Pharmacogenomics of HIV Therapy

1

Pharmacogenomics of HIV Therapy
David H. Haas, MDAssociate Professor of
MedicineVanderbilt University School of Medicine
International AIDS SocietyUSA
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
2
Objectives
Slide 2

• To provide a brief introduction to human
  genetics.
• To discuss current knowledge about human genetic
  variability and responses to HIV therapy.
• To suggest future directions for HIV
  pharmacogenomics.

From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
3
Slide 3
Question 1 Have you ever ordered a human
genetic test on a patient?

• Yes
• 2. No
• 3. Unsure
• 4. I dont order tests, so this doesnt apply to
  me

From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
4
Slide 4
Question 2 Have you ever had a human genetic
test done on yourself?

• Yes
• 2. No
• 3. Unsure

From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
5
Human Chromosomes
Slide 5
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
6
The four DNA bases
Slide 6

• Adenosine
• Cytosine
• Thymine
• Guanine

From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
7
Genetic Variants
Slide 7

• Polymorphism a common DNA variant (gt1 of
  population)
• Base substitution, deletion, or insertion.
• Most common are Single Nucleotide Polymorphisms
  (SNP).
• May be in coding or non-coding region.
• Alter amino acid (non-synonymous) or not
  (synonymous).
• May alter function or expression level of
  protein.
• Mutation a rare DNA variant (ltlt1 of population)

C/A
C/C
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
8
Haplotypes and Linkage Disequilibrium
Slide 8
NNNNNNNNN
NNNNNNNNN
NNNNNNNNN
NNNN
C A
T G
G T

• Certain SNPs tend to be inherited together
• LINKAGE DISEQUILIBRIUM

From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
9
Caveat of Genetic Association Studies
Slide 9
Identify Possible Genotype-Phenotype Association
Validate Association in Separate Dataset(s)
Establish Causation, Molecular Mechanisms,
Applications, etc
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
10
Some ARV Pharmacogenetic Variants
Slide 10

• Abacavir HSR (HLA-B5701) white gt black
• Efavirenz PK (CYP2B6) black gt white
• Nevirapine LFTs (ABCB1) black gt white
• Atazanavir jaundice (UGT) white gt black
• Atazanavir PK (PXR?) white gt black
• Nelfinavir (CYP2C19) Asian gt black, white

To date, every genetic variant that affects HIV
disease progression, ARV pharmacokinetics,
efficacy, or toxicity differs considerably in
frequency depending on geographic region of
ancestry.
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
11
Abacavir hypersensitivityHLA-B5701
Slide 11
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
12
PREDICT Double-Blind Study Design
1. retrospective high resolution typing 2.
prospective high resolution typing
Mallal et al NEJM 2008.
13
Performance Characteristics ofHLA-B5701
Screening for HSR
Immunologically Confirmed HSR1 HLA-B5701
Pos
Neg
23
0
Sens 100
25
794
Spec 97
Pos PV
48
1 Control Arm Data Only
Mallal et al NEJM 2008
14
DHHS Panel Guidelines (12/07)(http//aidsinfo.nih
.gov)
Slide 14

• The Panel recommends HLA-B5701 testing prior to
  initiating abacavir therapy... HLA-B5701-positive
  patients should not be prescribed abacavir,
  positive status should be recorded as an abacavir
  allergy in the patients medical record.

From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
15
Frequency of HLA-B5701
Slide 15
Nolan et al J HIV Ther 2003836
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
16
Drug Metabolism and Elimination
Slide 16
Nuclear receptor genes that control ADME
expression
Phase 1 enzymes (e.g. CYPs)
Phase 2 enzymes (e.g. UGTs)
Drug X
Drug X
Drug X
O
OH
R
Hydrophobic Hydrophilic
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
17
Hepatic Drug Transporters
Marzolini. Pharmacogenomics 20045273
18
EfavirenzCYP2B6
Slide 18
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
19
Slide 19
Background A5095 Time to Virologic Failure by
Race/Ethnicity and Adherence
Gulick et al. JAMA 2006296769.
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
20
Efavirenz Metabolism by CYP2B6
Slide 20
Ward et al. J Pharmacol Exp Ther 2003306,287.
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
21
Host Genetics and EfavirenzACTG studies
(A5095/5097s)
Slide 21

• Efavirenz Levels
• EFV plasma levels were greater in blacks than in
  whites (Ribaudo et al, 11th CROI).
• Median EFV AUC0-24h
• Blacks 58 µghrmL-1
• Whites 46 µghrmL-1
• Much overlap in the distribution of PK parameters
  between racial/ethnic populations.

From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
22
CYP2B6 516GgtT and Efavirenz Plasma Levels A5097s
Slide 22
Haas et al, AIDS 2004182391
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
23
Slide 23
Efavirenz Dose Reduction by CYP2B6 Genotype
Gatanaga Clin Inf Dis 2007451230
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
24
Efavirenz CNS Side Effects
Slide 24

• Genotype cant reliably predict CNS side effects
• Most patients with CNS side effects dont have
  high EFV levels.
• Most patients with high EFV levels dont have bad
  CNS side effects.

From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
25
Time to Virologic Failure Blacks (CYP2B6 516/983
Genotype)
Slide 25
blacks
N 219
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
26
Pharmacogenetics of NNRTIs in African
Americans(Vanderbilt-Meharry CFAR project)
Slide 26
Each interval 0.5, 1, 2, 4, 6, 8, 12, 24h, 2, 3,
4, 6, 8, 10, 14d
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
27
Single-Dose NNRTI Concentration-Time Profiles (34
Healthy African-Americans)
Slide 27
Haas et al. 9th HIV Clin Pharm Workshop
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
28
Slide 28
CYP2B6 and NNRTI PK Parameters (34 African
Americans)
Haas et al. JID 199872,2009
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
29
Slide 29
Efavirenz (single dose) Concentrations Just Among
CYP2B6 516/983 Rapid Metabolizers (n11)
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
30
NevirapineCYP2B6, ABCB1, HLA
Slide 30
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
31
Nevirapine Hypersensitivity HLA-DRB10101Marti
n et al AIDS 200519,93
Slide 31
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
32
Nevirapine Hypersensitivity Other HLAs

• Sardiniaa
• 13 with nevirapine HSR, 36 without HSR
• 46 with HSR had HLA-Cw8
• 5 without HSR had HLA-Cw8 (P 0.004)
• Japanb
• 12 with nevirapine HSR, 29 without HSR
• 42 with HSR had HLA-Cw8
• 10 without HSR had HLA-Cw8 (P 0.03)
• Thailandc
• HLAB3505 predicts skin rash (OR 20-39)
• Replicated in 2 cohorts.

aAIDS 2006201621 bAIDS 200721,264
cPharmacogenet Genom 200919139.
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
33
Tissue Distribution of P-glycoprotein
Slide 33
Encoded by ABCB1(formerly used to be called MDR1)
Marzolini C et al Clin Pharm Ther 20047513.
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
34
Nevirapine Liver Toxicity
Slide 34

• In a study in South Africa (FTC-302), grade 3 or
  4 LFT elevations affected 66 (17) NVP
  recipients.
• We explored ABCB1, CYP2B6, CYP3A4, and CYP3A5
  SNPs and NVP hepatotoxicity.
• Two matched controls identified for each case.
• 53 cases 108 matched controls

Haas et al, Clin Inf Dis 43783, 2006
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
35
MDR1 (ABCB1) Polymorphism and Nevirapine
Hepatotoxicity FTC-302 and ACTG Collaboration
Slide 35
Haas et al, Clin Inf Dis 43783, 2006
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
36
Slide 36
Ritchie Clin Inf Dis 200643779
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
37
Pharmacogenetics of Nevirapine Hepatotoxicity
Mozambique
Slide 37

• 161 pregnant women initiating ART.
• 73 NVP hepatotoxicity cases
• 88 controls
• 6 SNPs in MDR1, CYP2B6, CYP3A4, CYP3A5.
• (ABCB1) MDR1 3435CgtT associated with
  hepatotoxicity (p0.03, OR2.3).
• T allele protective.

Ciccacci et al. Am Soc Human Genet meeting,
Toronto, 2008
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
38
AtazanavirUGT1A1, PXR
Slide 38
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
39
UDP-glucuronosyltransferase (UGT1A1) and Jaundice
with Atazanavir
Slide 39
UGT1A1 promoter with 7 TA repeats is less
active 28 allele, Gilberts trait
Rodríguez-Nóvoa et al, Pharmacogenomics J
20066,234
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
40
Slide 40
UGT1A128 and Adjusted Bilirubin Levels
Rotger et al, Pharmacogenomics JID 2005192,1381
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
41
Drug Metabolism and Elimination
Slide 41
Nuclear receptor genes that control ADME
expression
Phase 1 enzymes (e.g. CYPs)
Phase 2 enzymes (e.g. UGTs)
Drug X
Drug X
Drug X
O
OH
R
Hydrophobic Hydrophilic
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
42
Slide 42

• Cohort of 47 HIV patients in Turin, Italy
  (Caucasian).
• Replicated in 62 HIV patients in Liverpool TDM
  Registry (?race)

From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
43
Associations Between Allelic Variants and HIV
Treatment Response
Slide 43

• Drug Phenotype Gene
• Abacavir Hypersensitivity HLA-B5701
• Lancet 2002359,727 1121 PNAS 2004101,4180
• Indinavir Jaundice UGT-1A1
• Atazanavir
• PNAS 200198,12671 ICAAC 2002 JID
  2005192,1381
• NRTI Lipoatrophy TNF-a promoter, HFE
• AIDS 200216,2013 AIDS 200317,121 JID
  2008197, 858
• Nevirapine Hypersensitivity HLA-DRB10101, -Cw8,
  -B3505
• Hepatotoxicity ABCB1
• Pharmacokinetics CYP2B6
• AIDS 200519,97 Pharmacogenet Genom 200515,1
  Clin Inf Dis 200643,779 783 AIDS
  200620,1621 AIDS 200721,264 Pharmacogenet
  Genom 200919,139

From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
44
Genetic Associations (continued)
Slide 44

• Drug Phenotype Gene
• Efavirenz CNS effects, Pharmacokinetics CYP2B6
• Viral response, Resistance ABCB1, CYP2A6
• Lancet 200235930 AIDS 2004182391
  Pharmacogenet Genom 2005151 JID 20051921931
  CID 200642401 CROI 2008 JID 2009199872
• Nelfinavir Viral response, Pharmacokinetics
  CYP2C19
• JID 20051921931
• PIs Dyslipidemia APOC, RETN
• JID 20051911419 PLoS Med 20063e52 AIDS
  2008221561.
• NRTIs Peripheral neuropathy Mitochondrial AIDS
  2005191341, AIDS 2006201503 haplogroup T,
• HFE
• HAART CD4 recovery Proliferation
• JID 20061941098 apoptosis

From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
45
Genetic Associations (continued)
Slide 45

• Drug Phenotype Gene
• Tenofovir Renal toxicity MRP2 (ABCC2)
• JID 2006941481
• Others
• ?
• ?
• ?
• ?
• ?
• ?
• ?

From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.
46
Approved Studies with ACTG Human DNA from US
(A5128)
Slide 46

• Project Papers
• NWCS 213 efavirenz, nelfinavir PK response
  ? 2
• NWCS 214 efavirenz CNS toxicity and PK ? 2
• NWCS 215 T cell turnover rates ? 1
• NWCS 224 metabolic complications 1
• NWCS 233 CD4 increase on ART ? 1
• NWCS 237 metabolic complications
• NWCS 238 peripheral neuropathy ? 3
• NWCS 239 efavirenz resistance after Rx
  interruption ? 1
• NWCS 243 HLA and viral evolution
• NWCS 248 efavirenz lopinavir PK 1
• NWCS 253 efavirenz response ?
• NWCS 254 efavirenz response ?
• NWCS 256 peripheral neuropathy ?
• NWCS 259 metabolic complications
• NWCS 262 innate immunity and responses to ART
• NWCS 266 treatment responses to ART
• NWCS 268 efavirenz PK ?
• NWCS 273 peripheral neuropathy ?

DNA banked on gt10,000 individuals
From DH Haas, MD, at San Francisco, CA April 20,
2009, IASUSA.