Ex. oxidation, reduction, hydrolysis
Drug Metabolism (see slide 25) Phase II: \_\_\_\_\_\_\_\_\_\_\_\_\_ reaction ◦ \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ attached to functional group ◦ Large increase in ? ◦ Ex = ?
Phase II: Conjugation reaction
◦ Large polar compound attached to functional group (covalent bond)
◦ Large increase in polarity
◦ Ex: acetylation, glucuronidation
Enzyme most commonly used for phase 1 of metabolism is ?
CYP3A4/5/7
Human Genome Project:
Coordinated by ?
Goals = ?
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
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
◦ 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
GINA stands for ?
Projects Americans from ?
Genetic information nondiscrimination act (2008)
Projects Americans from discrimination based on genetic information in health insurance and employment
Warfarin:
Class?
Anticoagulant Used to prevent and treat _________ in patients with ?
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)
Warfarin: Inhibits ? o \_\_\_\_\_\_\_\_\_\_\_ is a cofactor for GGCX which catalyzes the formation of functional clotting factors o Decreased clotting factors = ?
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
Warfarin mixture (slide 31 diagram): R-warfarin metabolized by ?
CYP3A4, 1A2, 1A1
Warfarin mixture (slide 31 diagram): S-warfarin metabolized by ?
CYP2C9
Warfarin mixture (slide 31 diagram): _-warfarin is _X more potent than _-warfarin
S- is 5X more potent than R-warfarin
How Warfarin Affects blood clotting:
o Vitamin K can’t form ?
o So, there’s a balance between ?
o Factors that affect the balance ?
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
Contributions to variable warfarin metabolism: CYP2C9 = _% VKORC1 = _% Sex, BMI, Age, Diet, Drugs = _% Unknown = _%
CYP2C9 = 10%
VKORC1 = 25%
Sex, BMI, Age, Diet, Drugs = 20%
Unknown = 45%
WARFARIN METABOLIZED BY ________ SNPs
o Wild type variant *1:
CYP2C9
Metabolizes warfarin normally
CYP2C9 SNPs (slide 33 diagram):
Two polymorphic variants:
▫ _ reduced warfarin metabolism by X%
▫ _ reduced warfarin metabolism by X%
2, 30
3, 90
Target enzyme for warfarin ?
◦ Many common polymorphisms
▫ Ex = ?
◦ Individuals with ? variant have lower levels of the ? enzyme
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
Clopidogrel: o Class = ? o Prevents ? o Given to patients with ? o Is a \_\_\_\_\_\_\_\_\_\_: absorbed in the liver, but not active until the liver
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
Clopidogrel:
MOA = ?
Absorbed in _______, activated in the ______.
Active metabolite binds to the _______ receptor, irreversibly blocks ___ binding and receptor
activation, inhibiting blood clotting
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
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
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
Clopidogrel:
Black-box warning added to label (slide 38)
About the patients CYP2C19 genotype
o Testing exists focusing on *2 variant
Clopidogrel:
Genetic testing exists for CYP2C19 variants, mostly focusing on *_ variant ← why do you think this may be?
Alternative = ?
◦ Ex = ?
2, higher prevalence
Alternative: Other drugs that do the same thing but don’t require CYP2C19 activity ◦ Ex: Prasugrel (Effient)
Codeine: Opiate for ?
pain, cough suppression, and diarrhea
Codeine: Low affinity for ____________, considered a _________.
Low affinity for opioid receptors, considered a PRODRUG
Codeine: Metabolized and ACTIVATED INTO _________ by __________.
Metabolized and ACTIVATED INTO MORPHINE by CYP2D6
◦ ~10% is converted to morphine, partially by CYP2D6
Codeine (see slide 41 chart):
o Poor metabolizers …………
o Ultra-rapid metabolizers …………..
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)
Tamoxifen:
_______________ antagonist, used to treat ?
_________, metabolized by _______, the rate-limiting enzyme in the catalysis of tamoxifen to metabolites with greater affinity for the ________ receptor.
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…..?
Vemurafenib (see chart on slide 45 & 46):
__________ drug for ___________ mutations only!
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!!!!
Research Challenges (slides 47-53):
- 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.
Drug Enzyme & Target:
Warfarin
Warfarin -> CYP2C9 & VKORC1
Drug Enzyme & Target:
Codeine
Codeine -> CYP2D6 & Prodrug (liver
Drug Enzyme & Target:
Tamoxifen
Tamoxifen -> CYP2D6 & Prodrug (liver)
PRODRUG = ?
a biologically inactive compound which can be metabolized in the body to produce a drug!
