L18: Pharmacogenetics and personalised medicine

Learning Objectives

  • Explain key terms used in pharmacogenomics;

  • Describe the effects of genetic polymorphism on drug metabolism and actions;

  • Appreciate the potential benefits of pharmacogenomics on healthcare and future drug development ;

  • Discuss the major obstacles for clinical application of pharmacogenomics

Pharmacogenetics and genetic variation

  • Pharmacogenetics: aiming to understand how the unique genetic composition of an individual can alter the pharmacokinetics and pharmacodynamic responses of that patien to a specific drug

  • Prodrug: becomes active after metabolism

  • Active drug: takes effect directly

Gene differences between individual humans

  • Mutations

    • frequency of variation at a particular locus in a population < 1%

      • point mutation

      • missense or nonsense silent mutation

      • insertion and deletion mutation

      • inversion

      • duplication

      • translocation

      • chromosomal aberration

    • often associated with rare diseases

      • cystic fibrosis

      • huntington’s disease

      • sickle cell anemia

  • Polymorphism

    • frequency of variation at a particular locus in a population > 1%

    • SNP is less likely to be the major cause of a disease

    • often no visible clinical impact

  • Single-nicleotude polymorphism (SNP)

    • linked SNPs (outside gene)

      • no effect in protein production or function

    • causative SNPs (in gene)

      • non-coding SNP: change amount of protein produced

      • coding SNP: change amino acid sequence → alter structure and function of protein

  • Other types of polymorphism

    • promoter polymorphisms

    • 5’ and 3’ UTR polymorphism

    • Slice-Site polymorphism

    • insertion-deletion polymorphism (indels)

    • STRs polymorphism

Linkage Disequilibrium (LD) and Haplotype

  • allele: one of a pair of genes on a specific locus that control the same trait

  • haplotype: groups of alleles on a single chromosome that are closely linked→ inherited as a unit

  • LD: multiple SNPs that always appear together→ allele that are inherited as a unit: haplotype block

Polymophisms occur in gene encoding

Drug metabolising enzyme——cytochrom P-450 enzymes (CYP)

Characteristics

  • superfamily of monooxygenases

  • a large and diverse group of enzymes that catalyse the oxidation of organic substances

  • 15 are known to be involved in drug metabolism

  • gene encoding of CYPs are highly polymorphic→ many isoenzyme

  • 40% of drugs metabolism is carried out by CYP2C9, CYP2C19, CYP 2D6 enzyme

Effect of polymorphism

  • ultrarapid or rapid metaboliser

    • 2 or multiple copies of functional allele and very high enzyme activity

    • lack of response (active drug)

    • adverse drug reaction (prodrug)

  • extensive or normal metaboliser

    • 2 functional alleles and normal activity

    • expected response (active drug; prodrug)

  • intermediate metaboliser

    • either 1 functional and 1 defective allele or 2 partially defective alleles

    • → reduced enzyme activity

    • exaggerated response (active drug)

    • reduced response (prodrug)

  • poor metaboliser

    • defective or deleted alleles and abolished enzyme activity

    • adverse drug reaction (active drug)

    • lack of response (prodrug)

AmpliChip CYP450 clinical test

  • genotype 29 known polymorphism in CYP2D6

    • including duplication and deletion

  • identify 2 major variants in CYP2C19

  • processes

    • PCR amplification

    • fragmentation or labelling of amplified products

    • hybridisation

    • staining

    • scanning od microarray

CYP2D6

  • Characteristics

    • mediate the most drug metabolism: 20-30%

    • polymorphism significantly affect the elimination of 50% of the currently-marketed drugs

  • Codeine (example of CYP2D6-mediated drug)

    • therapeutic use of codeine

      • opioid drug for analgesic, antitussive and anti-diarrhea

      • side effects: respiratory depression, constipation, sedation and addiction

      • pro-drug: needs to be metabolised to morphine

    • CYP2D6 polymorphism

      • poor metaboliser

        • unable to transform codeine to morphine

        • lack of pain relief → treatment failure

      • ultra-rapid metaboliser

        • convert codeine to morphine more quickly→ high exposure to morphine

        • breast feeding mom with CYP2D6 UM taking codeine→ risk health or even death to infants due yo morphine overdose via breast milk

CYP2C9

  • Characteristic

    • major role in oxidation of both xenobiotic (foreign) and endogenous (internal) compounds

    • make up ~18% of CYP450 proteins in liver

    • highly polymorphic with > 50 SNPs identified

    • major SNPs

      • CYP2C9*2: decrease activity by 30%

      • CYP2C9*3: decrease activity by 90%

  • warfarin (example of CYP2C9-mediated drug)

    • mechanism of warfarin

      • anti-coagulant drug for prevention of thrombosis

      • reduce body ability to make vitamin K, which helps synthesis of thrombocytes

        • inhibit vitamin K epoxide reductase complex 1 (VKORC1)

      • lower level of clotting protein makes blood cells less likely to clot

      • CYP2C9 enzyme metabolise warfarin

    • narrow therapeutic index (NTI)

      • effective daily dose: 0.5-80mg

    • CYP2C9 polymorphism

      • CYP2C9*2: reduces metabolism by 30%

      • CYP2C9×3: reduces metabolism by 90%

    • VKORC1 gene polymorphism (-1639 SNP)

      • G1639A → produce less VKORC1 enzyme

      • lower warfarin doses are required

Drug transportation / efflux

Adenosine triphosphate-binding cassette family (ABC)

  • Characteristics

    • present in cellular and intracellular membrane

    • import or remove substances form cells and tissue

    • ATP-dependent conformational change → substance transportation

  • ABCB1 transporter——P-glycoprotein (P-gp)

    • many drugs are transported across membranes

      • cytotoxic chemotherapeutic agents, protease inhibitors, anticonvulsants, antidepressants

    • expressed in intestine kidney liver, blood-brain barrier, spinal cord testes and placenta

  • drug efficiency

    • P-gp remove drug outside of cells in intestine

    • lower intestinal P-gp → increase bioavailability of drug

      • allow augmented drug effects and /or undesired effects due to prolonged drug exposure

  • polymorphism

    • 2677G>A/T: exon 21→ change amino acid sequence

    • 3435C>T: silent polymorphism in exon 26 → associate with ↓ expression of ABCB1

    • C1236T: silent polymorphism in exon 12

  • simvastatin

    • a lipid-lowering drug

    • response to this drug is affected by ABCB1 polymorphism

SLC transporter

  • types

    • OATs: organic anion transporter

    • OATPs: organic anion transporting polypeptides

    • OCTs: organic cation transporter

    • PepTs: peptide transport proteins

  • expressed in a variety of tissue.

    • liver, kidney, brain, intestine

Beta adrenergic receptors

  • ADRB2

    • important mediator of bronchodilation, ventilation and lipid metabolism

    • ADRB2 agonist: treat asthma

    • polymorphism

      • Arg16Gly, Gln27Glu, Thr164Ile

      • LD effect:

        • Arg16 is usually linked to Glu27

        • Gly16 is often linked with either Glu27 or Gln27

  • ADRB1

    • regulating heart rate contractility and renin release in kidney

    • common polymorphism

      • Ser49Gly

      • Arg389Gly

    • Ser49 and Arg389 shows enhanced receptor activity and increased response to beta blocker

    • Beta blocker

      • a class of drug target ADRB1

      • interfere with the binding to the receptor of epinephrine and other stress hormones

      • used for management of cardiac arrhythmias

      • examples

        • betaxolol

        • bisoprolol

        • metoprolol

Serotonin transporter protein (SERT)

  • 44 bp insertion/deletion in promoter region → longer or shorter allele

    • drug response: longer allele > shorter

  • VNTR polymorphism: SERT has 3 alleles with 9, 10 and 12 copies of tandem repeat in the 2nd intron

    • drug responseL 12 copy > 9/10 copy