Chapter 5: Pharmacogenomics

The inheritance of genetic information via the double DNA helix is now well-understood. The decoding of the human genome and of many animal and plant genomes has opened a field of research into the molecular basis of variations between individuals and among populations. The identification of the specific genes (or groups of genes) that affect drug responses is still incomplete, but knowledge about a small number of these genes of pharmacologic significance has suggested the possibility that “personalized medicine” is possible and may become practical in the near future.

Personalized medicine denotes clinical treatment that takes into account the genetic factors that contribute to disease and the pharmacogenomic factors that influence the response to drug treatment in specific individuals. Intense academic and commercial research is currently directed at discovering these factors. Research is also directed at developing accurate and inexpensive tests for pharmacogenetic factors in individual patients.

As noted in Chapter 4, important genetic variations in drug metabolism exist between individuals. Furthermore, genetic diseases alter many functions that are drug targets. The identification of specific genes that control the expression of the molecules involved and the variants (polymorphisms) of those genes has become the subject of intense research over the last 10–20 years. At present, much data are available regarding the variants of the genes for some phase I and phase II enzymes and some drug transporters. Examples of these genetic determinants of drug metabolism and transport are the subject of this chapter.

CYP2D6, CYP2C19, CYP3A4/5, and dihydropyrimidine dehydrogenase are among the drug-metabolizing enzymes most carefully studied (Table 5–1).

A. CYP2D6

This enzyme is responsible for the hepatic metabolism of 20% of commonly used drugs. More than 100 polymorphisms of the CYP2D6 gene have been discovered, but only 9 are common. CYP2D6 polymorphisms are especially important in patients receiving codeine because this enzyme converts codeine to its active metabolite, morphine. Several deaths due to respiratory depression have been reported in children who were believed to be ultrarapid metabolizers.

B. CYP2C19

CYP2C19 is responsible for the hepatic metabolism of a small number of very important drugs (clopidogrel, propranolol, omeprazole, diazepam, and tricyclic antidepressants). Because reduced metabolism of clopidogrel results in lower concentrations of its active metabolite, reduced function polymorphisms in this enzyme reduce the efficacy of clopidogrel and increase the risk of clotting in patients with coronary artery disease. Conversely, gain of function results in increased risk of bleeding. Poor metabolizers and IMs should receive alternative drugs prasugrel or ticagrelor, not clopidogrel.

C. CYP3A4 and CYP3A5

CYP3A4/5 are responsible for the metabolism of over 50% of drugs in common use. Some polymorphisms with important ethnic variability have been described, but relatively few appear to alter pharmacokinetics to a clinically significant degree.

D. Dihydropyrimidine Dehydrogenase (DPD)

DPD is responsible for the clearance of 5-fluorouracil (5-FU), a first-line prodrug agent for the treatment of colorectal cancer. Capecitabine and tegafur are oral prodrugs converted in the body to 5-FU. In the body, 5-FU is converted to cytotoxic 5-fluorouridine 5′-monophosphate (5-FUMP) and 5-fluoro-2′-deoxyuridine-5′-monophosphate (5-FdUMP) (see Chapter 54). Nonfunctional polymorphisms in the DYPD gene result in increased toxicity and require reduced dosage.

E. Multiple Enzyme Polymorphisms: CYP2C9 and VCORC1

CYP2C9 and vitamin K epoxide reductase complex subunit 1 (VCORC1) are responsible for the inactivation of S-warfarin. Some mutations of the VCORC1 gene lead to spontaneous bleeding disorders. Reduced function polymorphisms in both genes result in increased warfarin action and enhanced risk of bleeding. Algorithms have been developed to predict the optimal dosage of warfarin, but clinical trials of these algorithms have not shown improved anticoagulant control thus far.

A. Uridine 5′-diphospho-(UDP) glucuronosyltransferase (UGT1A1)

UGT1A1 is involved in the hepatic excretion of small molecules into the bile. UGT1A1 contributes to the clearance of SN-38, the bioactive metabolite of irinotecan, a cytotoxic agent used in the treatment of colorectal cancer. Reduced function polymorphisms result in increased irinotecan-induced bone marrow depression and diarrhea and require a reduction in dosage.

B. Thiopurine S-methyltransferase (TPMT)

TPMT is important in the inactivation of chemotherapeutic purine derivatives, eg, 6-mercaptopurine (6-MP), azathioprine, a prodrug of 6-MP, and 6-thioguanine (6-TG). Reduced function polymorphisms result in altered therapeutic efficacy as well as altered toxicity.

The organic anion transporter (OATP) 1B1 expressed by the SLCO1B1 gene transports drugs and endogenous compounds from the blood into hepatocytes. Substrates include statins and methotrexate. Numerous SNPs are recognized in the SLCO1B1 gene and some are associated with reduced function. Reduced function alleles result in elevated concentrations of some statins, especially simvastatin, and increased risk of skeletal muscle myopathy.

The P-glycoprotein is a very promiscuous transporter found in blood-tissue interfaces. Its former name, multidrug resistance transporter-1 (MDR1), reflects its importance in expelling cytotoxic drugs from resistant cancer cells. It is encoded by the ABCB1 gene and over 100 SNPs have been identified in its coding regions. Association studies with drug pharmacokinetics have yielded mixed results.

HLA polymorphisms are associated with variations in immunologic responses to drugs, including liver injury, Stevens-Johnson syndrome, and toxic epidermal necrosis. Examples are given in Table 5–1. Polymorphisms have been associated with reactions to abacavir, flucloxacillin, allopurinol, and carbamazepine.

A 17-year-old boy is admitted to the emergency department and acetaminophen overdose is suspected (See Chapter 4). What is the mechanism of acetaminophen toxicity and how is it treated? The Skill Keeper Answer appears at the end of the chapter.

1. A 59-year-old man with acute coronary syndrome is admitted to the hospital for emergency percutaneous insertion of a coronary stent. Which of the following drugs might cause unexpected results based on the patient’s CYP2C19 genotype?

   • (A) Clopidogrel

   • (B) Codeine

   • (C) Prasugrel

   • (D) Ticagrelor

   • (E) Warfarin

2. A 62-year-old woman with advanced colon cancer is treated with intravenous 5-fluorouracil. Within a few days, she develops severe diarrhea, and within a week, she shows severe neutropenia. Which of the following polymorphisms is most likely to be responsible?

   • (A) CYP2D6*1x3

   • (B) CYP2C19*2

   • (C) CYP2C9*3

   • (D) DYPD*2A

   • (E) UGT1A1*28

3. A 38-year-old man is being treated for HIV-induced acquired immunodeficiency syndrome (AIDS). When abacavir therapy is begun, he develops a severe skin rash. Which of the following pharmacogenomic diagnoses might explain this skin rash?

   • (A) CYP2D6*3 (PM)

   • (B) CYP3A5*3 (PM)

   • (C) HLA-B*57:01 (EM)

   • (D) SLCO1B1*5 (PM)

4. A college student volunteers to have his genome decoded as part of a population-wide study of polymorphisms. He receives a call from the principal investigator informing him that his genome unexpectedly contains an important single nucleotide polymorphism. Which of the following polymorphisms is associated with risk of hemolysis and increased resistance to malaria?

   • (A) CYP2D6*3

   • (B) CYP2D19*2

   • (C) TPMT*2

   • (D) UGT1A1*28

   • (E) G6PD-(A)–Canton

5. A 7-year-old child is brought to the emergency department in coma with cyanosis. Her mother states that the girl was given codeine with acetaminophen because of severe bruising after a fall. Shortly after the first dose, the child became unresponsive and “turned blue.” Which of the following alleles might be responsible for this presentation?

   • (A) CYP2D6*1x3

   • (B) CYP2C19*2

   • (C) CYP2C9*3

   • (D) DYPD*2A

   • (E) UGT1A1*28

1. Clopidogrel is a prodrug that must be metabolized to an active platelet-inhibiting metabolite by CYP2C19. Poor metabolizers achieve inadequate platelet inhibition, and EMs and UMs may have excess effect and bleed. Prasugrel and ticagrelor do not require P450 activation and are not subject to this risk. The answer is A.

2. CYP2D6*1x3 is a gain-of-function allele and is associated with increased effect and toxicity of codeine. CYP2C19*2 is a nonfunctional allele associated with reduced efficacy of clopidogrel. CYP2C9*3 with a reduced function allele of VCORC1 is associated with reduced warfarin clearance. UGT1A1*28 is a reduced function allele for uridine 5′-diphospho-(UDP) glucuronosyltransferase and enhances irinotecan toxicity. 5-Fluorouracil is cleared by dihydropyrimidine dehydrogenase (DPD). The DYPD*2A allele is nonfunctional. The answer is D.

3. Poor metabolizers of the CYP2D6*3 genotype are prone to reduced efficacy of codeine. Poor metabolizers of the CYP3A5*3 type show reduced tacrolimus clearance. Simvastatin toxicity (myopathy) is enhanced in SLCO1B1 poor metabolizers. Enhanced metabolizers of the HLA-B*57:01 type are prone to abacavir rashes and flucloxacillin liver damage. The answer is C.

4. CYP2D6 *3 is associated with reduced codeine efficacy. CYP2D19*2 results in reduced clopidogrel conversion to its active metabolite. TPMT *2 is associated with decreased clearance of 6-mercaptopurine and increased toxicity. UGT1A1*28 results in decreased clearance and increased toxicity of SN-38, the active metabolite of irinotecan. G6PD-(A)–Canton is a reduced function allele of the glucose 6-phosphate dehydrogenase gene that decreases intracellular stores of glutathione, increasing the risk of hemolysis but reducing susceptibility to malaria. The answer is E.

5. As noted in answer 4, SNPs in CYP2D6 may increase or decrease the efficacy and toxicity of codeine because the CYP2D6 enzyme is responsible for conversion of codeine to its active metabolite, morphine. CYP2D6*1xN and *2xN are gain-of-function polymorphisms that result in more efficient conversion to morphine and increased risk of opioid-induced respiratory depression. The answer is A.

In normal dosages, and in individuals with normal liver function, acetaminophen is converted to harmless glucuronide and sulfate conjugates and is excreted. Overdoses or high therapeutic doses in individuals with impaired liver function overwhelm the phase II systems and result in intracellular accumulation of a reactive intermediate that can combine with essential cellular proteins and cause hepatic necrosis. Treatment attempts to maximize free radical scavenger activity with N-acetylcysteine.

When you complete this chapter, you should be able to:

• ❑ Name 3 gene polymorphisms that increase or decrease drug efficacy or toxicity.

• ❑ Name 3 drugs that may require dosage adjustments in specific genetic populations.

• ❑ Name 1 drug that is more toxic due to a polymorphism.

• ❑ Name 1 drug that is less effective due to a loss of function polymorphism.