Lecture 5: Pharmacogenetics and Drug Toxicity PDF

Pharmacy (Honours) Year 1, Semester 2 Academic Session 2021/2022 Lecture 5 Pharmacogenetics and drug toxicity Zalina Bt Zahari ([email protected]) 12/04/2021 (2 pm – 5 pm) KeLIP ...

Pharmacy (Honours) Year 1, Semester 2 Academic Session 2021/2022 Lecture 5 Pharmacogenetics and drug toxicity Zalina Bt Zahari ([email protected]) 12/04/2021 (2 pm – 5 pm) KeLIP  Introduction Clinicians have long been aware that patients do not uniformly respond to medications. In some patients, one drug may not be as effective as expected, whereas in other patients, it may cause adverse reactions, sometimes life- threatening. The causes of these variations in drug response include clinical, environmental, and genetic factors. Pharmacogenetics is the study of genetic causes of individual variations in drug response. It is a hybrid between pharmacology (the science of drugs) and genetics (the science of genes and their action). Introduction  Pharmacogenetics and pharmacogenomics Pharmacogenetics – the study of variability in drug response due to heredity – largely used in relation to genes determining drug metabolism Pharmacogenomics – adding the suffix ‘… omics’ to areas of research – a broader based term that encompasses all genes in the genome that may determine drug response The distinction however, is arbitrary and both terms can be used interchangeably. A large number of articles have appeared on pharmacogenomics in various journals. This is because pharmacogenomics is viewed as a highly important area for improving drug therapy and prescribing in the future. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2014592/  Drug toxicity The development of severe, drug-related complications, which may require premature drug withdrawal or dose reduction can develop at normal therapeutic doses of a drug or as a result of an acute overdose. In some cases, toxicity occurs in the majority of treated individuals because of the nature of the drug (e.g. cytotoxic agents used for cancer chemotherapy), but significant toxicity is rare with the majority of commonly prescribed drugs when used at recommended dosages. There is considerable interindividual variability in both the nature and severity of adverse reactions, and toxicity can be reduced by taking into account factors that are known to increase susceptibility, such as age, concurrent disease or body weight, when selecting both the drug and the dosage. Genetic factors may also be taken into account for some drugs Usually a reduction in dosage or a change of drug during chronic treatment will reduce the severity of adverse effects. https://www.sciencedirect.com/topics/medicine-and-dentistry/drug-toxicity  Drug response Drug-response phenotypes include adverse drug events and therapeutic efficacy. Drug response can be impacted by several factors including diet, comorbidities, age, weight, drug–drug interactions, and genetics. Individual genetic variation in key genes involved in the metabolism, transport, or drug target can contribute to risk of adverse events or treatment failure. The study of genetic variation underlying pharmacokinetics and pharmacodynamics is known as pharmacogenetics, one of the pillars of the personalized medicine movement. https://www.sciencedirect.com/topics/medicine-and-dentistry/drug-response  Importance of pharmacogenetics to variability in drug response Clinical drug response represents a complex phenotype that emerges from the interplay of drug-specific, human body, and environmental factors. This complexity results in marked interindividual variation in drug response, affecting both efficacy and toxicity, and leading to patient harm and the inefficient utilization of limited healthcare resources. Pharmacogenomics is the study of the genetic determinants of interindividual drug response variation and aims to optimize drug efficacy and minimize adverse drug reactions through genotype(s)-informed drug stratification. https://www.sciencedirect.com/topics/medicine-and-dentistry/drug-response  Importance of pharmacogenetics to variability in drug response Currently, we prescribe drugs according to the model that ‘one dose fits all’. Using individual genetic profiling, it may possible to tailor drug prescription and drug dosage to the individual, thereby maximizing efficacy and minimizing toxicity. The promise of personalized medicines is also of obvious interest and importance to the pharmaceutical industry since it may allow streamlining of the drug development, drug testing and drug registration process, reducing the time from chemical synthesis to introduction into clinical practice, and therefore the cost of the drug development process. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2014592/  Types of genetic variants Variation within the human genome is seen about every 500– 1000 bases. Although there are a number of different types of polymorphic markers, most attention recently has focused on single nucleotide polymorphisms (SNPs), and the potential for using these to determine the individual drug response profile. SNPs occur at a frequency of 1% or greater in the population. A consortium between the pharmaceutical industry and charities was formed to create a library of SNPs. Theoretically, this could be used to create individual SNP profiles that correlate with individual drug response. https://www.ebi.ac.uk/training/online/course/human-genetic-variation-i-introduction-2019/what-genetic-variation  Types of genetic variants Genetic variation is the difference in DNA sequences between individuals within a population Mutations are the original source of genetic variation. A mutation is a permanent alteration to a DNA sequence. The term variant is used to refer to a specific region of the genome which differs between two genomes. https://www.ebi.ac.uk/training/online/course/human-genetic-variation-i-introduction-2019/what-genetic-variation  Types of genetic variants Different versions of the same variant are called alleles. For example, a SNP may have two alternative bases, or alleles, C and T. When working with genome scale data the term reference allele refers to the base that is found in the reference genome. Since the reference is just somebody’s genome, it is not always the major allele. In contrast, the alternative allele refers to any base, other than the reference, that is found at that locus. The alternative allele is not necessarily the minor allele and it may, or may not, be linked to a phenotype. There can be more than one alternative allele per variant. https://www.ebi.ac.uk/training/online/course/human-genetic-variation-i-introduction-2019/what-genetic-variation  Types of genetic variants https://www.ebi.ac.uk/training/online/course/human-genetic-variation-i-introduction-2019/what-genetic-variation  Types of genetic variants Genetic differences or variation between individuals leads to differences in an individual’s phenotype, trait or risk of developing a disease. An individual's phenotype is influenced both by their genotype and their environment. A mendelian trait is one that is controlled by a single locus, for example a single base-pair substitution. In most cases, associations between genetic variants and phenotypes/traits are not this simple. These are called complex phenotypes and may be influenced by multiple variants in the genome along with environmental factors. https://www.ebi.ac.uk/training/online/course/human-genetic-variation-i-introduction-2019/what-genetic-variation  Types of genetic variants Genetic variation is commonly divided into three main forms:  Single base-pair substitution There are also known as single nucleotide polymorphisms (SNPs) and can be any nucleic acid substitution: Transition – interchange of the purine (Adenine/Guanine) – or pyrimidine (Cytosine/Thymine) nucleic acids Transversion – interchange of a purine and pyrimidine nucleic acid (Figure 3) https://www.ebi.ac.uk/training/online/course/human-genetic-variation-i-introduction-2019/what-genetic-variation  Types of genetic variants Figure 3 SNPs result from the substitution of a single base-pair. In this example we have a transversion event substituting a Thymine nucleic acid in place of a Guanine.  Types of genetic variants  Insertion or deletion, also known as ‘indel’ Insertion or deletion of a single stretch of DNA sequence that can range from two to hundreds of base-pairs in length Figure 4 Indels affect a string of base-pairs. In this example the insertion string shows that GTA has been inserted, and the deletion string shows a deletion of CA. https://www.ebi.ac.uk/training/online/course/human-genetic-variation-i-introduction-2019/what-genetic-variation  Types of genetic variants  Structural variation Typically used to describe genetic variation that occurs over a larger DNA sequence. This category of genetic variation includes both copy number variation and chromosomal rearrangement events. https://www.ebi.ac.uk/training/online/course/human-genetic-variation-i-introduction-2019/what-genetic-variation  Copy number variation (CNV) A CNV is when the number of copies of a particular gene varies from one individual to the next. The extent to which copy number variation contributes to human disease is not yet known. It has long been recognized that some cancers are associated with elevated copy numbers of particular genes. https://www.genome.gov/genetics-glossary/Copy-Number-Variation  Chromosomal rearrangement Chromosomal rearrangements encompass several different classes of events: deletions, duplications, inversions; and translocations. A duplication, where part of a chromosome is copied. A deletion, where part of a chromosome is removed. An inversion, where chromosomal region is flipped around so that it points in the opposite direction. A translocation, where a piece of one chromosome gets attached to another chromosome. A reciprocal translocation involves two chromosomes swapping segments; a non-reciprocal translocation means that a chunk of one chromosome moves to another. https://www.ncbi.nlm.nih.gov/books/NBK21367/  Chromosomal rearrangement https://www.khanacademy.org/science/biology/classical-genetics/sex-linkage-non-nuclear-chromosomal- mutations/a/aneuploidy-and-chromosomal-rearrangements  Chromosomal rearrangement https://www.khanacademy.org/science/biology/classical-genetics/sex-linkage-non-nuclear-chromosomal- mutations/a/aneuploidy-and-chromosomal-rearrangements Chromosomal rearrangement  Codon A codon is a trinucleotide sequence of DNA or RNA that corresponds to a specific amino acid. The genetic code describes the relationship between the sequence of DNA bases (A, C, G, and T) in a gene and the corresponding protein sequence that it encodes. The cell reads the sequence of the gene in groups of three bases. There are 64 different codons: 61 specify amino acids while the remaining three are used as stop signals. https://www.genome.gov/genetics-glossary/Codon  Variants in coding regions If a variant falls within a coding region, it can be categorised based on how it would affect the codon it falls within Synonymous/silent - Due to redundancies in the genetic code, many nucleotide changes will not change the amino acid sequence, for example a GCT to GCC change would still encode an alanine. Missense - This change results in a change in amino acid, for example ACC threonine to AAC asparagine. Nonsense - These turn a coding codon, such as GGA glycine, to a stop codon, e.g. TGA. This will result in a truncated protein, which may or may not be subject to nonsense-mediated decay depending on where in the peptide it occurs. https://www.ebi.ac.uk/training/online/course/human-genetic-variation-i-introduction-2019/what-genetic-variation  Variants in coding regions Indels with a length divisible by three (i.e. whole codon indels) in coding regions will cause insertions or deletions of whole amino acids into the protein, and are known as in-frame deletions or insertions. Note that indels divisible by three may also cause a missense or nonsense variant if the variant falls across two codons. However, if the length is not divisible by three, this will cause a frameshift where all codons downstream of the indel are shifted, often resulting in a malformed protein or nonsense-mediated decay. https://www.ebi.ac.uk/training/online/course/human-genetic-variation-i-introduction-2019/what-genetic-variation  Variant effects on protein structure The effects of variants on protein structure can vary dramatically depending on the type of protein and the extent of variation. Take, for instance, a large, multi-domain protein with multiple variants. One variant could involve the deletion of a large region of protein sequence, corresponding to an individual domain. If the core function of these domains are independent, the function of the remaining domains may not be affected at all. Another variant of this protein, however, may involve the changing of only a single amino acid in the protein sequence. Despite the relative insignificance of this change to the overall protein sequence, if this residue is key to the function of the protein (for instance at the active site of an enzyme) then this could completely eradicate protein function, or modify it in some way, for instance to change the specificity of an enzyme. https://www.ebi.ac.uk/training/online/course/human-genetic-variation-i-introduction-2019/what-genetic-variation  Variant effects on protein structure An important factor in the effect of variation on protein structure is in the packing of the amino acids in the core of the protein structure. Most protein side chains are designated as either hydrophilic residues or hydrophobic residues. For a soluble protein, the outer surface of the protein is mainly composed of hydrophilic residues, whereas the core of the protein involves the packing of hydrophobic residues, away from the water in the solution. A variant that involves a change in the protein core from a hydrophobic residue to a hydrophilic one may destabilise the protein enough for function to be lost. Because the protein core is tightly packed, a change from a small amino acid (e.g. alanine) to a bulkier one (e.g. phenylalanine) may not be accommodated and may lead to the protein being unable to fold into its 3D form. An example of hydrophobic to hydrophilic variation is in human cystatin where a single variant, Leucine (L) to Glutamine (Q), destabilises the core of the protein. https://www.ebi.ac.uk/training/online/course/human-genetic-variation-i-introduction-2019/what-genetic-variation  Variant effects on protein structure Figure 8 In human cystatin a single variant causes Leucine (L) (purple) to be converted to a Glutamine (Q) in the variant structure, destabilising the core structure.  The 20 amino acids  Charged (side chains often form salt bridges): Arginine - Arg - R Lysine - Lys - K Aspartic acid - Asp - D Glutamic acid - Glu - E  Polar (form hydrogen bonds as proton donors or acceptors): Glutamine - Gln - Q Asparagine - Asn - N Histidine - His - H Serine - Ser - S Threonine - Thr - T Tyrosine - Tyr - Y Cysteine - Cys - C https://proteinstructures.com/Structure/Structure/amino-acids.html  The 20 amino acids  Amphipathic (often found at the surface of proteins or lipid membranes, sometimes also classified as polar): Tryptophan - Trp - W Tyrosine - Tyr - Y Methionine - Met - M (may function as a ligand to metal ions)  Hydrophobic (normally buried inside the protein core): Alanine - Ala - A Isoleucine - Ile - I Leucine - Leu - L Methionine - Met - M Phenylalanine - Phe - F Valine - Val - V Proline - Pro - P Glycine - Gly - G https://proteinstructures.com/Structure/Structure/amino-acids.html  Variants affecting surface residues Change of surface residues on a protein may affect its association with other proteins, though in practice changes in these regions have a less significant functional effect than changes in the core of the protein. Should a protein be involved in protein-protein, or protein-nucleic acid interactions, any variation of amino acids on the binding surface could lead to a loss of function. An example of this is Human DJ-1, which in rare forms of Parkinson's disease, contains single mutations that destabilise the homodimeric interface, leading to disruption of function (Figure 9) https://www.ebi.ac.uk/training/online/course/human-genetic-variation-i-introduction-2019/what-genetic-variation  Variants affecting surface residues Change of surface residues on a protein may affect its association with other proteins, though in practice changes in these regions have a less significant functional effect than changes in the core of the protein. Should a protein be involved in protein-protein, or protein-nucleic acid interactions, any variation of amino acids on the binding surface could lead to a loss of function. An example of this is Human DJ-1, which in rare forms of Parkinson's disease, contains single mutations that destabilise the homodimeric interface, leading to disruption of function (Figure 9) https://www.ebi.ac.uk/training/online/course/human-genetic-variation-i-introduction-2019/what-genetic-variation  Variants affecting surface residues Figure 9 Structure of Human DJ-1 from PDBe. Displayed in spheres is Methionine26. Mutation of Methionine26 to Isoleucine leads to destabilisation of the homodimeric interface in some forms of Parkinson's disease  Pharmacogenetics in clinical practice  Pharmacogenomics in general practice: The time has come Knowledge of the variants in pharmacogenomics is useful when prescribing a variety of medications. International guidelines have identified at least 15 genes for which testing can inform the prescribing of 30 different medications with good evidence of clinical benefit. Knowledge of the gene variants influencing exposure or response (ie pharmacogenomics) allows prescribers to move from the general to the particular, and provide a scientific basis for individualised prescribing. The goal is more effective and safer choices of medication and dose. https://www1.racgp.org.au/ajgp/2019/march/pharmacogenomics-in-general-practice  Pharmacogenetics in clinical practice  Pharmacogenomics in general practice: The time has come Nonetheless, pharmacogenomic tests should not be used as the sole basis for prescribing decisions, and should be considered in the context of other relevant clinical and laboratory features. General practitioners can incorporate pharmacogenomic tests into their clinical practice for patients with medication-related problems or those who are likely to require medications for which pharmacogenomics can provide guidance. https://www1.racgp.org.au/ajgp/2019/march/pharmacogenomics-in-general-practice  Pharmacogenetics in clinical practice  Pharmacogenomics in general practice: The time has come An important challenge in pharmacogenomics has been the lack of consistency in how laboratories report variations in different genes. This challenge was met by the Clinical Pharmacogenetics Implementation Consortium (CPIC) and the Dutch Pharmacogenetics Working Group (DPWG), which both provide frameworks for evaluating medication–gene associations and expert guidance about prescribing for patients with given variants. https://www1.racgp.org.au/ajgp/2019/march/pharmacogenomics-in-general-practice Clinical Pharmacogenetics Implementation Consortium (CPIC)  One barrier to implementation of pharmacogenetic testing in the clinic is the difficulty in translating genetic laboratory test results into actionable prescribing decisions for affected drugs.  CPIC’s goal is to address this barrier to clinical implementation of pharmacogenetic tests by creating, curating, and posting freely available, peer-reviewed, evidence-based, updatable, and detailed gene/drug clinical practice guidelines https://cpicpgx.org/ Clinical Pharmacogenetics Implementation Consortium (CPIC)  Guidelines  CPIC guidelines are designed to help clinicians understand HOW available genetic test results should be used to optimize drug therapy, rather than WHETHER tests should be ordered.  A key assumption underlying the CPIC guidelines is that clinical high-throughput and pre-emptive (pre-prescription) genotyping will become more widespread, and that clinicians will be faced with having patients’ genotypes available even if they have not explicitly ordered a test with a specific drug in mind. https://cpicpgx.org/  Implementing preemptive pharmacogenomics in clinical practice  Preemptive versus reactive genotyping  A first practical challenge related to implementing pharmacogenomic testing is the issue of when to genotype. Arguments have been made for both preemptive genotyping, which involves testing prior to prescribing so that results are available before the time of prescription consideration, and reactive genotyping, when a clinician orders a test only after he or she decides to prescribe a particular drug (but ideally in advance of the patient actually starting the medication).  While reactive genotyping is directly applicable to specific patient situations and more likely to be reimbursed by insurance companies, many believe the advantages of preemptive genotyping outweigh the current benefits of a reactive approach. https://www.aacc.org/publications/cln/articles/2018/april/implementing-preemptive-pharmacogenomics-in-clinical- practice  Implementing preemptive pharmacogenomics in clinical practice  Preemptive versus reactive genotyping  A first practical challenge related to implementing pharmacogenomic testing is the issue of when to genotype. Arguments have been made for both preemptive genotyping, which involves testing prior to prescribing so that results are available before the time of prescription consideration, and reactive genotyping, when a clinician orders a test only after he or she decides to prescribe a particular drug (but ideally in advance of the patient actually starting the medication).  While reactive genotyping is directly applicable to specific patient situations and more likely to be reimbursed by insurance companies, many believe the advantages of preemptive genotyping outweigh the current benefits of a reactive approach. https://www.aacc.org/publications/cln/articles/2018/april/implementing-preemptive-pharmacogenomics-in-clinical- practice Clinical Pharmacogenetics Implementation Consortium (CPIC)  Guidelines https://cpicpgx.org/ Clinical Pharmacogenetics Implementation Consortium (CPIC)  Genes-Drugs  CPIC assigns CPIC levels to genes/drugs with (1) PharmGKB Clinical Annotation Levels of Evidence of 1A, 1B, 2A and 2B, or (2) a PharmGKB PGx level for FDA-approved drug labels of “actionable pgx”, “genetic testing recommended”, or “genetic testing required”, or (3) based on nomination to CPIC for consideration.  The levels (A, B, C, and D) assigned are subject to change; only those gene/drug pairs that have been the subject of guidelines have had sufficient in-depth review of evidence to provide definitive CPIC level assignments.  Note that only CPIC level A and B gene/drug pairs have sufficient evidence for at least one prescribing action to be recommended. CPIC level C and D gene/drug pairs are not considered to have adequate evidence or actionability to have prescribing recommendations. https://cpicpgx.org/ Clinical Pharmacogenetics Implementation Consortium (CPIC)  Genes-Drugs https://cpicpgx.org/ Clinical Pharmacogenetics Implementation Consortium (CPIC)  Alleles Each allele in this table is discussed in the corresponding CPIC guideline manuscript or supplement listed below. https://cpicpgx.org/ Dutch Pharmacogenetics Working Group (DPWG) https://upgx.eu/guidelines/ Canadian Pharmacogenomics Network for Drug Safety (CPNDS) http://cpnds.ubc.ca/  Pharmacogenomics in Australia Most doctors recognise the value of genetic testing of cancer to predict whether patients are eligible for specific, targeted pharmacotherapy. Apart from these tests, there are only two items on the Medicare Benefits Schedule that inform individualised prescribing: a test for abacavir hypersensitivity (item 73323) and a test to guide dosing with thiopurines (item 73327). The clinical utility of pharmacogenomics is not widely appreciated in Australia. https://www1.racgp.org.au/ajgp/2019/march/pharmacogenomics-in-general-practice  Pharmacogenomics in Australia Pharmacogenomic testing by Australian laboratories is typically funded by patients. This is costly and prohibitive for some patients, although costs are decreasing all the time (a panel of common CYP enzymes costs $150–200). The disconnect between the evidence supporting pharmacogenomics and the availability of rebated testing is recognised in a recent position statement on pharmacogenomics developed by representatives from a number of major medical colleges and released by the Royal College of Pathologists of Australasia (www.rcpa.edu.au/Library/College- Policies/Position-Statements/Utilisation-of-pharmacogenetics-in- healthcare). Broader application of pharmacogenomics in general practice will occur when rebated tests become more widely available. https://www1.racgp.org.au/ajgp/2019/march/pharmacogenomics-in-general-practice  Summary 1. Importance of pharmacogenetics to variability in drug response Describe the contribution of genetic variation to drug response 2. Types of genetic variants Describe the types of genetic variants 3. Pharmacogenetics in clinical practice Illustrate the role of pharmacogenomics testing in clinical practice