Using genetics for drug prescribing: will it happen?

• Hype and hope• Relating DNA polymorphisms to variable

human physiology and drug responses: examples

• A view to the future

Take-home messages

• Diversity among human genomes can explain variability in human physiology, and its response to the environment.

• Pharmacogenetic information is now affecting drug development, and will enter clinical practice (a personal opinion).

• “Proving” genotype-phenotype relations requires collaborations among clinical investigators, basic biologists, information managers and statisticians, systems biologists, technologists, ethicists…

Case presentations

• A 68 year old man presents with a large anterior myocardial infarction, and has a VF arrest in the Emergency Room.

• Grade 4 diarrhea occurs in a 65 year old man receiving irinotecan for colon cancer.

• A 70 year old woman starts coumadin 5 mg/day for atrial fibrillation. One week later, her INR is 12.

• A 78 year man develops a QT interval of 700 msec and Torsades de Pointes a day after starting dofetilide.

• Life-threatening sepsis arises in a 9-year-old girl after 6-MP therapy for ALL.

“idiosyncratic” drug response

understand the biology

identify causative DNA variants

“idiosyncratic” response now predictable and

avoidable

Pharmacogenetics: Large single gene effects

cytotoxic

6-TGN concentrations

6-thioguanines (6-TGNs)

LL*3A/*3A(mutant)

HL*1/*3A

(heterozygote)

HH*1/*1

(wild-type)

1/300

*3A/*3A

*1/*3A *1/*1

“single nucleotide polymorphisms” (SNPs)

azathioprine

An “idiosyncratic” drug response

AR, 78 year old man• Chronic heart disease with history of bypass

surgery and valve replacement• Cardiac arrest 4 days after major abdominal

surgery; placed on dofetilide (a potent and highly selective blocker of a potassium current called IKr) to prevent recurrence. 2 days later:

Torsades de Pointes• Also characteristic of the

congenital long QT syndrome• Drug-induced QT

prolongation and torsades is the single commonest cause for drug withdrawal or relabeling in the past decade.

AR: An “idiosyncratic” drug response

• DNA variant resulting in R583C identified in KCNQ1, a gene controlling QT duration and mutated in a common form of the congenital Long QT Syndrome.

• R583C alters protein function in vitro: reduces IKs.

• Absent in >1000 controls “mutation”. This man has the congenital long QT syndrome, that remained asymptomatic for 78 years.

How did AR avoid arrhythmias for

2,000,000,000 heart beats? The concept of reduced repolarization

reserve• Redundancy (“reserve”) in cardiac repolarization allowed him to maintain a normal QT until other lesions (heart disease, dofetilide) were superimposed.

Patient 1 Patient 2

Same QT-prolonging drug

Drug ATPMT

inactive metabolite

Drug BCYP2C9

inactive metabolite

Drug C renal excretion

Drug DCYP3A4

inactive metabolite

transport by drug efflux pump

Redundancy in physiologic systems: “high risk pharmacokinetics”

6-MP

warfarin

digoxin

terfenadine (Seldane)

inhibitor drug

inhibitor drug

low margin between doses needed for efficacy and doses producing toxicity (therapeutic index)

a single pathway for drug elimination that is genetically variable or subject to inhibition by interacting drugs

PLUS

Drug ATPMT

inactive metabolite

Drug BCYP2C9

inactive metabolite

Drug C renal excretion

Drug DCYP3A4

inactive metabolite

Drug ECYP2C9

inactive metabolite

transport by drug efflux pump

Redundancy in physiologic systems: “high risk pharmacokinetics”

transporterrenal excretion

CYP3A4inactive metabolite

TPMTinactive metabolite

6-MP

warfarin

digoxin

terfenadine (Seldane)

inhibitor drug

inhibitor drug

Drug E will be an especially attractive agent if it also has a

high therapeutic index

Redundancy in physiologic systems as a protective

mechanism• arrhythmia susceptibility• susceptibility to adverse drug reactions

and interactions • “multi-hit” requirement for

carcinogenesis

“idiosyncratic” drug response

understand the biology

identify causative DNA variants

“idiosyncratic” response now

predictable and avoidable

Pharmacogenetics: Large single gene

effects

unusually variable drug response

identify associated DNA polymorphisms

• adjust dose or change drugs

• discover new biology and new drug targets

Pharmacogenomics:Discovering new

biology

1950 20201980

PHARMACOGENETICS

PHARMACOGENOMICS

Single gene Small number of genes

Complex biologic pathway

Large single variant effect

Smaller effect; multiple variants

Whole genome

PHARMACOGENOMICS(large populations)

Single gene Small number of genes

Complex biologic pathway

Large single variant effect

Smaller effect; multiple variants

Whole genome

• Rare coding region variants (polymorphisms or mutations)

• Commoner coding and regulatory variants• Detectible effects of polymorphisms in >1 gene• Pathway analysis and whole genome approaches

PHARMACOGENOMICS

PHARMACOGENETICS(snlall groups)

Variants in the warfarin target

25 = 32 possible combinations

Haplotype A: CCGATCTCTGHaplotype B: TCGGTCCGCG

Variants in the warfarin target – 2

Single Nucleotide Polymorphisms (SNPs) in the VKORC1 promoter

CG TCCT

AG

TCCGTCGReider et al.NEJM 2005

Variants in both drug metabolism (CYP2C9) and drug target (VKORC1)

genes affect warfarin dose requirement

• 554 patients on chronic warfarin; early dropouts not included

• CYP2C9 genotype predicts 9% of dosage variability

• VKORC1 haplotype accounts for 23%• Illustrates

• Multi-gene effects can be detected• Understanding mechanisms in rare syndromes can

inform the study of common biologic problems • Increasing importance of haplotypes

Reider et al., NEJM 2005

A 68 year old man presents with a large MI, and has a VF arrest in the

ERPatient 1 Patient 2

Same acute MI

?“reduced antifibrillatory reserve”

Reduced cardiac sodium current predisposes to serious arrhythmias

Hypothesis: Variable sodium channel expression is a candidate mechanism for variability in basal conduction velocity, and in susceptibility to slowed conduction with exogenous stressors (drugs, myocardial ischemia). Slow conduction predisposes to sudden death due to VF.

Loss of function mutations in the sodium channel gene cause a

distinctive ECG and ↑↑risk of VF

Brugada syndrome

Sodium channel blocking drugs increase mortality

Days from randomization

% s

urvi

val

encainide orflecainide (n=730)

Placebo (n=725)

6 sodium channel promoter variants, found only in Asians

intron 1promoter

0-1000-2000 bp 1000

T-1

41

8C

T-1

06

2C

T-8

47

G

-83

5in

sGC

G-3

54

C

C2

87

T

exon 1 (non-coding)

intron 1promoter

-1000-2000 bp 1000-1000-2000 bp 1000

T-1

41

8C

T-1

06

2C

T-8

47

G

-83

5in

sGC

G-3

54

C

C2

87

T

exon 1 (non-coding)

exon 1 (non-coding)

6 variants: 26 = 64 possible combinations

6 sodium channel promoter variants, found only in Asians, in very tight linkage disequilibrium

intron 1promoter

0-1000-2000 bp 1000

T-1

41

8C

T-1

06

2C

T-8

47

G

-83

5in

sGC

G-3

54

C

C2

87

T

exon 1 (non-coding)

C C G ins C TC C G ins C T

T T T --- G CT T T --- G C 75.5%Haplotype A

24%Haplotype B

C T T --- C CC T T --- C C 0.5%Haplotype C

Frequency*

intron 1promoter

-1000-2000 bp 1000-1000-2000 bp 1000

T-1

41

8C

T-1

06

2C

T-8

47

G

-83

5in

sGC

G-3

54

C

C2

87

T

exon 1 (non-coding)

exon 1 (non-coding)

C C G ins C TC C G ins C T

T T T --- G CT 75.5%75.5%

24%24%

C T T --- C CC T T --- C CC T T --- C CC T T --- C C

Frequency

Haplotype B ↓↓promoter activity

0

3

6

9

12

15

18

Wild Type 6-changehaplotype

Wild Type 6-changehaplotype

Fo

ld a

ctiv

ity

CHO cells Cardiomyocytes

n=13, p=0.04 n=9, p=0.006

A B A B

80

100

120

140

AA AB BB

AA AB BB80

100

120

140

normals

71 probands with Brugada Syndrome

QR

S d

urat

ion

(mse

c)

60 34 8

45 21 5

Ventricular conduction is slower with the reduction of function

allele

QRS duration (msec)

Genotype-dependent incremental conduction slowing by sodium channel

blockers

AA AB BB

200

80

120

160

200+20

msec+17

msec+29

msec

Who has the longest QRS duration?Brugada Syndrome mutation + drug exposure + BB haplotype

“Genes load the gun, environment pulls the trigger”

“idiosyncratic” response now

predictable and avoidable

“idiosyncratic” drug response

understand the biology

identify causative DNA variants

Pharmacogenetics: Large single gene

effects

1950

unusually variable drug response

identify associated DNA polymorphisms

• adjust dose or change drugs

• discover new biology and new drug targets

Pharmacogenomics:Discovering new

biology

20201980 2050

Routine patient visit

identify or look up DNA variants in

that patient

adjust dose or change drugs

The futureMoving to widespread

practice

NatureOct. 5, 2005

Genotypes:CYP2D6: *4/*4CYP2C9: wt/*2NAT: slowTPMT: wt/wtUGT1A1: 6/6ACE: IDCETP: BBBRCA1: negative1 AR: S49/G3892 AR: R16/G27KCNQ1: R583CHERG: wt/wtKCNE1: wt/wtKCNE2: wt/wtApo: 2/3ABCA1: wt/wt

Genotypes:CYP2D6: *4/*4CYP2C9: wt/*2NAT: slowTPMT: wt/wtUGT1A1: 6/6ACE: IDCETP: BBBRCA1: negative1 AR: S49/G3892 AR: R16/G27KCNQ1: R583CHERG: wt/wtKCNE1: wt/wtKCNE2: wt/wtApo: 2/3ABCA1: wt/wt