What are introns?
- Regulatory piece of DNA/RNA
- Transcription factors bind here
- non coding
What are exons?
- coding region
- Map for proteins
What is splicing?
where introns are removed and exons put together
What is alternative splicing?
initial RNA can be modified to make slightly different proteins (different mRNA, depending on how splicing occured)
Order of events for protein transcription?
Gene (DNA)–> Transcription –> primary transcript (RNA)–> splicing–> mature transcript (mRNA)–> translation–> protein
What 4 bases make up DNA?
- Adenine- Thymine
- Guanine- Cytosine
What is the sugar backbone of DNA?
Deoxyribose sugar phosphate backbone
What nucleotide bases make up RNA?
- Adenin- uracil
- Guanine- cytosine
What backbone does RNA consist of?
What makes an amino acid?
3 nucleotides= 1 codon–> 1 amino acid
What does an amino acid sequence start with? End with?
end- stop codon
What is a SNP?
- 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
What is G6PD?
- part of pentose phosphate pathway
- provides reducing energy (NADPH) to cells to protect them from ROS
- makes glutathione (rely on it for detoxifying acetaminophen)
What is G6PD deficiency?
- 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
What is the survival advantage to G6PD deficiency?
Provides protection against malaria
Heavily found genetically from countries where malaria is a higher risk
What does a BChE deficiency cause?
- prolonged apnea after succinylcholine administration
- BChE= butycholinesterase aka pseudocholinesterase aka plasma cholinesterase
What are some drugs metabolized by plasma cholinesterase?
What type of variant is BChe deficiency?
- autosomal recessive
- not an all-or-nothing variant. varying degree of butylcholinesterase activity
What is porphyria?
- 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
What is the main porphryia type we encounter? Symptoms?
- Acute Intermittent Porphyria
- pain in abdomen, back
- tachycardia without fever
- urine normal to dark amber
What is NAT2? What happens when deficient in NAT2 or increased NAT2?
- 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
What is heredity of NAT2 deficiency mutation?
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
What is phase I drug metabolism?
- Functionalization reaction
- 80% of drugs metabolized this way
- exposes a functional group
- small increase in polarity
- ex- oxidation, reduction, hydrolysis
What is phase II drug metabolism?
- Conjugation reaction- more invovled
- large polar compound attached to functional group (covalent bond)
- large icnrease in polarity
- ex- acetylation, glucoronidation
What are some main enzymes involved in phase I metabolism?
- CYP 3A,4,5,7
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
What are some main enzymes involved in phase II metabolism?
(also COMT is phase II, side note)
What were some goals of the human genome project?
- Coordinated by US dept of energy and NIH
- 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
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%
What is GINA?
- Genetic information nondiscrimination act (2008)
- protects americans from discrimination based on genetic information in health insurance and employment
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%
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
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
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
What enzyme is involved in codeine metabolism? Implications?
- 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
What enzyme is tamoxifen metabolizes by?
- 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
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
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