Pharmacogenetics PDF

Pharmacogenetics Maitham Bahman  Basics Humans inherit traits from their parents in the form of DNA −DNA: A double stranded molecule that is responsible for the storage and transfer of genetic information.  Nucleotides are the building blocks o...

Pharmacogenetics Maitham Bahman  Basics Humans inherit traits from their parents in the form of DNA −DNA: A double stranded molecule that is responsible for the storage and transfer of genetic information.  Nucleotides are the building blocks of DNA and RNA. Nitrogenous base: Purines (adenine and guanine) and pyrimidines (thymine, cytosine and uracil) 5 nucleobases in total; DNA and RNA only have 4 each. − DNA: thymine (T), guanine (G), adenine (A), and cytosine (C). Base pairs; A-T and G-C. − RNA: uracil (U), guanine (G), adenine (A), and cytosine (C). Base pairs; A-U and G-C  Each parent passes down DNA to their offspring in the form of chromosomes − A chromosome is a packed thread-like structure of DNA − One chromosome from the father and one chromosome from the mother pair up to form chromosome pairs. Humans have 46 chromosomes, or 23 pairs, in every cell.  Within chromosomes, there are regions that carry instructions which determine our features and characteristics, known as genes. −Sections of the DNA that encode for specific proteins. − Genes are responsible for our inherited traits (e.g. eye colour). −A person has two copies of every gene, one on each corresponding chromosome.  Genes of the same function come in different forms, known as alleles −Variations of a given gene (e.g. eye colour). A person may carry the gene for brown eyes and a gene for blue eyes; they are both genes but in relation to each other they are alleles.  RNA reads the gene codes within DNA to produce proteins that make up enzymes and receptors. Some alleles can result in the production of enzymes or receptors with altered function or affect the quantities in which they are produced. Variations from the ‘normal’ pattern in the general population (polymorphism) can lead to varied responses to pharmacotherapy in sub-populations.  Gene polymorphisms occur due to mutations − Substitution − Deletion − Insertion − Duplication Most common form of mutation is single nucleotide polymorphisms (SNPs), i.e. changes to a single base. SANE  Genotype: The underlying genetic make-up that is responsible for an organism’s traits. Phenotype: The physical expression of traits relating to the underlying genes and environmental factors. These are observable characteristics such as hair colour, eye colour, height etc.  Pharmacogenetics ① The study of how variations of individual genes can affect drug handling and - response (i.e. pharmacodynamics and pharmacokinetics). individual Pharmacogenetic studies are usually born out of an aberrant response to a drug, leading to a genetic investigation to understand the cause. In terms of application, pharmacogenetics is more applicable to individual patients rather than a general population. The goal is to understand genetic polymorphism to individualise therapy and limit variability. ITEM Ian  Pharmacogenomics to understandPD 0 The study of how all the genes in a genome relate to drug handling and response. more applicable to a population Why Pharmacogenomic studies are usually undertaken to understand drug pharmacodynamics and pharmacokinetics in the broader population. e in The application of pharmacogenomics is directed more towards the development of new drugs and to better our understanding of existing drugs.  History Known for a long time that uncooked fava beans are toxic to some people − Acute haemolytic anaemia − ‘favism’ I Mid-1920s; acute haemolytic anaemia observed in some people receiving antimalarial drugs. Mid to late 1950s; discovered that patients who had haemolytic anaemia from using the antimalarial drug primaquine had a deficiency in the enzyme glucose- F 6-phosphate dehydrogenase (G6PD). GGPDI hemolytic a anemia  G6PD deficiency is hereditary, mainly affects males, and is one of the most common enzyme deficiencies in humans. The G6PD gene is located in the X chromosome; a mutation in this gene leading to deficiency is inherited in an X-linked recessive manner. Bait's x linked Males (XY) are more susceptible than females (XX) − Males only need to inherit one mutated gene to be affected − Females need to inherit two mutated genes; much less likely to occur. Females with one mutation don’t usually have G6PD deficiency; one normal ‘dominant’ gene/allele is enough for healthy G6PD enzyme expression. Impact of Genetic Polymorphism  Cytochrome P450 Large family of enzymes Involved in ~70-80% of drug metabolism Common practice to italicize the expression when referring to a gene that encodes for an enzyme, e.g. CYP2D6 for the enzyme and CYP2D6 for the gene  O CYP2D6 Most well-studied drug metabolising enzyme. Over 100 alleles identified. Polymorphism of this enzyme leads to individuals being broadly categorized as: 6 2 4classes −Poor metabolisers −Intermediate metabolisers −Extensive metabolisers −Ultrarapid metabolisers  Involved in ~ 40% of first-pass metabolism and in the metabolism of 20-25% of all medications. In the 1970s, some participants in clinical studies involving debrisoquine (anti- hypertensive) and sparteine (anti-arrhythmic) experienced exaggerated side- effects. −Found to have higher plasma concentrations than expected. SET −Later attributed to polymorphisms in the CYP2D6 gene. −Inter-ethnic variations in CYP2D6 phenotypes are reported with up to 10% I of Caucasians being poor metabolisers. ethically linked  ifcodienewas Codeine converted into morphine for theactive form ifCyp2Donotellative Ttoxic analgesic effect. notfunctioning tefficacy ~5-15% of codeine converted into morphine. changes any these Poor metabolisers; low morphine in may concentration → reduced analgesic effect. wait Rapid metabolisers; high morphine concentration → dangerous side effects active (e.g. respiratory depression, cardiac arrest). someactivity  Codeine also metabolised into active (codeine-6-glucuronide) and inactive (norcodeine) metabolites. Morphine further metabolised : − Morphine-6-glucuronide (active); contributes to analgesic effect. − Normorphine; some analgesic effect. − Morphine-3-glucuronide (inactive). Due to the good correlation between metaboliser phenotype and codeine t dosage, CYP2D6 genotyping can help with individualised therapy. o  CYP2D6 Activity Score (AS) system; each allele given a score based on activity: - AS = 0; No function - AS = 0.5; Reduced function -AS = 1; Normal function s s os as Sum value of alleles in gives a score that indicates the phenotype: ff S AS score Genotype Phenotype 0 No functional alleles Poor metabolizers 0.5 One reduced function + one non-functional alleles Intermediate Two normal function alleles Two reduced function alleles 1.0-2.0 Extensive One normal function + one reduced function alleles the Norm One normal function + one no function alleles >2 More than two copies of normal function alleles Ultrarapid  C CYP2C9 Four enzymes make up the CYP2C subfamily of enzymes. CYP2C9 most abundant and most involved in drug metabolism. CYP2C9 regarded as one of the most important drug metabolising enzymes, right after CYP3A4 and CYP2D6. Accounts for ~15-20% of CYP450 metabolised drugs Responsible for the metabolism of many narrow therapeutic index drugs (e.g. phenytoin, S-warfarin, tolbutamide, losartan) and NSAIDs.  Polymorphism results in reduced enzymatic activity. Individuals classified as: rapid bio − Normal metabolisers (two normal gene copies) D I decreased function alleles) − Intermediate metabolisers (one normal + one i − Poor metabolisers (two reduced function alleles) classes Inter-ethnic variability. Carriers of the less active allelic variants of CYP2C9 may require dosing adjustments.  CYP2C9 polymorphisms play an important role in warfarin dosing −Main enzyme responsible for the metabolism of the more highly active S enantiomer. −CYP2C9 deficient patients receiving warfarin are more prone to bleeding events; lower activity of the enzymes →higher systemic concentrations. Patients with CYP2C9 deficiencies may have a higher incidence of gastrointestinal bleeding with certain NSAIDs, and an increased risk of hypoglycaemia associated with the use of sulfonylureas for diabetes Tolbutamide management.  CYP2C19 CYP2C19 polymorphism − Poor metabolisers (~2-15%) t − Intermediate metabolisers (~18-45%) − Extensive metabolisers (~35-50%) − Rapid metabolisers (2-30%) − Ultrarapid metabolisers (~2-5%)  Expression of CYP2C19 significantly varies between ethnic groups. delicacy if ICypzag Metabolism by CYP2C19 enzymes can either activate (e.g. clopidogrel) or inactivate (e.g. amitriptyline) a drug depending on the concerned drug. Itoxicicity  Clinical Relevance Phenotype Genotype(s) Prodrug Active Drug Poor Two non-functional alleles metaboliser ↓ Efficacy Potential toxicity One normal + one non-functional alleles Possibly Sub- ↓ Dose may be Intermediate One increased + one non-functional therapeutic levels needed metaboliser alleles a Extensive Two normal alleles Normal dosing Normal dosing metaboliser Rapid One normal + one increased activity Potential toxicity ↓ Efficacy metaboliser alleles ↓ Dose may be Possibly Sub- Ultrarapid Two increased function alleles needed therapeutic levels metaboliser  Individuals carrying one non-functional + one increased function, or one reduced function + one increased function alleles are rarely encountered, and their metaboliser phenotype is unknown. Using CYP2C19 as an example, the star-allele nomenclature is introduced here: − Allelic variants are given a *number and classed based on their activity. CYP2C19*1 is the normal ‘wild-type’ gene, while CYP2C19*2 and CYP2C19*3 are allelic variants that have been classified as non-functional. each number  represent y − Humans inherit one copy of each gene from each parent, and therefore have two copies of any given gene in each cell. − Genotype is written with two *numbers based on which alleles an individual expresses. CYP2C19*1/*1; two normal copies of CYP2C19 gene = extensive (normal) metaboliser. Two of the same allele (*1/*1) = homozygous genotype. CYP2C19*2/*3; two non-functional copies of CYP2C19 gene = poor metaboliser. Two different alleles (*2/*3) = heterozygous genotype.  CYP2C19 Allele Variant Functionality *1 (wild-type) Normal *2, *3, *4, *6, *7, *8 Non-functional *5, *9, *10 Decreased *17 Increased Wild type gene: The ‘normal’ allele that encodes for the most prevalent phenotype in a population.  Clopidogrel (antiplatelet); Clinical application depends on studies −Prodrug that requires activation to exert an effect, mainly mediated by CYP2C19. −Negligible effect in poor metabolisers; alternative so antiplatelet therapy (e.g. prasugrel, ticagrelor) recommended. −Intermediate metabolisers; increased dose or alternative therapy may be needed. B Ias −Extensive and ultrarapid metabolisers; no dosage changes recommended. WIstudies no need toincrease dosefor ultra clinical trying to build it it up to consider it  as guideline The Clinical Pharmacogenetics Implementation Consortium (CPIC) has guidelines covering 18 drugs including clopidogrel, tricyclic antidepressants (TCAs), proton pump inhibitors (PPIs), selective serotonin reuptake inhibitors (SSRIs), and voriconazole (antifungal). its not a must recommendations − Poor metabolisers; TCAs, SSRIs, PPIs, and voriconazole generally require dose reduction not a well established science − Intermediate metabolisers; no change initially − Ultrarapid metabolisers; may need an increase in dose or alternative drugs that are not dependent on CYP2C19 metabolism.  o CYP3A4 CYP3A subfamily; most abundant group of enzymes from CYP450 superfamily. − Found mainly in liver and intestines. CYP3A4 considered as most important drug metabolising enzyme; involved in metabolism of >50% of drugs. Foetal expression of CYP3A4, enzyme activity, and enzyme quantity are extremely low which appear to reach maturity levels at 1 years old.  Expression of CYP3A4 in females is two-fold higher than in males. Polymorphs widely reported; effect on enzymatic activity appears insignificant. doesn't mean it doesn't exist Variability in enzyme activity; likely due to intrinsic regulatory mechanisms. Alleles reported to reduce CYP3A4 activity; appear ethnically linked. Non-CYP450 Enzymes  UDP-Glucuronyltransferase (UGT) Involved in the metabolism of ~40-70% of drugs through a process known as glucuronidation. UGT nomenclature follows the same rules as the CYP labelling system. UGT1A and UGT2B are the most important subfamilies in relation to drug metabolism, found mainly in the liver.  Genetic polymorphism results in individuals being categorised into: − Fast glucuronidators − Intermediate glucuronidators − Slow glucuronidators High ethnic variability in phenotype expression.  Polymorphism linked with several diseases: −UGT1A1 polymorphism; reduced glucuronidation directly linked to unconjugated hyperbilirubinemia, a condition where there is a build-up of toxic unconjugated bilirubin from the breakdown of red blood cells. −Gilbert’s syndrome, a mild condition, and Crigler-Najjar syndrome, a severe condition, are both due to inherited UGT1A1 alleles with reduced glucuronidation, resulting in unconjugated hyperbilirubinemia.  notecan yay Irinotecan (anticancer): active procty Swat − Converted to the active metabolite SN-38 via hydroxylation by carboxylesterases. − SN-38 then metabolised by UGT1A1 mediated glucuronidation into inactive metabolites. notONEproof − Allelic variants resulting in decreased UGT1A1 functionality lead to toxic blood levels of SN-38, causing myelosuppression and severe diarrhoea. − A reduced dose is recommended in patients with less active UGT1A1 alleles.  Thiopurine Methyltransferase (TPMT) Responsible for the metabolism of thiopurines (mercaptopurine, thioguanine, azathioprine). Genetic polymorphisms in the population cause changes in enzyme activity where ~90% have high activity, ~10% have intermediate activity, and ~ 0.3% having low activity.  Thiopurines; Immunosuppressants; rheumatoid arthritis, irritable bowel syndrome, Crohn’s disease Anticancer; acute lymphoblastic leukaemia Prodrugs; activated by several enzymes and metabolised into inactive metabolites by TPMT.  Hematopoietic toxicity is an associated risk with thiopurine therapy; patients with a TPMT deficiency are at an even greater risk. TPMT deficiency; ↓ clearance of active metabolites; ↑ circulating concentration; ↑toxicity. CPIC guidelines suggest dosage adjustments for thiopurines in TPMT deficient individuals (CPIC Guideline for Thiopurines and TPMT and NUDT15).  N-Acetyltransferase (NAT) Acetylation is the main mechanism responsible for the metabolism of several drugs: −Isoniazid (antibiotic). −Procainamide (antiarrhythmic). −Hydralazine (antihypertensive). −Dapsone (antibiotic). −Sulfasalazine (DMARD).  Genetic polymorphisms result in individuals being: − Slow acetylators − Intermediate acetylators − Fast acetylators High inter-ethnic variability in NAT phenotypes.  NAT2 deficiencies have been linked with increased risk of several cancers. Slow acetylator phenotype is an autosomal recessive trait; two abnormal alleles inherited. Some reports have suggested that slow acetylators are at a significantly increased risk of idiopathic systemic lupus erythematosus (SLE), ~71% in slow acetylators vs ~52% in the general population. idiopathic  Slow acetylators at higher risk of developing drug induced SLE like syndrome, with hydralazine and procainamide being the main culprits. − Hydralazine induced lupus syndrome (HILS) is almost only observed in slow acetylators, where up to 10% of all patients develop HILS. − Linked to increased drug concentration due to poor metabolism, leading to toxicity. Slow  Isoniazid induced peripheral neuropathy and liver toxicity occur at higher rates in slow acetylators compared to intermediate and rapid metabolisers. − Previously believed that rapid acetylators have an increased risk of isoniazid induced hepatotoxicity. SLOW − Later studies showed that slow acetylators were at a higher risk. − Ethnic variability for isoniazid phenotype is high, but isoniazid induced hepatotoxicity rates do not differ significantly between populations. − Role of NAT2 polymorphisms in isoniazid induced hepatotoxicity remains unclear and underlying mechanisms have not been established. Watz acetylat  Amonafide (anticancer) −Was under investigation but has since been discontinued after failing phase 3 trials. −Fast acetylators more susceptible to myelosuppression. fast −↑ plasma concentrations and ↑ toxicity associated in fast acetylators was unexpectedly found. −Further investigation; faster metabolism of amonafide into n-acetyl amonafide metabolite by NAT2, which inhibits the oxidation of amonafide by CYP1A2. mutationof main −Recommendations: ↓ doses in fast acetylators; ↑ doses in slow acetylators.  Drug Transporters Transporters move drug: − into a cell (influx transporters). − out of a cell (efflux transporters). − bidirectionally (influx/efflux). ATP-binding Cassette (ABC) Transporters Efflux transporters. jelled G's Play a vital role in ADME. systemic The ABCB1 subfamily is the most extensively studied efflux transporter due to its wide expression in human tissues. P Bio an M − Also known as multidrug resistance protein 1 (MDR1) or P-glycoprotein. − Various polymorphs have been reported and their expression differs between different ethnicities. − Polymorphs have been shown to alter transporter function and drug pharmacokinetics.  ABCC2 −Also known as multidrug resistance protein 2 (MDR2). −Important transporter of anticancer drugs. −Polymorphisms in ABCC2 genes are uncommon although a few have been identified without an obvious effect on function or drug pharmacokinetics. −Some reports have shown that ABCC2 polymorphs can result in decreased risk of antiepileptic drug resistance, increased exposure to high dose methotrexate, and increased exposure to pravastatin in multi dose regimens.  ABCG2 Also known as breast cancer resistant protein (BCRP) Polymorphisms linked to pharmacokinetic alterations of several drugs; camptothecin analogues (anticancer), anthracyclines (anticancer), taxanes (anticancer), statins, DMARDs, anti-HIV drugs, and sulfonylureas (antidiabetic). BLIMPPicancerdrugs MDR GI BCRP Solute Carrier (SLC) transporters inllut Kellum Influx transporters. ballet Polymorphism has been demonstrated to alter their function. hydroguillic The organic cation transporter (OCT), organic anion transporter (OAT), and organic anion transporting polypeptides (OATPs) are all SLC transporters. MEI Biu aud  OATP polymorphisms were shown to affect the glucose-lowering capacity of O− Certain polymorphs increased exposure to repaglinide by ~70% and had an repaglinide (antidiabetic). enhanced glucose lowering effect. − Other polymorphs decreased exposure by ~30% and had a less pronounced effect on blood glucose when compared to the wild-type gene. Some OATP polymorphs result in increased statin exposure; pravastatin, pitavastatin, atorvastatin, rosuvastatin and active simvastatin acid. The clinical significance of drug transporter polymorphisms has not been well-established, however, future studies may yet demonstrate valuable findings that could shape future dosing recommendations.  Genetic Polymorphism in Pharmacodynamics Drugs interact with specific targets in the body, mainly enzymes and receptors, to exert an effect. Genetic polymorphism can change the properties of these target sites and in turn affect the therapeutic response and/or experience of side effects. Phenylthiocarbamide (PTC) E TASZR Accidentally found to taste bitter to some individuals and tasteless to others. This taste perception was associated with polymorphisms in the taste receptor gene TAS2R. There is a large inter-ethnic variation in ratio of tasters to non-tasters, where non-tasters can be as low as ~3% in some ethnicities and as high as~67% in other ethnicities. This early example highlights how changes to receptor genes can affect receptor function. β1 adrenergic receptors (ADRB1) Associated with an increased adrenergic effect. Atenolol (angina) and metoprolol (hypertension); selective beta-blockers that interact with β1 receptors to induce their effects. Hypertensive patients with certain ADRB1 variants show greater reductions in blood pressure in response to metoprolol therapy. Coronary heart disease patients carrying certain alleles were at an increased risk of death, where the heightened death risk was reversed following treatment with atenolol.  In heart failure patients, carriers of a specific genotype showed superior improvements in left ventricular ejection in response to carvedilol (non- selective β-blocker) or metoprolol, while bucindolol (non-selective β-blocker) was associated with higher survival rates in the same genotype. Interestingly, Caucasians respond better to beta blockers than people of African lineage, which may in part be due to higher prevalence of the more active β1 receptor genotype in Caucasians. Vitamin K epoxide reductase (VKOR) Warfarin acts by inhibiting VKORC1, which inhibits downstream carboxylation of clotting factors, leading to its anticoagulant effect. VKORC1 polymorphs can either result in warfarin sensitivity or resistance. Warfarin sensitivity; ↓VKORC1 expression; ↓dose to minimise risk of bleeding events. Gphamacodynamic  Warfarin resistance; ↑VKORC1 expression; ↑dose for effective anticoagulation or no response. Asian populations have a higher prevalence of the VKORC1 gene associated with warfarin sensitivity which may explain why lower doses are needed for effective anticoagulation in Asian ethnicities.  Pharmacogenetic/Pharmacogenomic Testing Pharmacogenetic testing has the potential to be at the forefront of personalised medicine. Pharmacogenetics/pharmacogenomics field is still in its infancy Some recommendations have made their way into drug labels to guide dosing.  The information contained in drug labels can describe (source: fda.gov): − Drug exposure and clinical response variability − Risk for adverse events − Genotype-specific dosing − Mechanisms of drug action − Polymorphic drug target and disposition genes − Trial design features  The inclusion of pharmacogenetic/pharmacogenomic information in drug labels aims to: Identify responders and non-responders Avoid adverse events Optimise drug dose The tests can be classified into ‘required’, ‘recommended’, or ‘information only’.  Cetuximab: - Monoclonal antibody that binds to human epidermal growth factor receptor (EGFR). - Used in the treatment of some forms of cancer. - Testing required: EGFR expression in tumours.  Maraviroc: - Chemokine receptor antagonist used in the management of HIV infections. - Indicated for CCR5 tropic HIV-1 strain only. - Testing required: Confirmation of CCR5 tropic HIV1 strain.  Dasatinib: - Selective tyrosine kinase inhibitor. - Indicated for Philadelphia chromosome-positive (Ph+) chronic myelogenous leukaemia (CML) and acute lymphoblastic leukaemia (ALL). - Testing required: Philadelphia chromosome-positive (Ph+) cancer cells.  Carbamazepine: - Anticonvulsant used to prevent and manage seizures. - Allele (HLA-B*1502) associated with increased risk of carbamazepine induced Stevens-Johnson syndrome. - Testing recommended: Presence of HLA-B*1502 allele in Asian population to optimize dose and avoid serious adverse events.  Irinotecan: - Topoisomerase 1 inhibitor used as an anticancer drug. - Some UGT1A1 genotypes associated with reduced UGT activity which causes a build up of the active metabolite SN-38. - Testing recommended: UGT1A1 alleles with lower activity to avoid serious adverse events.  to gout Other examples of recommended tests include: outgo −CYP2C9 and VKORC1 for warfarin. −TPMT for thiopurines. odds −G6PD for rasburicase. do add of  Summary Genetic polymorphism can have a significant impact on drug pharmacokinetics and pharmacodynamics. Ethnic variabilities in genetic polymorphism should be considered in therapy choice. Pharmacogenetic testing can help guide dosing for effective therapy and prevention of adverse events.