Pharmacogenetics of Statin Therapies Daniel I. Chasman, Ph.D. Division of Preventive Medicine Brigham and Women’s Hospital Johanna and Ralph DeStefano Personalized Health Care Conference OSU Medical Center Columbus, OH Oct 6, 2011
Nov 02, 2014
Pharmacogenetics of Statin Therapies
Daniel I. Chasman, Ph.D.Division of Preventive Medicine
Brigham and Women’s Hospital
Johanna and Ralph DeStefano Personalized Health Care
Conference OSU Medical CenterColumbus, OH
Oct 6, 2011
Disclosure
Funding for this research provided by
AstraZenecaCelera
Background and research questions
• BackgroundThere is large inter-individual response to statin therapy as
measured by LDL-C reduction. Some of this variation may be correlated with genetic variation.
• Research questionsWhat genes, in the entire genome, carry common genetic
variation associated with LDL-C lowering on statin therapy?
What are the magnitudes of these effects?
Are there interactions involving these gene variants?
To what extent do the genetic effects explain variation in inter-individual statin response?
Some previous genetic analyses of LDL-C lowering with statin treatment
• Candidate gene analysis1
HMGCR – target of statin therapy
APOE – major apolipoprotein of VLDL, IDL, chylomicrons
LDLR – LDL receptor
ABCG5/8 – sterol transporters
CYP7A1 – cytochrome P450 family metabolizing enzyme
ABCG2 – transporter in liver, kidney
• Genome-wide association studies (GWAS)2
CLMN association in GWAS of PRINCE, CAP, and TNT (pravastatin, simvastatin, atorvastatin)
GRIK4 association in GWAS of TNT (atorvastatin)
SLCO1B1 association myopathy GWAS of SEARCH (simvastatin)
References1JAMA. 2004 291:2821, ATVB 2010 30:1485, Circ. 2008 117:1537; Athero. 2004 175:287; Am J Cardi. 2004 93:104. Athero. 2001 158:183. Circulation Cardiovascular genetics 2010 doi: 10.1161. 2PLoS One. 2010 5:e9763 , N Engl J Med. 2008 ;359:789, Circ Cardio Genet. 2009 2:173.
CYP’s
LDLRAPOEABCG5/8
HMGCR
degradation
hepatocyte
inhibition of cholesterol
synthesis
hepatocyte
effects on cholesterol
transport
hepatocyte
vascular system
peripheral tissues
Known pharmacologic pathways for statin therapy
uptake
intestine
hepatocyte
excretion
hepatocyte
renal cells
temporal sequence of statin pharmacology
ABCB1ABCG2
SLCO1B1
Genome-wide association study (GWAS)
• Focus on single nucleotide polymorphisms (SNPs), the most prevalent form of genetic variation in people
• SNPs typically have two alleles, the major allele signified here as “A” and the minor allele signified as “a”
• In a single experiment, examine all common SNPs at once. For 1% allele frequency, approx. 1 million SNPs
• Test for association of the minor allele with LDL-C response among individuals taking statin
Population with genome-wide data from JUPITER
• JUPITER trial enrolled 17,802 participants with LDL-C < 130mg/dL and C-reactive protein (CRP) ≥ 2mg/L for primary prevention with random allocation to rosuvastatin (20 mg/day). Treatment highly effective in this population1
• Genotyping on the Illumina Omni 1M Quad platform by Illumina• 8,782 of the 12,649 JUPITER participants with genotype had
verified European ancestry• Compliance limits sample to 6,934• SNPs excluded when failing Hardy-Weinberg equilibrium test at
P < 10-6, with the exception of rs7412 at APOE (E2 v. E3)• 820,411 SNPs pass QC with minor allele frequency > 1%
1N Engl J Med. 2008 359:2195.
Clinical characteristics of study sample(all European ancestry)
characteristic placebo statin p*
3414 3520
age (yrs) 66.0 (60.0-71.0) 66.0 (60.0-71.0) 0.52
sex (N (%) female) 1086 (31.8) 1112 (31.6) 0.86
BMI (kg/m^2) 28.7 (25.6-32.1) 28.7 (25.8-32.1) 0.76
hypertension (N (%)) 1886 (55.2) 1985 (56.4) 0.35
smoking_cigs (N (%)) 443 (13.0) 460 (13.1) 0.94
LDL-C (mg/dL) 110.0 ( 97.0-120.0) 110.0 ( 96.0-120.0) 0.16
HDL-C (mg/dL) 50.0 (41.0-61.0) 49.0 (41.0-60.0) 0.40
triglycerides (mg/dL) 115.5 (84.0-163.0) 117.0 (85.0-167.0) 0.10
Δ LDL-C (mg/dL) 3.0 (-15.0-7.0) -54.0 (41.0-66.0)
Δ HDL-C (mg/dL) 1.0 (-5.0-3.0) 3.0 (-8.0-1.0)
Δ triglycerides (mg/dL) 0 (-24-25) -18.5 (-3.0-50.0)
Defining LDL-C response to statin therapy
Absolute LDL-C response:
LDL-C at 12 months – LDL-C baseline
Fractional LDL-C response:
LDL-C at 12 months – LDL-C baseline = absolute ΔLDL-C
LDL-C baseline LDL-C baseline
Statistical power: JUPITER sample with genome-wide genetic information is the largest to date with a single statin administered at a single dose ΔLDL-C (mg/dL) Δ fr. LDL-C (%)
MAF p=0.05 5x10-8 p=0.05 5x10-8
0.05 3.8 8.5 3.7 8.3
0.1 2.8 6.2 2.7 6.0
0.2 2.1 4.7 2.0 4.5
0.5 1.7 3.7 1.6 3.6
Genome-wide association of baseline LDL-C
~820K SNPs
Genome-wide association ofLDL-C lowering with rosuvastatin
< Absolute LDL-C reduction
Fractional LDL-C reduction >
Genome-wide association of LDL-C lowering with placebo
< Absolute LDL-C reduction
Fractional LDL-C reduction >
Magnitude of effects: best SNP at each locus
absolute LDL-C reduction (mg/dL) fractional LDL-C reduction (%)
chr. pos. gene SNP MAF effect (se) p SNP MAF effect (se) p*
1p32.3 PCSK9 rs17111584 0.05 4.3 (1.4) 5.8E-04 rs11591147 0.03 -4.5 (1.7) 3.1E-04
4q22.1 ABCG2 rs2199936 # 0.11 -5.2 (0.9) 2.1E-12 rs1481012# 0.11 -5.1 (0.9) 1.7E-15
6q26 LPA rs10455872 0.05 6.2 (1.3) 3.5E-09 rs10455872 0.05 6.8 (1.2) 5.0E-15
19q13.32 APOE rs71352238 0.10 4.2 (1.0) 2.9E-04 rs7412 0.15 -5.1 (0.8) 5.8E-19
baseline LDL-C (mg/dL)
chr. pos. gene SNP MAF effect (se) p
1p32.3 PCSK9 rs11591147 0.03 -5.0 (0.8) 4.7E-11
4q22.1 ABCG2 N.S.
6q26 LPA N.S.
19q13.32 APOE rs7412 0.15 -6.1 (0.4) 1.6E-53
LDL-C lowering
Baseline LDL-C
# high LD
Distribution of effect by genotype
Total genetic effect: proportion of variance explained at genome-wide loci
“●” indicates locus with genome-wide association (p<5x10-8)
For comparison, age, BMI, sex, smoking status, region explain:3.5% of absolute LDL-C response3.7% of fractional LDL-C response
Genes from genome-wide analysis
• PCSK9 (chr. 1)Serine protease with functions in LDLR protein degradation
• ABCG2 (chr. 4)Widely-expressed (hepatic, renal, elsewhere) transporter studied for multi-
drug resistance phenotype in chemotherapy (as BCRP). Variation also associated with plasma urate levels. Effects observed in candidate analysis of LDL-C lowering with rosuvastatin*.
• LPA (chr. 6)Apolipoprotein(a) component of Lp(a). Plasma Lp(a) levels almost entirely
determined by genetic variation at LPA. LDL-C includes contribution from cholesterol in Lp(a) particles.
• APOE (chr. 19)Major apolipoprotein component of VLDL, IDL, chylomicrons.
*Circ Cardiovasc Genet. 2010 Jun 1;3(3):276-85.
Validation
No replication, but …• Genome-wide standard of significance (p<5x10-8) imposed• All loci previously recognized in genetics of statin response literature• Winner’s curse probably not a strong influence on effect estimates• Associations not merely due to individuals with extreme LDL-C since
such individuals were excluded by the trial design• No effects at all in placebo
Sub-genome-wide significant loci(5x10-8<P<5x10-6)
absolute LDL-C reduction(mg/dL)
fractional LDL-C reduction(%)
chr. SNP pos maf beta (se)* p* beta (se)* p* genes
2q21.3 rs6730157 135623558 0.35 3.4 (0.6) 3.0E-05 3.7 (0.6) 8.2E-07 RAB3GAP1
6p22.3 rs6924995 16269404 0.21 4.1 (0.7) 5.3E-07 3.8 (2.9) 1.4E-06 IDOL (MYLIP)
6q23.1 rs7769153 131298057 0.03 8.9 (1.9) 1.1E-04 10.3 (1.8) 1.7E-07 EPB41L2
9q22.1 rs1875620 90729879 0.45 2.8 (0.6) 7.2E-07 2.2 (0.6) 3.7E-04 C9orf47, S1PR3, SHC3
19p12 rs931608 22405962 0.12 4.2 (0.9) 2.7E-07 3.6 (0.9) 7.9E-07 LOC342994, ZNF98
IDOL (inducible degrader of LDL receptor)
•IDOL (originally named MYLIP)
Sterol responsive ubiquitin-mediated pathway for post-transcriptional regulation (degradation?) of the LDL receptor1
Regulated by LXRRecently associated with baseline LDL-C2
Candidate therapeutic target for “statin-like” regulation of LDL-C levels mediated through the LDL receptor
•EPB41LD
Unknown function but shares band 4.1 homology with IDOL
1Science 2009 325:100-1042PLoS Genetics 2009 5:e1000730. Nature 2010 466:707-13.
Candidate associations absolute LDL-C reduction (mg/dL) fractional LDL-C reduction (%)chr gene SNP pos maf effect* (se) p* effect* (se) p*
5 HMGCR rs17244841 74678611 0.05 1.9 (2.0) 5.00E-01 1.8 (2.0) 5.70E-01
rs17238540 74691254 0.02 1.7 (2.0) 6.20E-01 1.6 (2.0) 8.30E-01
rs12916 74692295 0.39 1.1 (0.6) 3.10E-01 1 (0.6) 3.90E-01
rs6989121 74717529 0.20 1.2 (0.7) 9.7e-02 (9.5e-01) 0.99 (0.7) 1.3e-01 (9.8e-01)
rs104744332 74652599 0.33 1.0 (0.6) 2.6e-01 (1e+00) 1.1 (0.6) 9.5e-02 (9.4e-01)
12 SLCO1B1 rs4149056 21222816 0.16 2.7 (0.8) 1.70E-04 2.6 (0.8) 7.70E-05
rs4363657 21259989 0.17 2.8 (0.8) 1.80E-04 2.8 (0.7) 4.00E-05
rs123172681,2 21243808 0.16 3.2 (0.8) 2.9e-05 (3.8e-03) 3.2 (0.8) 4.1e-06 (5.3e-04)
19 LDLR rs6511720 11063306 0.15 -1.7 (0.8) 1.50E-01 -2.6 (0.8) 4.60E-03
rs688 11088602 0.43 -0.58 (0.6) 5.50E-01 -0.4 (0.6) 9.50E-01
rs1433099 11103658 0.27 0.023 (0.7) 5.90E-01 0.28 (0.6) 6.30E-01
rs116721231 11055823 0.05 4.4 (1.0) 6.6e-04 (2.4e-02) 4 (1) 5.9e-03 (2.0e-01) rs116684772 11056030 0.24 -1.9 (0.7) 9.2e-03 (2.9e-01) -2.1 (0.7) 1.8e-03 (6.4e-02)
No associations at GRIK4, CLMN, CYP3A5, CYP2C9
1,2locus-wide best SNP for absolute (1) or fractional (2) LDL-C reduction
Interaction analysis
• No interaction among lead SNPs at genome-wide loci• No interaction between lead SNPs and other SNPs across
genome• No interaction with sex• No evidence for conditional associations within top loci• However, evidence for PCSK9 X LDLR interaction with
fractional LDL-C reduction (pint=0.002)
rs11668477 (LDLR)
rs11591147 (PCSK9) non-carrier carrier (~15%)
non-carrier -51.6% -52.0
carrier (~6%) -51.5 -57.0
CYP’s
HMGCR
degradation
hepatocyte
inhibition of cholesterol
synthesis
hepatocyte
effects on cholesterol
transport
hepatocyte
vascular system
peripheral tissues
APOE
PCSK9
LPA
LDLR
IDOL
APOB
Influence of common genetic variation on rosuvastatin therapy in JUPITER
uptake
intestine
hepatocyte
SLCO1B1
excretion
hepatocyte
renal cells
ABCG2
temporal sequence of statin pharmacology
Genetic score: sum of inherited “risk alleles”
absolute LDL-C response fractional LDL-C response
Effects of genetic score
beta
(95% CI) R2 OR > median
absolute ΔLDL-C-5.0 (mg/dL)(-6.06- -3.93) 2.3
1.54(1.41-1.69)
fractional ΔLDL-C-5.5 (%)
(-6.57- -4.5) 3.11.93
(1.75-2.12)
Estimates per unit of score, i.e. per inherited allele
Another candidate (KIF6)
KIF6 gene non-synonymous variant (rs20455, MAF=34.7%). Minor allele (719Arg) has greater CV risk and greater response to atorvastatin (CARE, WOSCOP).
No effect observed in JUPITER. See: Ridker et al. Circ Cardiovasc Genet. 2011 Apr 14. Lack of association may be related to differences between rosuvastatin and other statins
Summary
• In JUPITER, three (3) loci genome-wide significant association for LDL-C reduction with random rosuvastatin (20mg/dL) allocation: ABCG2, LPA, APOE
• An additional locus (PCSK9) for LDL-C reduction arises from genome-wide association with baseline LDL-C.
• Per allele, the lead SNPs are associated with a -5.2 mg/dL (ABCG2) and a +6.2 mg/dL (LPA) change in absolute LDL-C; a -5.1 mg/dL change in fractional LDL-C change (APOE)
• In total, 2.8% and 6.7% of the variance explained by four loci in absolute and fractional LDL-C reduction respectively
• A sub-genome-wide association at IDOL is consistent with current understanding of LDL receptor regulation
• Additional candidate analysis supports a role for variation in SLCO1B1 and LDLR
• A genetic risk score reveals dependence of median LDL-C response on genetics but only explains a small proportion of the variance
• No interaction effects with rosuvastatin observed for KIF6 variant
Collaborators and support
• BWHPaul M Ridker, MD, MPHAudrey Chu, PhDFranco Guilianini, PhDJean MacFadyen, BS
• AstraZenecaFredrik Nyberg, MD, PhD, MPHBryan Barratt, PhD
• SupportAstraZeneca
Celera