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HIV and Host Genetics. Amalio TELENTI Institute of Medical Microbiology CHUV – UNIL www.chuv.ch/imul. Genetic risk Predicting appropriate drug levels Treatment choice What comes next A view on human populations. Genetic frequency in a population.
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Amalio TELENTIInstitute of Medical Microbiology
CHUV – UNILwww.chuv.ch/imul
HIV and Host HIV and Host GeneticsGenetics
•Genetic riskGenetic risk
•Predicting appropriate drug levelsPredicting appropriate drug levels
•Treatment choiceTreatment choice
•What comes nextWhat comes next
•A view on human populationsA view on human populations
>5%1%<<<<<<1%
Severe ????? Mild
Primary immuno-deficiencies
?????????Common trait disease
Genetic frequency in a populationGenetic frequency in a population
Disease manifestation / riskDisease manifestation / risk
Understanding genetic riskUnderstanding genetic riskHow do we do it?How do we do it?
• DNA from a large number of individuals
• Large scale genotyping of common human variation (500’000 – 1 million polymorphisms).
• Association analysis with correction for the large number of tests (significative p-values should be <10-7 to 10-8 ).
Homozygous 1
Heterozygous
Homozygous 2
Genome-wide genotypingGenome-wide genotyping
500.000 to 1.000.000 SNPs/individual
HCP5/HLA-B*5701HLA-C –35ZNRD1/HLA-A10CCR532
Fellay et al.
Genome-wide results (2554 individuals) Genome-wide results (2554 individuals) Genetic score and HIV-1 progressionGenetic score and HIV-1 progression
Elite controllersElite controllersLTNP-viremic controllersLTNP-viremic controllersLTNP-non viremic controllersLTNP-non viremic controllersProgressorsProgressorsRapid progressorsRapid progressors
Clinical definition Clinical definition Genetic markers Genetic markers
CD4 evolution of Rapid Progressors (n=73) CD4 evolution of Rapid Progressors (n=73) during 3 years after seroconversion during 3 years after seroconversion
Red: associated with an AIDS event/death
<350 CD4 T cells
0 365 730 10950
100
200
300
400
500
600
700
800
900
1000
Days post SC
CD
4 T
cel
l co
un
t
Martinez-Picado & Telenti
Rapid progression – a genetic extreme Rapid progression – a genetic extreme
ECLTNP
CNP P RP
0.0
0.5
1.0
CCR2 V64ICCR5 32
HLA-C
ZNRD1HLA-A+
HLA-B+
CCR5_HHE/HHE
HLA-B-
CCR5_H+/H+
CCR5_P1/P1
Alle
lic f
req
uen
cy o
r p
rop
ort
ion
Casado et al.
Integrating host and viral parametersIntegrating host and viral parameters
Casado et al.
Results - IResults - I• We can now explain up to 22% of
population differences in viral load on the basis of common variants, demographics and population factors.
• At the individual level, these type of data may translate into prediction of disease progression.
•Genetic riskGenetic risk
•Predicting appropriate drug levelsPredicting appropriate drug levels
•Treatment choiceTreatment choice
•What comes nextWhat comes next
•A view on human populationsA view on human populations
Cou
nt
0
5
10
15
20
25
30
35
log10 EFV AUC (µg*h/ml)
0.5 1.0 1.5 2.0 2.5 3.0 3.5
Cum
ulat
ive
Fre
quen
cy
1
10
30
50
70
90
99
99.9
99.99
Cou
nt
0
5
10
15
20
25
30
35
log10 EFV AUC (µg*h/ml)
0.5 1.0 1.5 2.0 2.5 3.0 3.5
Cum
ulat
ive
Fre
quen
cy
1
10
30
50
70
90
99
99.9
99.99
Distribution of Efavirenz AUC valuesRotger et al. Clin Pharm Ther 2007
Extensive metabolizer
Slow metabolizerRapid metabolizer
8-OH-EFV
N
CF 3
O
H
Cl
OH
CYP2A6>2B6
CYP2B6> 3A5>3A4
EFV 7-OH-EFV
8,14-(OH)2-EFV
CYP2B6>2D6>2C19>2A6>2C9
8-OH-EFV-O-gluc
7-OH-EFV-O-sulf
7-OH-EFV-O-gluc
EFV-N-gluc
…UGT?
8,14-(OH)2-EFV-O-gluc
…UGT? …UGT?
…UGT?
…SULT?
7-OH-EFV-O-sulf
…SULT?
7-OH-EFVN
CF3
O
Cl
OH OHOH
OHOOC
N
CF3
O
H
Cl OH
OH
O
OHOH
OH
HOOC
OH
N
CF3
O
H
Cl
ON
CF3
O
H
Cl
OO
OHOH
OH
HOOC
N
CF 3
O
H
Cl
OSO 3-
OH OHOH
OHOOC
N
CF3
O
H
Cl
O
N
CF3
O
H
Cl
SO 4-
N
CF3
O
H
Cl
N
CF3
O
H
Cl
OH
EFV metabolic pathways
8-OH-EFV
N
CF
O
H
Cl
OH
CYP2A6>2B6
CYP2B6> 3A5>3A4
EFV 7-OH-EFV
8,14-(OH)2-EFV
CYP2B6>2D6>2C19>2A6>2C9
8-OH-EFV-O-gluc
7-OH-EFV-O-sulf
7-OH-EFV-O-gluc
EFV-N-gluc
…UGT?
8,14-(OH)2-EFV-O-gluc
…UGT? …UGT?
…UGT?
…SULT?
7-OH-EFV-O-sulf
…SULT?
7-OH-EFVN
CF3
O
Cl
OH OHOH
OHOOC
N
CF3
O
H
Cl OH
OH
O
OHOH
OH
HOOC
OH
N
CF3
O
H
Cl
ON
CF3
O
H
Cl
OO
OHOH
OH
HOOC
N
CF 3
O
H
Cl
OSO 3-
OH OHOH
OHOOC
N
CF3
O
H
Cl
O
N
CF3
O
H
Cl
SO 4-
N
CF3
O
H
Cl
N
CF3
O
H
Cl
OH
3
EFV metabolic pathways
8-OH-EFV
N
CF
O
H
Cl
OH
CYP2A6>2B6
CYP2B6> 3A5>3A4
EFV 7-OH-EFV
8,14-(OH)2-EFV
CYP2B6>2D6>2C19>2A6>2C9
8-OH-EFV-O-gluc
7-OH-EFV-O-sulf
7-OH-EFV-O-gluc
EFV-N-gluc
…UGT?
8,14-(OH)2-EFV-O-gluc
…UGT? …UGT?
…UGT?
…SULT?
7-OH-EFV-O-sulf
…SULT?
7-OH-EFVN
CF3
O
Cl
OH OHOH
OHOOC
N
CF3
O
H
Cl OH
OH
O
OHOH
OH
HOOC
OH
N
CF3
O
H
Cl
ON
CF3
O
H
Cl
OO
OHOH
OH
HOOC
N
CF 3
O
H
Cl
OSO 3-
OH OHOH
OHOOC
N
CF3
O
H
Cl
O
N
CF3
O
H
Cl
SO 4-
N
CF3
O
H
Cl
N
CF
O
H
Cl
OH
3
3
EFV metabolic pathways
CYP2A6 CYP2A6 & CYP3A4 and Efavirenz Pharmacokinetics
4.00
4.25
4.50
4.75
5.00
5.25
5.50
5.75
6.00
Lo
g1
0 E
FV
pla
sm
a A
UC
(u
g*h
/ml)
Hom LOF Het LOFCYP2B6: Het GOF Normal funct.
4321-321-CYP2A6CYP3A4
Total LOF: 4321-321-
Di Iulio, PGG 2009, Arab CPT 2009
CYP2B6CYP2B6
CYP2A6/3ACYP2A6/3A
0
2000
4000
6000
8000
10000
12000
14000Pre-adjustment
Screening Baseline Week 6 Week 10 Week 24
EF
V c
on
ce
ntr
ati
on
[n
g/m
l]
CDB076 – Calmy et al -Therapeutic drug monitoring (TDM) enables efavirenz dose reduction in virologically-controlled patients
Therapeuticrange
600200 « LOF » genotype 600200 « DOF » genotype600400 « DOF » genotype 600400 « LOF » genotype
TDM vs Genotype-driven efavirenz dose adjustementTDM vs Genotype-driven efavirenz dose adjustement
Low Low OutliersOutliers (n=121) (n=121)
Extreme (>P85%) Extreme (>P85%) (n=92)(n=92)
CasesCases ControlsControls
Lopinavir/r Pharmacokinetic-GeneticsLopinavir/r Pharmacokinetic-Genetics
Lubomirov et al.
Lopinavir/r Pharmacokinetic-GeneticsLopinavir/r Pharmacokinetic-Genetics
CYP3AOATP1B1
MRP2
LPV
Lubomirov et al.
Manolio Nat Genet 2009
Dyslipidemia as common genetic traitDyslipidemia as common genetic trait
Rotger et al. 2009
Results - IIResults - II• For a number of drugs, we have a
good understanding of the genetic determinants of plasma drug levels.
• It helps evaluate the correlation of drug levels-genes-toxicity.
• This information could lead to dose adjustement.
•Genetic riskGenetic risk
•Predicting appropriate drug levelsPredicting appropriate drug levels
•Treatment choiceTreatment choice
•What comes nextWhat comes next
•A view on human populationsA view on human populations
We have a problem
B. Ledergerber, SHCS
Tools for initiating antiretroviral Tools for initiating antiretroviral therapy in HIV-1 infected individualstherapy in HIV-1 infected individuals
• CD4 cell count • Viremia• Clinical symptoms• Viral genetics (primary drug
resistance)
Can host genetic information add Can host genetic information add something?something?
Can host genetic information add Can host genetic information add something?something?
DRUGS WITH GENETIC MARKERS
Efavirenz
Atazanavir
Lopinavir
Tenofovir
Abacavir
INTERMEDIATE PHENOTYPE
High plasma levels
Increased bilirubin
Increased lipid levels
Phosphaturia, glucosuria, etc…
CLINICAL EFFECT
CNS toxicity
Gilbert syndrome
Cardiovascular diseases
Renal proximal tubulopathyHypersensitivity
HypothesisHypothesisIndividuals carrying risk genetic markers will discontinue the initial treatment more frequently/earlier than individuals without
0 60 120 180 240 300 3600
1020
304050
60708090
100without GR
with GR
Estimated rates of global (n = 577)discontinuation at 1 yearaccording to genetic risk
506
71
No. at Riskwithout GR
with GR
458
59
432
51
411
44
380
38
347 305
35
50.2%
31.2%
aHR = 1.76 (CI95%: 1.18 - 2.63)
Pa= 5.65 x 10-3
29
Time to discontinuation (days)
Glo
bal d
isco
ntinuat
ion (%
)
Analysis of 577 individuals starting first line Analysis of 577 individuals starting first line ART 2004-2007ART 2004-2007
b)a) a) b)
0 60 120 180 240 300 3600
20
40
60
80
100without GRwith GR
Estimated rates of EFV (n = 272)discontinuation at 1 yearaccording to genetic risk
259
13
No. at Riskwithout GR
with GR
239
11
225
9
216
8
203
6
191
6 3
71.2%
28.1%
aHR = 3.43 (CI95% 1.48 - 7.95)
P= 0.004
177
Time to discontinuation (days)
EFV discontinuation (%)
0 60 120 180 240 300 3600
20
40
60
80
100without GRwith GR
Estimated rates of EFV (n = 272)discontinuation at 1 yearaccording to genetic risk
259
13
No. at Riskwithout GR
with GR
239
11
225
9
216
8
203
6
191
6 3
71.2%
28.1%
aHR = 3.43 (CI95% 1.48 - 7.95)
P= 0.004
177
Time to discontinuation (days)
EFV discontinuation (%)
a) b)
0 60 120 180 240 300 3600
20
40
60
80
100without GR
with GR
Estimated rates of LPV (n = 184)discontinuation at 1 year
according to genetic score 2gRn
168
16
No. at Riskwithout GR
with GR
159
15
148
12
136
11
124
10
109
9 6
46.5%
33.1%
aHR = 1.28 (CI95%: 0.53 - 3.12)
P = 0.587
87
Time to discontinuation (days)
LPV discontinuation (%)
a) b)
0 60 120 180 240 300 3600
20
40
60
80
100without GR
with GR
Estimated rates of LPV (n = 184)discontinuation at 1 year
according to genetic score 2gRn
168
16
No. at Riskwithout GR
with GR
159
15
148
12
136
11
124
10
109
9 6
46.5%
33.1%
aHR = 1.28 (CI95%: 0.53 - 3.12)
P = 0.587
87
Time to discontinuation (days)
LPV discontinuation (%)
a) b)
0 60 120 180 240 300 3600
20
40
60
80
100without GR
with GR
Estimated rates of ATV (n = 121)discontinuation at 1 year
according to UGT1A1*28, *37 (rs8175347)
103
18
No. at Riskwithout GR
with GR
97
14
94
12
93
10
87
8
81
7 6
62.5%
18.9%
68
aHR = 6.10 (CI95%:2.78 - 13.32)
P = 6.00 x 10-6
Time to discontinuation (days)
ATV discontinuation (%)
a) b)
0 60 120 180 240 300 3600
20
40
60
80
100without GR
with GR
Estimated rates of ATV (n = 121)discontinuation at 1 year
according to UGT1A1*28, *37 (rs8175347)
103
18
No. at Riskwithout GR
with GR
97
14
94
12
93
10
87
8
81
7 6
62.5%
18.9%
68
aHR = 6.10 (CI95%:2.78 - 13.32)
P = 6.00 x 10-6
Time to discontinuation (days)
ATV discontinuation (%)
Tenofovir Efavirenz
Lopinavir/r Atazanavir/r
•Genetic riskGenetic risk
•Predicting appropriate drug levelsPredicting appropriate drug levels
•Treatment choiceTreatment choice
•What comes nextWhat comes next
•A view on human populationsA view on human populations
•Telenti A. F1000 Biology Reports 2009
Integration of large scale genome/cellular dataIntegration of large scale genome/cellular data
•Bushman et al. PLoS Pathogen 2009
Integrating expression and Integrating expression and genetic variationgenetic variation
Viral control (Phenotype)Viral control (Phenotype)Viral control (Phenotype)Viral control (Phenotype)
Genetic variationGenetic variationGenetic variationGenetic variation
Expression variationExpression variationExpression variationExpression variation
Co-factorsCo-factorsCo-factorsCo-factors
How do we do it?How do we do it?• Choice of tissue/cell type
• Clinical/lab conditions (perturbations)
• Genome-wide transcription analysis
• Gene and pathway analysis
• Search for genetic variants influencing gene expression.
Transcriptome analysis in
CD4 T cells from 127 HIV-infected
individuals
Low
High
Rotger et al.
Hea
lthy
cont
rols
Elite
co
ntro
llers
Roger et al.
Expression variants influencing HIV-1 disease?
48000 transcripts
260 genes differentially
expressed during HIV-1 infection
190 genes under cis-acting SNP
modulating expression
300K gene-centric SNPs
1
OAS1
Susceptibility to West Nile Virus Susceptibility to HIV?
The next frontierThe next frontier
http://www.ipadrblog.com/BlindMenandElephant.jpg
>5%1%<<<<<<1%
Severe ????? Mild
Primary immuno-deficiencies
RARE AND RARE AND PRIVATE PRIVATE
MUTATIONSMUTATIONS
Common trait disease
Genetic frequency in a populationGenetic frequency in a population
Disease manifestation / riskDisease manifestation / risk
“…some 11,000 of Watson’s SNPs (15% novel) are predicted to change the amino-acid sequence — and so, perhaps, the function — of a protein.”
Whole Genome SequencingWhole Genome Sequencing
James WATSON
•Genetic riskGenetic risk
•Predicting appropriate drug levelsPredicting appropriate drug levels
•Treatment choiceTreatment choice
•What comes nextWhat comes next
•A view on human populationsA view on human populations
The genomics of human ancestryThe genomics of human ancestry
Tishkoff et al. Science 2009
Human ancestry in genetic studiesHuman ancestry in genetic studies
ATTENTION!ATTENTION!• Genetic/genomic studies need to take population origin into account (« pop. stratification »).• Frequencies of alleles may vary substantially (eg. HLA, Cytochrome P450). • Less information available on non-Caucasians.
HOWEVER!HOWEVER!• More differences found across individuals than across populations.•Causal variants are equally functional across populations.• Markers (non-causal) may not work across populations.
ConclusionsConclusions• We can know explain 22% of population
variance in viral load by genetics, population effects, gender and age.
• We can explain pharmacokinetics for an increasing number of drugs in ART
• Useful predictive strategies might be brought to clinical use.
• Integrating data and understanding the role of rare and private mutations is the next step
University of LausanneM. Rotger J. di IulioS. ColomboR. LubomirovL. DecosterdC. CsajkaT. BuclinP. TarrM. Cavassini
University of GenevaA. Calmy P. Descombes
Duke UniversityJ. FellayK. DangE. Heinzen D. Goldstein
SHCSA. RauchH. GünthardB. LedergerberH. FurrerB. Hirschel
CNM – Carlos III MadridC. Lopez-Galindez