Transcript Immune Functions of B Cells

Expanding the Research Domains of
Rheumatoid Arthritis Clinical Databases:
The Promise of Pharmacogenetics
Jeffrey Greenberg, MD, MPH
NYU Hospital for Joint Diseases
New York University School of Medicine
December 2006
Outline
• Why Pharmacogenetics
• Case Study: TNF Antagonists
• Issues of Study Design and Analysis
• Future Directions
How Variable is the Human Genome?
Size:
3 billion base pairs of DNA
Content:
39,114 genes
Variation: 1% of base pairs are polymorphic
(i.e. 30 million base pairs)
Pharmacogenetics and “Personalized” Medicine
Marsh, S. and McLeod HL. Hum. Mol. Genet. 2006 15:R89-93.
Why Is Pharmacogenetics Important?
“ Let us […] imagine the despair of the mouse experimentalist
when we suggest that he or she randomly allocate treatments to
animals of different genetic backgrounds and immunized with
different disease triggers.”
….[This is essentially how we treat RA in 2006]
Klareskog, L. Nature Clinical Practice Rheumatology (2006) 2, 517.
Arthritis Clinical Databases and Pharmacogenetics
• 6 biologic agents have been FDA approved for RA.
• Only 1 RCT (Early RA Trial) has published pharmacogenetic
studies.
• Arthritis clinical databases may represent the ONLY practical
approach to advancing the field of pharmacogenetics.
• As more biologic agents are approved, biomarkers that can
predict response will be increasingly important.
GENETIC
POLYMORPHISMS
Pharmacokinetic
•Transporters
•Plasma protein binding
•Metabolism
Pharmacodynamic
•Receptors
•Ion channels
•Enzymes
•Immune molecules
Potential Consequences of Different
Drug Metabolism and Drug Receptor Genotypes
Evans WE and Relling MV. Science 286:487-491, 1999.
Polymorphic Drug Metabolizing Enzymes
ALDH2
Acetaldehyde dehydrogenase
CYP1A2
Caffeine, acetaminophen
demethylation
CYP2C9
Warfarin hydroxylation
CYP2C19
Mephenytoin hydroxylation
CYP2D6
Debrisoquine hydroxylation
UGT2
Ibuprofen and naproxen
glucuronidation
Isoniazide acetylation
NAT 2
Proof of Principle: Warfarin and Cytochrome P450 Cyp2C9 Alleles
Dervieux T et al, Mutat Res 2005:180-194.
Methylene Tetrahydrofolate Reductase (MTHFR)
Dervieux T et al, Mutat Res 2005:180-194.
Effect of the MTHFR C677T Polymorphism on
Methotrexate Toxicity in RA Patients
Urano W et al. Pharmacogenetics 2002: 12(3): 183-190
Pharmacogenetics of TNF Antagonists
for the Treatment of RA
Case Study
How Can We Predict Response (or Failure) of
Methotrexate or TNF Antagonists in RA Patients?
ACR20 Response
ACR50 Response
90
80
ACR70 Response
85
76
75
69
70
60
50
48
43
43
40
30
24
19
20
10
0
MTX
Etanercept
Etanercept + MTX
Source: Klareskog L et al. Lancet 2004; 363: 675-81.
Comparison of RA Studies
% Achieving ACR Response
MTX + TNF Antagonist in Established Disease
80
70
ACR20 Drug+MTX
60
ACR20 PBO+MTX
50
ACR50 Drug+MTX
40
30
ACR50 PBO+MTX
20
ACR70 Drug+MTX
10
ACR70 PBO+MTX
0
Inflix-10m
g/kg/q8w
Infliximab
D2E7 40 q2w
Adalimumab
Etanercept 25 m g
Etanercept
10 mg/kg/q4w
40 q2w
25 biw
Lipsky
Weinblatt
Weinblatt
NEJM 2000
A & R 2003
NEJM1999
biw
Can We Predict Response to Abatacept, but not anti-TNF?
Abatacept in TNF Inadequate Responders (ATTAIN)
ACR20
ACR50
ACR70
60
% of patients
50.4
40
19.5
20.2
20
10.2
3.8
1.5
0
Placebo
Genovese et al. N Engl J Med. 2005;353:1114.
Abatacept 10mg/kg q 4w
Can We Predict Risk of Serious Infection for RA Patients
Treated with TNF Antagonists?
Meta-analysis of Risk of Serious Infection
from Adalimumab and Infliximab RCTs
Bongartz, T. et al. JAMA 2006;295:2275-2285.
Effect of HLA-DRB1 on ACR 50 Response
Etanercept vs Methotrexate in the Early RA Etanercept Trial
80
70
60
50
40
2 copies SE
30
1 copy SE
20
0 copy SE
10
0
Methotrexate
Etanercept
10 mg
Etanercept
25 mg
N=151 in the Etanercept 25 mg arm; OR (95% CI) for effect of SE = 4.3 (1.8 – 10.3)
Criswell LA et al. Arthritis Rheum. 2004; 50(9): 2750-2756.
HLA-DRB1 and Response to TNF Antagonists
Summary of Published Literature
Study
Drug
Outcome
Criswell et al. (2004)
Etanercept
Positive association
Kang et al (2005)
Etanercept
No association
Marotte et al (2006)
Infliximab
No association
Martinez et al (2004)
Infliximab
No association
Miceli-Richard et al (2006)
Adalimumab
No association
Effect of the TNF –308 G/A Polymorphism
on Clinical Response to Infliximab (n=53)
EULAR Good Response (Decrease of DAS-28 by 1.2)
100
80
60
80.5
71.7
40
41.7
20
0
Overall
AA and A/G
genotypes
G/G genotype
P=0.0086
Mugnier B. Arthritis Rheum. 2003; 48(7): 1849-1852
TNF Polymorphisms and Response to TNF Antagonists
Summary of Published Literature
Study
Drug
Outcome
Mugnier et al. (2003)
INF (N=59)
Positive association
Fonseca et al (2005)
INF (N=22)
Positive association
Cuchacovich et al (2004)
INF (N=22)
No association
Martinez et al (2004)
INF (N=78)
No association
Padyukov et al (2003)
ETA (N=123)
Positive association*
Criswell et al (2004)
ETA (N=151)
Positive association†
* Combination of TNF and IL-10 SNPs.
** Extended Haplotype that included TNF/LTA and HLA-DRB1region
Genetic Risk Factors are Stronger Predictors of
Developing Infections (UTIs) than Clinical Risk Factors
Etanercept vs Methotrexate in the Early RA Etanercept Trial
Odds Ratio
95% CI
Age >65
1.49
0.63 – 3.52
Elevated ESR
1.26
0.62 – 2.56
RF positive
1.32
0.43 – 4.06
Steroid use
1.15
0.58 – 2.27
ETA vs MTX
1.05
0.58 – 1.91
TNF –238 A
2.45
0.99 – 6.13
LTA +365 C
1.70
1.04 – 2.77
FcGR3a F
1.76
1.01 – 3.10
Hughes LB et al.
Genes and Immunity
2004; 5: 641-647.
Study Design and Analysis Issues
in Pharmacogenetics
SNP Selection for Pharmacogenetics
• “Functional” SNP of candidate gene
• High density genotyping of coding and non-coding SNPs of a
specific candidate gene
• SNP(s) of multiple genes in a metabolic pathway
• Whole genome scan
High Density Genotyping Project across the Whole Genome:
Insights into the Correlation Structure of Alleles
Insights from the HapMap Project and Related Studies
Allele Frequencies of Drug Metabolizing Enzymes and
Other Genes Vary across Different Population Groups
CYP1A1
GSTM1
CYP2C19
DIA4
NAT2
CYP2D6
A. Bantu, Ethiopian,
Afro-Caribbean
B. Norwegians,
Ashkenazi Jews,
Armenians
C. Chinese,
New Guineans
From Wilson, et al. Nature Genet
29:265-269, 2001
Relative power (%)
Efficiency and power
tag SNPs
random
SNPs
~300,000 tag SNPs
needed to cover common
variation in whole genome
in CEU
Average marker density (per kb)
P.I.W. de Bakker et al. (2005) Nat Genet Advance Online Publication 23 Oct 2005
Can We “Tag” Candidate Inflammatory Gene SNPs
Hypothesized to Modulate TNF Antagonist Response?
Gene
Common
SNPs
genotyped
Related
Haplotypes
Haplotype
Tag SNPs
Haplotype
Coverage
by Tag
SNPs
TNF-α
9
4
4
87%
IL-1β
20
4
3
100%
IL-6
26
4
3
99%
CTLA-4
11
12
5
100%
73
30
15
--
Future Directions
Example of a diagnostic DNA microarray of polymorphisms of candidate
genes to predict response and risk of toxicity (e.g. chemotherapeutic agent)
Evans WE, Relling MV. Pharmacogenomics: Translating functional genomics into rational therapeutics.
Science 286:487-491, 1999.
Pharmacogenomic Studies May Be More Relevant to Predicting
Response for Pleiotropic Drugs such as TNF Antagonists
Roden, D. M. et. al. Ann Intern Med 2006;145:749-757
Gene Profiling in White Blood Cells Predicts Infliximab
Responsiveness in Rheumatoid Arthritis
• 33 RA patients treated with Infliximab
• Responders vs nonresponders (decrease of DAS-28  1.2)
• PBMC isolated from venous blood and total RNA extracted
• mRNA collected at baseline hybridized to a microarray of
10,000 non-redundant cDNAs.
• Real-time, quantitative reverse transcription PCR of selected
mRNA also performed.
• Statistical analysis included t- test and SAM (Significance
Analysis of Microarrays) with a false discovery rate of <1%.
Lequerre T et al. Arthritis Research and Therapy 2006: 8 R105
Gene Profiling in White Blood Cells Predicts Infliximab
Responsiveness in Rheumatoid Arthritis
Results
• Overall 16/33 (48%) were EULAR responders.
• The 33 patients randomly divided into:
a) “Training” cohort (n=13)
b) “Validation” cohort (n=20)
• 41 mRNAs were differentially expressed in responders versus
nonresponders s a function of the response to treatment
• Differentially expressed genes were confirmed by qRT-PCR:
– 20 transcript set
– 8 transcript set
Lequerre T et al. Arthritis Research and Therapy 2006: 8 R105
Gene Profiling in White Blood Cells Predicts Infliximab
Responsiveness in Rheumatoid Arthritis
20 transcript set
8 transcript set
Sensitivity
90
80
Specificity
70
100
PPV
75
100
NPV
88
83
The Future: Incorporate Biomarkers into Clinical Trials
Evans and Johnson, Ann Rev Genom Hum Genet 29-39, 2001
Pharmacogenetics and “Personalized” Medicine
Marsh, S. and McLeod HL. Hum. Mol. Genet. 2006 15:R89-93.