Lecture 18: Pharmacogenomics

Question 1

What is pharmacogenomics? = 6

Answer 1

1 * Pharmacogenomics used interchangeably with pharmacogenetics
…2 * defined as the study of how a person’s genetic make-up affects their response to a drug.
…3 * effective, safe medications, prescribed based on a person’s genetic makeup

4 * Pharmacogenomics - an important example of ‘precision medicine’, which tailors medical treatment to each person. (Obama)

5 * Move from ‘one drug fits all’ and prevent ADR. Pharmacogenomics can inform you ahead of time whether a drug is likely to be a benefit and is safe.

6 * The field is growing and developing through clinical trials.

7 * In the future, pharmacogenomics will be used to develop tailored drugs to treat a wide range of health problems, including cardiovascular disease, Alzheimer disease, cancer, and asthma

Question 2

What is genetic variation? What is the effect on drugs? = 5

Answer 2

1. Genetic variation in the regulatory and coding regions of genes determines drug response.

2.The ten highest-grossing drugs in the USA, for every the person helped between 3 and 24 individuals failed to show a response. Rough data!

3. ADRs account for ~6.5% of hospital admissions in adults, increasing to >15% in people with multimorbidity.
   (UK figures, similar to other countries)

4.~50% of prescriptions in the
The USA and UK are affected by actionable germline pharmacogenes.

5. 90% of patients older than 70 years will be exposed to at least one drug with pharmacogenomics guidance.

Question 3

Sources of Variation in Response ..flow chart = 12

Answer 3

all:
1. Age
2. Pregnancy
3. race
4. obesity
5. gender
6. disease states
7. adherence
8. drug interactions
9. environmental factors

10. Pharmacogenomics —> Genetic differences

= VARIABILITY IN DRUG RESPONSE

Question 4

History of Pharmacogenomics: more detail of timeline on slide 6

Answer 4

510 BC
-First described by Pythagoras around 510 BC
*Ingestion of fava beans causing haemolytic anemia.
*Due to deficiency of G6PD (1950s) affecting ~400 million people

• The term pharmacogenomics
  appeared in 1990s.
• 2005
  The first FDA approval of a
  pharmacogenetic test was in 2005 (for
  alleles in CYP2D6 and CYP2C19)

Question 5

Benefits of Pharamcogenomics:

‘Integrating pharmacogenomics into clinical practice will ultimately enable healthcare providers to: 4’

Answer 5

1 * Maximize use of a medications

2 * Reduce ADR

3 * Speedup time to achieve the therapeutic benefit of a drug

4 * Decrease the chance of side effects or dependency

Question 6

Benefits of Pharmacogenomics

‘Decrease the cost of healthcare expenditures by: 7’

Answer 6

1 * Using genomics to identify the most appropriate and affordable drug the first time

2 * Reducing ADR early in treatment, thus

3 * Reduce hospital length of stays

4 * Reduce hospital readmissions

5 * Reduce ED visits

6 * Reduce the risk of morbidity and death, and

7 * Be cost-effective

Question 7

Benefits of Pharamcogenomics:

Answer 7

Pharmacogenomics will enable development of tailor-made therapeutics for treating widespread health problems like
- neurodegenerative,
- cardiovascular disorders,
- HIV,
- cancer,
- asthma, etc

Question 8

Pharmacogenomic landscape…what can it do? = 6

Answer 8

1. Predict Drug dose
2. Prevent adverse drug reactions
3. enabling drug discovery/development
4. predicting the activation of pro-drugs
5. developing targeted drugs for cancer therapy
6. enabling drug discovery/development

Question 9

Pharmacogenomic information contained in drug labels from different regulatory agencies

Answer 9

diagram on slide 9

Question 10

Selected pharmacogenetic tests in the context of US FDA-approved drug labels.

Answer 10

table on slide 10

Question 11

Knowledge Information… 8

Answer 11

1 * Dutch Pharmacogenetics Working Group (DPWG)
…2 * information on drug–gene pairs, including drug labels and clinical
guidelines.

3 * Clinical Pharmacogenetics Implementation Consortium (CPIC)
guidelines
…4* help clinicians understand genetic test results should be used to optimize drug therapy.

5. • PharmVar
     …6* centralized data repository on pharmacogene variation.

7 * FDA lists 517gene/drug associations that have been included on drug labels.

8 * Much of the content in drug labels is for information only, rather than guidance on drug dosages.

Question 12

CPIC and DPWG Guidelines for Stroke
Medications

Answer 12

slide 12…table

Question 13

Comparison of methods for testing:

Answer 13

IMPORTANT…DIAGRAM ON SLIDE 13

Question 14

How does pharmacogenomics work?

‘DRUG PHARMACOKINETICS’ = 7

Answer 14

Drug Pharmacokinetics

1 * Four main processes involved in drug pharmacokinetics—
2* absorption,
3* distribution,
4 * Metabolism and
5 * Excretion

6 * These factors determine inter-individual variability in drug handling.

7 * Genetic variants can have a role in determining drug pharmacokinetics at each of these stages.

Question 15

How does pharmacogenomics work?

‘DRUG RECEPTORS’

Answer 15

• Drug Receptors.
• DNA variants determine the type of receptors, how many, and efficiency. As a result, a higher or lower amount of the drug is needed or a different drug.

Question 16

Understanding Drug Receptors on drugs …….4

Answer 16

DRUG ON RECEPTOR…

1. MANY RECEPTORS —> ‘strong response to drug’
2. FEW RECEPTORS —> ‘Weak response to drug’
3. NO RECEPTORS —> ‘ NO response to drug’
4. DIFFERENT TYPE OF RECEPTORS –> ‘NO response to drug’

Question 17

Example: Breast Cancer and T-DM1.
= 5

Answer 17

1 * Some breast cancers make too many HER2 receptors, which helps the cancer develop and spread.

2 * T-DM1 (Trastuzumab-DM1 is an antibody-drug conjugate) used to treat these cancers and works by attaching to HER2 receptors on cancerous cells and
killing them.

3 * Tumour tissue is tested to determine if T-DM1 is the right treatment.

4 * If there is a high number of HER2 (HER2 positive), TDM1 can be used.
- If the tumor is HER2 negative, TDM1 will not work.

5. *Human epidermal growth factor receptor 2

Question 18

How does pharmacogenomics work?… DRUG UPTAKE = 4

Answer 18

1. • Some drugs need to be actively taken into cells.
2. • DNA variants can affect uptake of certain drugs.
     
     3. • Decreased uptake means the drug does not work as well and can cause it to build up in other parts of your body, which may be a problem.

4 * DNA variants can affect how quickly some drugs are removed from the cells. If
drugs are removed too quickly, they might not have time to act.

Question 19

DRUG UPTAKE… NORMAL UPTAKE VS DECREASED UPTAKE

Answer 19

1. Normal uptake —> the drug works as expected
2. Decreased uptake —> drug can build up and cause problems

Question 20

Example: Statins and Muscle Problems = 6

…drug uptake

Answer 20

1 * Statins act in the liver to lower cholesterol.

2 * To work, they must first be taken into the liver cells.

3 * Statins are transported by a protein made by the ‘SLCO1B1’ gene.

4 * A DNA variant causes reduced simvastatin to be absorbed by cells.

5 * When taken at high doses, simvastatin can build up causing muscle weakness and pain.

6 * Genetic testing the ‘SLCO1B1’ gene can be done to determine if simvastatin is the best statin and what dose would work best

Question 21

How does pharmacogenomics work?

Drug Breakdown = 3

Answer 21

1. DNA variants can affect the speed of a drug break down.
2. • If the drug is metabolized more quickly than most people, a higher dose may be required or a different drug used.
3. • If the drug is metabolized more slowly, a smaller dose may be required.

Question 22

How does pharmacogenomics work?… DRUG BREAKDOWN…

RATE OF BREAKDOWN =3

Answer 22

1. NORMAL BREAKDOWN —> Nedd the normal dose of the drug
2. FAST BREAKDOWN —> Need more drug or a different drug
3. SLOW BREAKDOWN —> Need less drug

Question 23

Example: Depression & Amitriptyline…drug breakdown = 4

Answer 23

1. The breakdown of the antidepressant drug amitriptyline is influenced by two
   genes ‘CYP2D6’ and ‘CYP2C19.’
2. • Genetic testing for these genes can help decide what dose of the drug is needed.

3 * Fast metabolizers will need a higher dose or a different drug.

4. • Slow metabolizers will need a smaller dose or a different drug to avoid a bad reaction.

Question 24

Cytochrome Oxidase P450 Enzymes = 5

Answer 24

1 * 57 Different active genes

2 * 17 Different families

3 * CYP1, CYP2 and CYP3 are primarily involved in drug metabolism.

4 * Six metabolize 90% of drugs. The two most significant enzymes are ‘CYP3A4 and CYP2D6.’

5 * ‘CYP2A6, CYP2B6, CYP2C9 ,CYP2C19, CYP2D6, CYP2E1
and CYP3A4’ are responsible for metabolizing most clinically important drugs

Question 25

Genetic Variability Influences Drug Metabolism Enzymes

Answer 25

*75% of all drugs are metabolized by ‘CYP3A4 + CYP2D6’

*2D6 contributes~20% of all drugs, although it is only 1.5% of total liver content

diagram on slide 24

Question 26

CYP2D6 and CYP2C19:

Answer 26

CYP 2D6 in Caucasians:
– PM: 7% High plasma drug level, toxicity
– IM: 40% Lower dose in some patients
– EM: 50% Normal metabolizers STD dose
– UM: 3% Very low drug level, higher dose

CYP 2C19 in Caucasians:
– PM: 3%
– IM: 27%
– EM: 70% Normal metabolizers

Question 27

Drug Dose..understanding = 6

Answer 27

1 * The dose determines both efficacy and safety of a drug.
Genetic factors play a role.

2 * An example is warfarin:
* SNPs in CYP2C9 (enzyme metabolizing warfarin) & VKORC1 (enzyme inhibited by warfarin) determine the dose requirement.
Loss-of-function SNPs in either or both genes cause reduced enzyme activity and lower warfarin doses is required, to avoid
overexposure, and achieve therapeutic anticoagulation.

3 * Other examples are with anticancer drugs:
4 * TPMT and NUDT15 SNPs and thiopurines,
5 * DPYD polymorphisms and fluoropyrimidines, and
6 * UGT1A1 polymorphisms and irinotecan.

6 * In these cases, a SNP either reduces or abolishes the activity of the relevant enzyme resulting in reduced metabolism of the anticancer drug, overexposure and
dose-dependent toxicity, causing bone marrow suppression and/or severe diarrhoea.

Question 28

Examples of dose adjustments based on PGDx… DIAGRAM ON SLIDE 27

Answer 28

Genetic SNPs in cytochrome P450 enzymes CYP2D6, CYP2C19 and CYP2C9, thiopurine Smethyltransferase (TPMT), and N-acetyltransferase
type 2 (NAT2).

UM: ultra-rapid metabolizer; RA: rapid acetylator;

EM: extensive metabolizer; IA: intermediate

acetylator; IM: intermediate metabolizer; SA: slow

acetylator; PM: poor metabolizer; AUC: area under the curve;

Question 29

Targeted Drug Development = 8

Answer 29

1 * Some diseases are due to specific mutations in a gene.

2. Can be many other mutations that have different effects.

3 * The protein may not work correctly, or not be made at all.

4 * Drugs can be created based on how the mutation affects the protein. The drug only works for the specific mutation,
eg ‘Cystic Fibrosis’

5 * Ivacaftor, trialled in the 4% of patients carrying G551D mutation, led to a 55% reduction in the pulmonary exacerbation rate.

6 * Combination of elexacaftor, tezacaftor and ivacaftor, used in patients with at least one copy of Phe508del, reduced the
exacerbation rate by 63%.

• CVD
  7 * Gain-of-function mutations in the PCSK9 gene lead to high LDL-C levels and premature CVD & vise versa.

8 * Anti-PCSK-9 antibodies, reduce LDL-C by 54% when given fortnightly and CVD events.

Question 30

Effects of variation in CYP2D6 metabolism with clinical response to two therapeutic agent

Answer 30

CODEINE AND NORTRIPTYLINE

TABLE/DIAGRAM ON SLIDE 30

Question 31

Metabolism of warfarin

Answer 31

DIAGRAM ON SLIDE 31

Question 32

Warfarin = 5

Answer 32

1 * Warfarin is the most common oral anticoagulant in the world

2 * Therapeutic range: INR 2-3 (2.5-3.5 for prosthetic heart valves)

3 * INR <2: risk of thromboembolic event

4 * INR >3: risk of bleeding complications

5 * 30 to 35% of the variability in warfarin response is due to genetic variants, which is more than clinical variables alone.

Question 33

Warfarin.. UNDERSTANDING IN DETAIL

= 4

Answer 33

1 * Metabolism of warfarin is dependent on
CYP2C9 and CYP2C9 LOF alleles (CYP2C92 and CYP2C93) have been associated with over-anticoagulation and an increased risk of bleeds.

2 * Pharmacogenetic algorithm; age, sex, weight, height, self-declared race, use of amiodarone, use of enzyme inducers, VKORC1 genotypes, and predicted phenotypes according to CYP2C9 polymorphisms

3 * Three recent RTCs have produces conflicting results. Possibly due to different populations groups.

4 * Warfarin use has dropped over the last 10 years from 77 to 12% in specific indications like atrial fibrillation.

Question 34

Jason 4-year-old boy - TPMT

= 10

Answer 34

1 * Presented with 2 weeks of extensive bruising & back pain.

2 * Pale, tachycardic, no fever, ↓ Hb, ↑ WCC, ↓ platelets

3 * Blood film → ↑ lymphocytes → acute lymphocytic leukaemia, (bone marrow)

4 * Responded well to chemotherapy

5 * Maintenance dose of 6-mercaptopurine & MTX

6 * Prior to treatment blood taken for TPMT – level OK

7 * Severe neutropenic sepsis – treated with antibiotics

8 * Had a blood transfusion for anaemia – gave false TPMT level

9 * TPMT genotype – homozygous for TPMT*3A

10 * Reduced dose of 6MP and remained disease free

Question 35

Metabolism of 6-Mercaptopurine

Answer 35

FLOWCHART SLIDE 35

Question 36

TPMT Activity & Personalized Dosage

Answer 36

DIAGRAM TO GRAPH ..SLIDE 36

Question 37

Peripheral blood leukocyte count (WBC) and azathioprine
(AZA) dose in TPMT deficient heart transplant recipients
Lancet 341:436, Feb 13, 1993

Answer 37

DIAGRAM/GRAPH ON SLIDE 37

Question 38

WHAT IS TAMOXIFEN = 2

Answer 38

1. Tamoxifen known as the most important adjuvant endocrine treatment in patients with estrogen receptor (ER) positive breast cancer.
2. It inhibits tumor growth and promotes apoptosis in ER-positive tumors, resulting in a reduced risk of recurrence and death from breast cancer.

Question 39

Tamoxifen controversy: 4

Answer 39

1. Between 2018 and 2021, 2 studies showed a relation between CYP2D6 genotype and breast cancer recurrence as well as breast cancer-specific mortality after tamoxifen treatment.

2 * Four studies reported no association with clinical outcome in tamoxifen treatment.

3 * The controversy regarding the association of CYP2D6 genotype and tamoxifen- related clinical outcome continues.

4 * This controversy will exist until large RCTs are performed.

Question 40

UNDERSTANDING Drug Safety…4

Answer 40

1. • ADRs can be divided into Type A and Type B reactions, both can be affected by genetic factors.
2. • A great deal of progress has been made in identifying genetic predisposing factors for ADRs over the past 20 years.
3. • Type A, ADRs are an augmentation of the pharmacological actions of a drug and show typical dose dependency, with a reduction in dose leading to improvement in ADRs.
4. • The examples given in the previous slides on dose are illustrations of Type A ADRs.

Question 41

Type B ADRs = 5

Answer 41

1 * Type B ADRs cannot be easily explained based on the pharmacology of the drug,
2 * There is no clear dose dependency and drug discontinuation stops the ADR.
3 * Many of these ADRs are immune mediated.
4 * HLA alleles predispose to these reactions.

5 * Such as associations with flucloxacillin hepatitis and carbamazepine hypersensitivity.

Question 42

Pharmacogenomics in clinical practice = 3

Answer 42

1. Implementation of pharmacogenomics into clinical practice has been slow, and pharmacogenomic testing has been restricted to certain specialist centres.

2 * Due to a perceived lack of clinical evidence, inability to access genotyping tests, lack of clarity on costeffectiveness, lack of knowledge on how to interpret
pharmacogenomic tests and the actions to take when a patient has a variant allele, education, funding, worries about disruption to the normal clinical pathways and concerns over confidentiality issues.

3 * Evidence needed on polypharmacy (≥5 concomitant drugs) and multimorbidity in the elderly.

Question 43

Diversity…6

Answer 43

1. Genomic studies are highly Eurocentric and to lack ethnic diversity
   …2. exacerbates already-existing health in equalities.
2. 97% of GWAS data participants are of European ancestry with only 2.2% Asian,
   0.02% African.
3. Lack of diversity is a problem in pharmacogenomic studies eg
   ….5. * Most warfarin dosing algorithms have been based on CYP2C92 and CYP2C93 SNPs, which are prevalent in European populations but largely absent in African-ancestry populations. Studies that have evaluated the role of CYP2C9 SNPs that are more prevalent in African populations are scant.
4. Lack of consideration of ethnic diversity is also seen in drug labels.

Question 44

Drug discovery and drug safety = 5

Answer 44

1. In oncology, MPS has identified driver mutations in somatic cancer genomes.
   Leading to the development of drugs that target these mutations.
   
   2. • Eg Vemurafenib, inhibits BRAF and crizotinib, inhibits ALK.
2. • Most successful drug classes developed are tyrosine kinase inhibitors, eg imatinib, which targets the BCR–ABL1 fusion gene in CML. Transforming
     prognosis of CML be similar to age matched individuals.
3. • This is not the case with most solid tumours. Initially there is a dramatic response that relapses due to the development of new mutations.
4. • The challenge - identify best combination of therapies targeting the aberrant pathway(s) to lead to increased overall survival.

Question 45

Conclusions:

Answer 45

1 * Genetic variation contributes to inter-individual differences in drug response

2 * Through personalized or precision medicine, pharmacogenomics is expected to give:
3 * Better, safer drugs the first time
4 * More accurate methods of determining appropriate drug dosages

5 * Implementation into clinical practice has been slow.

6 * Genomics data will help in the early stages of drug development, identifying hazards that might not be detectable otherwise.

7 * Multimodal algorithms using clinical (eg, age, sex & BMI) + genetic factors, and other -omic biomarkers, are needed.

8 * HOWEVER, MANY CASES ARE NOT YET READY FOR PRIME TIME!!! But with research, pharmacogenomics will lead to improved human health.