PHARMACOGENOMICS IN

OTHER DRUG THERAPY

Dr Dzul Azri Mohamed Noor
OBJECTIVES

• Identify gene function in drug therapy

• Explain the effect of gene polymorphism in drug therapy
• Give recommendation based on the available
pharmacogenomic data
EFAVIRENZ & CYP2B6
 EFAVIRENZ
• Potent inhibitor of HIV-1 replication
• MOA: inhibit reverse transcriptase  prevent formation of viral
double strand DNA  inhibit replication
• In Malaysia  part of first line and alternative therapy
- Tenofovir + Emtricitabine + Efavirenz
- Zidovudine + Lamivudine + Efavirenz
- Abacavir + Lamivudine + Efavirenz
• In US  use has been replaced with HIV-I integrase inhibitor
• It can be used in pregnant patient or desiring pregnancy
• It can also be used in patient who are also taking rifampicin-
based tuberculosis therapy
Problem?

• Narrow therapeutic index (therapeutic range: 1- 4 ug/mL)

• Large interindividual variability
• Prone for toxicity – CNS toxicity, hepatic injury, QT
prolongation
• Have more drug-drug interaction
• Autoinduction?
CYP2B6 & EFAVIRENZ
 CYP2B6 polymorphism
• ~28 alleles, 50 haplotype and > 100 SNPs

64 516 593 777 785 983 1132 1459 Function

*2 C>T Normal
*3 C>A uncertain
*4 A>G increased
*5 C>T normal
*6 G>T A>G Decreased
*9 G>T Reduced
*18 T>C Null
*27 T>C uncertain
*28 C>T null
PREVALENCE

Malay Chinese Indian

CYP2B6*1 60.7% 67.8% 61.7%

CYP2B6*2 0.8% 1.3% 4.1%

CYP2B6*4 7.6% 6.4% 9.9%

CYP2B6*6 25.4% 13.9% 18.5%

CYP2B6*9 4.6% 10.2% 5.9%

CYP2B6*27 0.8% 0.0% 0.0%

CLINICAL IMPLICATIONS

• Considerable autoinduction observed in CYP2B6*1 and

*1/*6 but little or no autoinduction in *6/*6
• CYP2B6 PM (especially those with 516 G>T and/or 983 T>C)
associated with decreased EFV clearance and increased in
toxicity
• CYP2B6 RM and UM may experience slightly lower dose
adjusted trough concentration but the effect observed are
modest
 RECOMMENDATION

* Also applies for children >3 years and >40kg

 • Children less 3 years
Metaboliser phenotype Weight (kg) Dosage

Poor metabolizer (516 TT) 5 – less than 7 50 mg

7 – less than 14 100 mg

14 – less than 17 150 mg

More than 17 150 mg

Normal & Intermediate 5 – less than 7 300 mg

metabolizer (516 GG and 516
GT)
7 - less than 14 400 mg

14 – less than 17 500 mg

More than 17 600 mg

* Also applies to 983 T>C genotype

Important consideration

• For those currently on combination pills, dosing changes

may cause patient to take more pills  increase pill burden
• In those patient that concurrently taking drug that have
significant effect on efavirenz plasma concentration  may
not require dosing reduction based on genotyping data
• Therapeutic drug monitoring (if available) can be used to
guide dosing adjustment
TACROLIMUS & CYP3A5
TACROLIMUS

• Indicated for anti-rejection therapy in

patient undergoing solid organ
transplantation
• It binds to its cytoplasmic protein
receptor forming complexes that will
bind to calcineurin
• This will prevent dephosphorylation
and nuclear translocation of the
activated T cell  inhibit activation of
IL-2 production and T lymphocyte
activation
Problems?

 highpatient variability
 narrow therapeutic index
 undergoes first-pass metabolism
 patient at risk of rejection if subtherapeutic
 patient at risk of toxicity such as nephrotoxicity,
neurotoxicity, hypertension and hyperglycaemia if
supratherapeutics
 TDM is conducted but cannot be used to
determine initial dosing
TACROLIMUS PK
PATHWAY
CYP3A5 polymorphism & enzyme function
Allele Nucleotide Effect on protein Enyzme function
variation
*1 - - Normal

*2 27289 G>T T398N Unknown

*3 6986 C>T Splicing defect No function

*4 14665 T>C Q200R Unknown

*5 12952 A>G Splicing defect Unknown

*6 14690 C>T Splicing defect No function

*7 27131_27132insA 346 Frameshift No function

*8 3699G>A R28C Unknown

*9 19386 C>T A337T Unknown

6986 T>C Splicing defect
CYP3A5 genotype and phenotype
Clinical Implication

• CYP3A5 non-expressor was found to have higher dose-

adjusted trough concentration vs CYP3A5 expressor
• Using genotyping-guided dosage, more patient achieve
target serum concentration earlier but no difference in
terms of survival, rejection and toxicity at 3 months.
• Meta-analysis study suggest that CYP3A5 expressor are at
higher risk of rejection and have lower dose-adjusted trough
concentration 1-year post transplantation
 Recommendation

Other factors such as drug-drug interaction, patient clinical factor

that can also affect tacrolimus PK need to be taken into
consideration
HEPATITIS C THERAPY & IFNL3, ITPA
HEPATITIS C

• Hepatitis C affects 3% of world population (~ 170mil)

• Prevalence high in African and Asian with more than
5%
• 70-80% patient are asymptomatic clinically diagnosed
HepC is low
• It have tendency to persist and develop into chronic
hepatitis, hepatic carcinoma and cirrhosis which require
liver transplant
LIFE CYCLE OF HEP C VIRUS
HepC THERAPY

• Interferon monotx  ribavirin + pegylated interferon.

• Success of therapy are defined by:
a) Sustained virological response
- undetectable HCV RNA in serum 6 month after
treatment completion
b) Rapid virological response
- lack of detection ofHCV RNA after 4 weeks of
treatment
• Only less than 50% will achieve desired SVR
• Only HepC genotype 2 and 3 are best predictor for
succesful outcome
Predictors of Hepatitis C therapy poor
outcome
• Age
• Male
• High viral load
• Co-infection with HIV
• Poor adherence
• Insulin resistance
• Liver fibrosis
• High level of AST and/or ALT (> 3 times UNL)
• HCV Genotype 1
PEGYLATED INTERFERON & IFNL3
PEGINTERFERON ALPHA
• Has a potent antiviral activity by inducing IFN-stimulated genes
• Proteins transcribed from these genes will inhibit various stages of
viral replication
• Also interact with adaptive and innate immune response
• Promote T- helper cell differentiation which will lead to increase
production of interleukin-2 and IFN-gamma
• Dose Peginterferon alpha 2a
- SC 180 mcg/weekly (can decrease to 135 mcg/weekly in
those patient who cannot tolerate 180 mcg dose)
• Dose Peginterferon alpha 2b
- SC 1.5 mcg/kg/weekly
IL28B aka IFNL3
• Members of type III IFN-λ family
• recognized by heterodimer of IL-10 and IFN-λ receptor
which is widely expressed in epithelial tissue and in the
liver
• Activation of these receptor - activate JAK-STAT
pathway  activate set of IFN-stimulated genes 
antiviral and antiproliferative property
IFNL3 polymorphism

• 2 major SNPs : rs 12979860 and rs8099917

• Rs 12979860
- located 3kb upstream of IFNL3 promoter region
- more prevalent in European, USA and part of Asian population
- change from Cytosine (C) to Thymidine (T)
• Rs 8099917
- located in between IFNL2 and IFNL3
- 8kb downstream IFNL3 and 16kb upstream of IFNL2
- more prevalent in part of Asian population
- change from Thymidine (T) to Guanosine (G)
• In individual with rs 12979860 CC genotype, low
expression of IFNL and ISGs are observed  lead to
high viral load and increase sensitivity to IFN therapy
• In individual with CT or TT genotype, higher ISGs
detected  activate negative feedback loop to
inactivate JAK-STAT pathway unable to eliminate virus
and unable to stimulate powerful ISGs from IFN therapy
• This polymorphism association with therapeutic
response has been replicated in HepC genotype 1 and 4
but less in genotype 2 and 3.
• Association between therapy response with rs 8099917
is not conclusive.
RIBAVIRIN & ITPA
Ribavirin

• Has no benefit if given alone  usually given in combination with

Peginterferon alpha or DAAs
• Dose of ribavirin:
- minimum effective dose: 10.6 mg/kg/day
- In patient <75kg body weight : 1000 mg/day (400mg OM,
600mg ON)
- In patient >75kg body weight : 1200 mg/day (600mg OM,
600mg ON)
Mechanism of Action

• Postulated mechanism of action:

1) Binding of ribavirin triphosphate (RTP) to the nucleotide
binding site of RNA polymerase  reduced viral replication/
defective virions productions
2) competitively inhibit Inosine Monophosphate
Dehydrogenase (IMPDH)  inhibit synthesis of guanosine
triphosphate (GTP) needed for RNA replication
3) act as a mutagen  RTP incorporate into nucleotide 
promote viral mutation
4) immunomodulation  inhibit antibody production and
humoral response
Ribavirin-induced anemia

• 50% of patients receiving ribavirin will experience decrease

of >3 mg/dL of Hb
• May require dose reduction (usually within the first 12
weeks therapy)
Factors associated with ribavirin-induced
anemia
• Age
• Female
• Baseline platelet level (<150,000 platelets/mm3)
• Baseline Hb level
• Dose and plasma concentration of ribavirin (dose >12mg/kg)
• Creatine > 1.5mg/dL; creatinine clearance <80ml/min
ITPA variants

• Located in chromosome 20
• 2 major SNPs
• Rs 1127354 – change from C to A
• Rs 6051702 – change from A to C
• Both variants leads to decrease in ITPA function
• ITPase deficiency (in homozygous/heterozygous variants) will
lead to accumulation of ITP in the erythrocytes and
competes with ribavirin  avoidance of ATP reduction and
oxidative stress damage.
 Inositol ITPase Inositol
triphosphate diphosphate ITPase
(ITP) (IDP)
Inositol
monophosphate
(IMP)
PO4 PO4

Ribavirin
monophosphate Ribavirin
diphosphate
Ribavirin
triphosphate
Ribavirin
erythrocytes
plasma
• Accumulation of Ribavirin Triphosphate in erythrocyte
• Leads to reduce ATP level and glutathione concentration
• Decrease in protection from oxidative stress damage of RBC membrane
Management of ribavirin-induced anemia
DIRECT ANTIVIRAL AGENT & NS’s
POLYMORPHISM
TRIPLE THERAPY
• Currently new class of drug has been introduced for
HepC therapy called direct-acting antiviral (DAA) drug
• Eg: boceprevir, telaprevir
• Class of protease inhibitor that inhibit NS3/4 and NS5
protease required for viral replication
• Side effects: taste disturbances, LOA, anemia, fever,
chills
IMPACT OF TRIPLE THERAPY

Boceprevir Telaprevir

SVR Before SVR SVR SVR

After Before After
CC 78% *80% 64% 90%

CT 27% 59% 25% 71%

TT 28% 71% 23% 73%

CLINICAL IMPLICATIONS

• In those patient with HepC and with IFNL3 CT/TT

genotype, DAAs introduction may help to achieve SVR
desired
• However, cost and adverse effects of DAAs need to be
considered as well
• Emergence of resistance to DAA also need to be
considered
 NS3, NS4, NS5

• Non-structural protein
• Contains protease enzyme crucial for structural cleaving and
viral replication
NS3 polymorphisms
 CLINICAL IMPLICATIONS

• Presence of one mutation usually confer low resistance - eg in

telaprevir, V36M or T54A alone

• Higher number of mutation  higher resistance

- eg in telaprevir, V36M + A156T combination

• Believed to affect the binding of the protease inhibitor to the

enzyme site

• Individuals with this variants usually showed virologic

breakthrough or incomplete virologic response
Mrs HRT, a 60-year-old lady (weight 55 kg, height 160cm) was diagnosed twelve
weeks ago, with Hepatitis C genotype 4 and was eventually started on SC
Peginterferon Alpha 2-b and T. Ribavirin. This morning, she came to the Hepatology
Clinic for her 12-weeks follow-up. She looked pale and complained of constant
tiredness.
Social History: Retired teacher and currently living with her husband.
Past Medical History: Hypertension X 5 years
Current Medication: 1) Atenolol 100 mg OD
2) Perindopril 4 mg OD
3) Peginterferon Alpha 2-b 80 µg/week
4) Ribavirin 600 mg BD
Vital sign: BP 120/70 mmHg
Liver Biopsy: Some inflammation noted
Genetic Test: 1) IFNL3 rs12979860 : CT genotype
2) ITPA rs1127354 : CC genotype
Lab Values: 1) Serum creatinine : 75 µmol/L
2) Hemoglobin : 8 g/dL
3) AST : 200 U/L
4) ALT : 180 U/L
5) Viral load : 300,000 copies (target for week 12 is less than
100,000)
Discuss the relevance of the genetic tests performed in this patient. Based on the
information given above, give your assessment and recommendation pertaining to this
patient’s Hepatitis C therapy (15 marks)