Pharmacogenomics Flashcards
1
Q
What are introns?
A
- Regulatory piece of DNA/RNA
- Transcription factors bind here
- non coding
2
Q
What are exons?
A
- coding region
- Map for proteins
3
Q
What is splicing?
A
where introns are removed and exons put together
4
Q
What is alternative splicing?
A
initial RNA can be modified to make slightly different proteins (different mRNA, depending on how splicing occured)
5
Q
Order of events for protein transcription?
A
Gene (DNA)–> Transcription –> primary transcript (RNA)–> splicing–> mature transcript (mRNA)–> translation–> protein
6
Q
What 4 bases make up DNA?
A
- Adenine- Thymine
- Guanine- Cytosine
7
Q
What is the sugar backbone of DNA?
A
Deoxyribose sugar phosphate backbone
8
Q
What nucleotide bases make up RNA?
A
- Adenin- uracil
- Guanine- cytosine
9
Q
What backbone does RNA consist of?
A
Ribose sugar
10
Q
What makes an amino acid?
A
3 nucleotides= 1 codon–> 1 amino acid
11
Q
What does an amino acid sequence start with? End with?
A
Start= methionine
end- stop codon
12
Q
What is a SNP?
A
- Single nucleotide polymorphism is a DNA sequence variation that occurs when a single nucleotide in the genome is altered
- Frequency: mutation found in at least 1 % of the population
- accounts for 90% of human genetic variation
- can occur in coding or non-coding regions
- generally not a huge deal UNLESS the SNP inserts an extra nucleotide or removes nucleotid.
- if it does this, it causes a frameshift and can be a huge deal
13
Q
What is G6PD?
A
- part of pentose phosphate pathway
- provides reducing energy (NADPH) to cells to protect them from ROS
- makes glutathione (rely on it for detoxifying acetaminophen)
14
Q
What is G6PD deficiency?
A
- Subject to oxidative stress, causing hemolysis, RBC breakdown–> hemolytic anemia
- RBC borken down faster than body can produce them
- generally goes unnoticed until oxidative stress
- Men more likely to suffer from G6PD def. because it resides on the X chromosome
- X-linked ressessive pattern
15
Q
What is the survival advantage to G6PD deficiency?
A
Provides protection against malaria
Heavily found genetically from countries where malaria is a higher risk
16
Q
What does a BChE deficiency cause?
A
- prolonged apnea after succinylcholine administration
- BChE= butycholinesterase aka pseudocholinesterase aka plasma cholinesterase
17
Q
What are some drugs metabolized by plasma cholinesterase?
A
- succinylcholine
- mivacurium
- chloroprocaine
- tetracaine
- procaine
18
Q
What type of variant is BChe deficiency?
A
- autosomal recessive
- not an all-or-nothing variant. varying degree of butylcholinesterase activity
19
Q
What is porphyria?
A
- one of several mutation in the biosynthetic pathway of heme
- clinical symptoms result from buildup of pre-cursors
- precursors can be very dangerous and can be fatal in buildup
- exacerbation can be spontaneous or result from exposure to drugs, hormones and other compounds
20
Q
What is the main porphryia type we encounter? Symptoms?
A
- Acute Intermittent Porphyria
- Symptoms:
- pain in abdomen, back
- nausea
- tachycardia without fever
- seizures
- urine normal to dark amber
21
Q
What is NAT2? What happens when deficient in NAT2 or increased NAT2?
A
- Found that with isoniazid (1st effective drug for TB) that the concentration of isoniazid in urine depended on individual’s ability to convert isoniazid to acetylisoniazid (by NAT2= n- ACETYLTRANSFERASE)
- Slow acetylators- (Low NAT2) prone to isoniazid toxicity (peripheral neuropathy)
- fast acetylators- (High NAT2) more prone to hepatotoxicity
- acetyltransferase also important in metabolism of hydralazine, procainamide, dapson and sulfonamides
- deficiency can lead to lupus type syndrome
22
Q
What is heredity of NAT2 deficiency mutation?
A
single recessive gene
- 2 most common alleles (NAT2*5 AND 2*6)
- acocund for 90% of slow acetylators
- 27 known variables, so variation is hard to determine
- most variant alleles involve 2-3 point mutations
23
Q
What is phase I drug metabolism?
A
- Functionalization reaction
- 80% of drugs metabolized this way
- exposes a functional group
- small increase in polarity
- ex- oxidation, reduction, hydrolysis
24
Q
What is phase II drug metabolism?
A
- Conjugation reaction- more invovled
- large polar compound attached to functional group (covalent bond)
- large icnrease in polarity
- ex- acetylation, glucoronidation
25
What are some main enzymes involved in phase I metabolism?
* CYP 3A,4,5,7
* CYP2D6
26
What are some pharmacogenmoic implications with wafarin?
* Wafarin is a racemic mixture
* R-warfarin- metabolized by CYP3A4, 1A2, 1A1
* S-warfarin- metabolized by CYP 2C9
* 5 x more potent than R warfarin
* Warfarin inhibits vitamin K epoxide reductase
* reduced vitamin K is a cofactor for GGCX, which catalyzes the formation of functional clotting factors
* decreased clotting factors--\> decreased coags
27
What are some main enzymes involved in phase II metabolism?
UGT
NAT1/2
(also COMT is phase II, side note)
28
What were some goals of the human genome project?
* Coordinated by US dept of energy and NIH
* Goals
* id all gnees
* determine sequences of base paird that make up human DNA
* store this info
* improve data analysis toolds
* transfer technologies to private sector
* address ethical, legal and social issues that may arise form project
29
What are factors contributing to warfarin metabolism?
unknown\> VKORC1\> sex/BMI/age/diet/drugs \>cyp2C9
* *the contribution of warfarin metabolism by CYP2C9 is rather small, esimated to be approximately 10% warfarin dose variations*
* *contribution of VKORC1 is 25%*
* *clinical factors such as age, sex, diet, drgus, BMI contribute 20%*
* *thus, the identified factors that contribute to variable warfarin responses account for approx. 50%, the other, as yet unidentified factors reach almost 50%*
30
What is GINA?
* Genetic information nondiscrimination act (2008)
* protects americans from discrimination based on genetic information in health insurance and employment
31
What is the role of CYP2C9 SNP in drug metabolism?
* This enzyme metabolizes S- warfarin ( 5 x more potent than R)
* Wild-type variant \*1- metabolizes warfarin normally
* Two polymorphic variants \*2 and \*3
* \*2 reduces warfarin metabolism by 30%
* \*3 reduces warfarin metabolism by 90%
*
32
What is VKORC1?
* Vitamin K expoxide reductase
* reduces vit K in order to make coagulation factors
* common polymorphism is G1639A
* This variant has lower level of VKOR enzyme
* more sensitive to Coumadin
* If you have more robust VKORC1- you would need more drug to have an effect
33
What is clopidogrel MOA?
* Binds to ADP receptors on plt and prevent aggregation and thrombosis
* However, clopidogrel is a prodrug and it is the active metabolite that actually binds to the P2RY12 receptor
* Prodrug mdae active by CYP2C19
* this enzyme has many different variants
* 2,3,4,5 have NO activity and drug is ineffective
* 17 has increased actiivty and exaggerated response
34
What are some CYP2C19 variants and what is a drug is impacts?
* CYP2C19 impacts clopidogrel metabolism
* \*2 and \*17 are most common
* \*2- this variant causes CYP2C19 activity to be decreased- clopidogrel to not work because it can't be transformed into its active form
* *why clopidogrel has black box warning for recommendaiton of genetic testing*
* \*17 causes CYP2C19 activity to be increased
35
What enzyme is involved in codeine metabolism? Implications?
CYP2D6
* Low affinity for opioid receptors. considered a prodrug
* 10% of codeine is converted to morphine, partially by CYP 2D6
* Poor metabolizers- can't convert codeine--\> morphine and do not feel pain relief (placebo, no CYP2D6)
* Ultra rapid metabolizers: metabolize codeine too efficiently, which can cuase morphine intoxication (robust cyp2d6)
* *Usually noted ethnic difference, with ethiopian being the highest percentage of ultrarapid metabolizers*
36
What enzyme is tamoxifen metabolizes by?
CYP2D6
* Prodrug, metabolized by CYP2D6
* CYP2D6 is rate limiting enzyme in caralysis of tamoxifen to metabolites with greater affinicty for estrogen receptor
* if have low activity of CYP2D6, likely giving placebo
* do enzyme acitivty test before admin
37
What can vemurafenib be used for? What is the mutation involved?
* Melanoma drug for BRAF V600E mutations only
* B-raf mutated in 80% melanomas (commonly BRAF V6003, \>60% of melanomas--\> constitutive activaiton of Braf
* braf important in signaling bathway
* drug stops clelular proliferation
* shows lots of drug resistance
38
What are some reasons pharmacogenomics hasn't really taken off as much as expected?
* gap in translation between research and putting results into clinical practice
* associations between genotype and phenotype not always reproducible
* hard to get companies to invest
* many mutations are rare and the tests would only benefit some people
* takes time
