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Pharmacogenetics to Pharmaco-omicsPrecision Medicine
andDrug Response
Richard Weinshilboum, M.D.Dasburg Professor of Cancer Genomics Research
Professor of Pharmacology and MedicineMayo Clinic College of Medicine and Science
Mayo Clinic, Rochester, MN, USA
http://www.pharmacometabolomics.org/
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Pharmacogenetics to Pharmaco-omicsPrecision Medicine
andDrug Response
• Introduction• Pharmacogenetics• Pharmacogenomics• Pharmaco-omics• Conclusions
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Application of “omic” science to study variation in drug response phenotypes.
Critical component of Precision Medicine.
Pharmacogenetics to Pharmaco-omicsPrecision Medicine
andDrug Response
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Evolution ofPharmacogenetics-Pharmaco-omics
Pharmacogenetics(candidate genes)
Pharmacogenomics(genome-wide studies)
Pharmaco-omics(Multiple “omics”)
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Goals• Avoid adverse drug reactions• Maximize drug efficacy• Select responsive patients• Drugs as molecular probes
Pharmacogenetics to Pharmaco-omicsPrecision Medicine
andDrug Response
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Pharmacogenetics to Pharmaco-omicsPrecision Medicine
andDrug Response
• Introduction• Pharmacogenetics• Pharmacogenomics• Pharmaco-omics• Conclusions
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Julie Axelrod
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CatecholamineBiosynthesis and Metabolism
Dopamine β-Hydroxylase
HO
HO CHCH2NH2
HO
HO CH
OH
CH2NH2DBH
Dopamine Norepinephrine
-
CatecholamineBiosynthesis and Metabolism
Dopamine Catabolism
3,4-Dihydroxy-phenylacetaldehyde
3-Methoxy-tyramine
Dopamine
SULT1A3MAO
HO
HO
Dopamine-3-O-Sulfate
HO
HO3SO
CH2CH2NH2 HO
HO
CH2CHO HO
CH3O
CH2CH2NH2
CH2CH2NH2
COMT
PAPS
PAP
SAM
SAH
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DBH and COMTSib-Sib Correlations
DBH COMT
Science 181: 943-45, 1973 Nature 242: 490-491, 1974
R=0.57P
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Plasma DHB Pedigrees
Am J Hum Genet. 1975 Sep; 27(5): 573–585
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COMTFrequency Distribution
Thermal Stability and Genotype
Lachman et al, Pharmacogenetics 6:243-50, 1996
COMT Polymorphisms – 1947 Publications by 2017
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©2016 MFMER | slide-15
Metabolism of 6-Mercaptopurine
N
N
N
NH
SH
N
N
N
NH
SCH3
N
N
N
NH
SH
HO
OH
N
N
N
NH
SCH3
OHOH
Xanthine Oxidase(XO)
ThiopurineMethyltransferase
(TPMT)
XO TPMT
2,8-Dihydroxy-6-Methylmercaptopurine
AdoHcy
AdoHcy
AdoMet
AdoMet
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©2016 MFMER | slide-16
Human RBC TPMT
10
5
00 5 10 15 20
TPMT Activity, Units/ml RBC
298 Unrelated Adults
TPMTH/TPMTH
TPMTL/TPMTH
TPMTL/TPMTL
% O
f Sub
ject
s Pe
r0.
5 U
nits
of A
ctiv
ity298 Unrelated Adults
Amer. J. Human Genetics, 32:651-62,1980
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Pharmacogenetics to Pharmaco-omicsPrecision Medicine
andDrug Response
• Introduction• Pharmacogenetics• Pharmacogenomics• Pharmaco-omics• Conclusions
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SSRIPharmacogenomics
and Pharmaco-omics
Variation in SSRI Therapeutic Outcomesand
SSRIs as Molecular Probesfor MDD Molecular Mechanisms
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©2016 MFMER | slide-19
Mayo-NIH PGRN SSRIPharmaco-omics Research Program
Pharmacometabolomics Pharmacogenomics
Replication
Discovery StudyMayo PGRN SSRI
Clinical Trial
STAR*D PGRN ISPC
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Week 0• Consent
• Clinical assessment
• Start at escitalopram 10 mg or citalopram 20 mg
• DNA and baseline metabolomics blood draw
Week 4• Clinical assessment
• Potential dose increase to 20 mg or 40 mg, depending on symptoms.
• Blood draw for metabolomic and plasma drug level assays
Week 8• Clinical assessment
• Blood draw for metabolomic and plasma drug level assays
…
Follow-up phone call at Weeks 24
Mayo PGRN Citalopram-Escitalopram Clinical Trial
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QIDS-C16 Score
Baseline8 weeks
Num
ber o
f Sub
ject
s at
bot
h Ba
selin
e an
dLa
st V
isit
Eval
uatio
ns
Mayo PGRN Citalopram-EscitalopramClinical Trial Outcomes
No DepressionBaseline n=0
Last visit n=212
MildSymptoms
Baseline n=40Last visit n=173
ModerateSymptoms
Baseline n=216Last visit n=56
SevereSymptoms
Baseline n=172Last visit n=21
Very SevereSymptoms
Baseline n=35Last visit n=1
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Adherent EA PatientsCharacteristic and Measure Last visit (N = 499) 8 weeks (N = 398)
DemographicsAge 39.91 (±13.8) 40.64 (±13.5)Female gender 312 (62.5%) 255 (64.1%)Clinical CharacteristicsQIDS-C Baseline 15.08 (±3.47) 14.99 (±3.31)QIDS-C Week 4 8.46 (±4.41) 8.34 (±4.41)QIDS-C Week 8 6.24 (±4.05) 6.24 (±4.05)HAMD Baseline 22.31 (±5.08) 22.09 (±4.92)Baseline MedicationCitalopram 155 (31.2%) 124 (31.2%)Escitalopram 342 (68.8%) 274 (68.8%)OutcomesRemitter (QIDS ≤ 5) 206 (41.3%) 198 (49.7%)Response (%QIDS ≤ 50%) 287 (57.5%) 274 (68.8%)
Mayo PGRN SSRI Clinical TrialInitial 529 Patients
Ji et al., Pharmacogenomics J. 2013 13(5):456-63.
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Citalopram Biotransformation
Ji, et al. Brit J. Clin. Pharmacology. 78.2, 373-383, 2014
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Citalopram Pharmacokinetic GWAS
Ji, et al. Brit J. Clin. Pharmacology. 78.2, 373-383, 2014
CYP2C19 CYP2D6
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MDD and SSRIPharmacogenomics
GoalsBiomarkers for
SSRI Pharmacokineticsand
SSRI Pharmacodynamicsand
SSRI Mechanisms
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SSRI ResponsePharmacogenomic GWAS
Lack of Replication• Possible explanation- phenotypic
heterogeneity• Possible approach- use
pharmacometabolomics to inform genomics
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Pharmacogenetics to Pharmaco-omicsPrecision Medicine
andDrug Response
• Introduction• Pharmacogenetics• Pharmacogenomics• Pharmaco-omics• Conclusions
-
©2016 MFMER | slide-29
MetabolomicsInformed PGx
Genomics
Transcriptomics
Proteomics
Metabolomics
Clinical Phenotypes
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LCECA Metabolomics
Mayo PGRN Citalopram-Escitalopram
Clinical Trial
• 918 patient samples (290 subjects, 3 timepoints)
• 37 LCECA metabolites assayed• Dr. Wayne Matson, Bedford, MA
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Challenges
Plasma Pharmacometabolomics
• Merging metabolomics and genome-wide genomics
• Relationship of peripheral metabolites to CNS function
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Pharmacometabolomics Informed Pharmacogenomics
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Plasma Serotonin and Change in Plasma Serotonin were Associated with SSRI
Clinical Response
4 weeks 8 weeks 4 weeks 8 weeks 4 weeks 8 weeks
Baseline p = 0.012 p = 0.028 p = 0.007 p = 0.047 p = 0.015 p = 0.019
Changes after 4 weeks p = 0.011 p = 0.041 p = 0.026 p = 0.060 p = 0.021 p = 0.024
Changes after 8 weeks p = 0.069 p = 0.147 p = 0.037 p = 0.130 p = 0.041 p = 0.06
Remssion Response % ChangeClinical OutcomesPlasmaSerotonin
Association of Plasma Serotonin Concentrationwith Clinical Outcomes in Mayo Study
Remission: post-treatment QIDS < 5 or HAMD < 7.Response: >50% reduction in QIDS or HAMD.
Gupta M.*, Neavin D.*, Liu D.*, et al. Mol Psychiatry. 2016 Dec;21(12):1717-1725(* Co-first Authors.)
Sheet1
RemssionResponse% Change
4 weeks8 weeks4 weeks8 weeks4 weeks8 weeks
Baselinep = 0.012 p = 0.028 p = 0.007 p = 0.047 p = 0.015 p = 0.019
Changes after 4 weeksp = 0.011 p = 0.041 p = 0.026 p = 0.060 p = 0.021 p = 0.024
Changes after 8 weeksp = 0.069 p = 0.147 p = 0.037 p = 0.130 p = 0.041 p = 0.06
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Plasma Serotonin ConcentrationsAfter SSRI Therapy
• Plasma Serotonin concentrations, and change in plasma serotonin, were highly associated with SSRI outcomes.
• Higher baseline serotonin and greater change were both associated with better SSRI outcomes.
Gupta M.*, Neavin D.*, Liu D.*, et al. Mol Psychiatry. 2016 Dec;21(12):1717-1725(* Co-first Authors.)
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Serotonin-Kynurenine Balanceand
Major Depressive Disorder
L-Tryptophan
Serotonin
(SerotoninNeurotransmission)
Kynurenine
(GlutamateNeurotransmission)
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ERICH3p = 9.28E-08
Chromosome Position (BP)
-log
10 (p
Valu
e)
1 2 3 4 5 6 7 8 9 10 11 12 1314 16 18 20 22
15 17 19 21 23
2
3
4
5
6
7
8
Baseline Plasma Serotonin GWASTSPAN5
p = 7.84E-09
Gupta M.*, Neavin D.*, Liu D.*, et al. Mol Psychiatry. 2016 Dec;21(12):1717-1725(* Co-first Authors.)
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Baseline Serotonin Concentrations by ERICH3 and TSPAN5 SNP Genotypes
Gupta M.*, Neavin D.*, Liu D.*, et al. Mol Psychiatry. 2016 Dec;21(12):1717-1725(* Co-first Authors.)
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ERICH3 and TSPAN5 Locus Zoom Plots
Gupta M.*, Neavin D.*, Liu D.*, et al. Mol Psychiatry. 2016 Dec;21(12):1717-1725(* Co-first Authors.)
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TSPAN5 GTEx Tissue ExpressionR
PKM
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ERICH3 GTEx Tissue ExpressionR
PKM
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TSPAN5 SNPs are cis-eQTLs
Gupta M.*, Neavin D.*, Liu D.*, et al. Mol Psychiatry. 2016 Dec;21(12):1717-1725(* Co-first Authors.)
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Tryptophan Pathway
L-Tryptophan
5-OH tryptophan
Serotonin
Formyl-kynurenine
3-OH Kynurenine
Kynurenine
Quinolinic Acid
TPH 1/2
DDC
Kynurenic Acid
KATIII
IDO/TDO2
Multiple Steps
5-OH Indole acetic acid Melatonin
AANAT
ASMT
KFA
MAO(A/B)
KMO
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©2016 MFMER | slide-43
SK-N-BE(2) Neuroblastoma cellsEx
pres
sion
fold
cha
nge
SLC6
A4
TPH
1
TPH
2
DDC
MAO
A
MAO
B
HTR1
A
HTR3
A
HTR3
B
HTR6
HTR7
SLC1
8A2
*
*
*** **** *
*P < 0.05; **P < 0.005N=3; Mean+SEM
*
TSPAN5 Knockdown (72 hrs)TSPAN5 Over-expression (72 hrs)
TSPAN5 Function
Gupta M.*, Neavin D.*, Liu D.*, et al. Mol Psychiatry. 2016 Dec;21(12):1717-1725(* Co-first Authors.)
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ERICH3 nsSNP Expression
WT
ERICH3
GAPDH
GAPDH
ERICH3
DM
SOM
G13
23M
AD
MSO
MG
132
3MA
DM
SOM
G13
23M
AD
MSO
MG
132
3MA
EVL1056V P264A
L1056V + P264A
WT
EV
L1056V P264AL1056V + P264A
Gupta M.*, Neavin D.*, Liu D.*, et al. Mol Psychiatry. 2016 Dec;21(12):1717-1725(* Co-first Authors.)
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Culture Media Serotonin ERICH3 and TSPAN5 KD and OE
SerotoninConcentration
KD and OEEfficiency
SK-N-BE(2) Neuroblastoma Cells
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PGRN-AMPS ISPC STAR*D
rs11580409 (ERICH3 ) 0.16 0.022 0.041
SSRI Response at Four or Six WeeksP Values
PGRN-AMPS: Mayo Clinic Pharmacogenomics Research Network-Antidepressant Medication Pharmacogenomics Study
ISPC: International SSRI Pharmacogenomics ConsortiumSTAR*D: Sequenced Treatment Alternatives to Relieve Depression
ERICH3 SNPs and Clinical Outcomes in SSRI GWAS
Gupta M.*, Neavin D.*, Liu D.*, et al. Mol Psychiatry. 2016 Dec;21(12):1717-1725(* Co-first Authors.)
Sheet1
PGRN-AMPSISPCSTAR*D
rs11580409 (ERICH3)0.160.0220.041
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Tryptophan Pathway
L-Tryptophan
5-OH tryptophan
Serotonin
Formyl-kynurenine
3-OH Kynurenine
Kynurenine
Quinolinic Acid
TPH 1/2
DDC
Kynurenic Acid
KATIII
IDO/TDO2
Multiple Steps
5-OH Indole acetic acid Melatonin
AANAT
ASMT
KFA
MAO(A/B)
KMO
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Association of HAMD Scores with Baseline Metabolite Concentrations
Metabolite r P-value PathwayKynurenine -0.157 0.008 Tryptophan3-Hydroxykynurenine -0.143 0.015 TryptophanCysteine -0.134 0.023 CysteineMethionine 0.106 0.072 MethionineSerotonin -0.099 0.093 TryptophanGuanosine 0.099 0.095 Purine5-Hydroxytrptophan 0.098 0.097 Tryptophan(+)-delta-Tocopherol 0.094 0.112 AntioxidantsXanthosine 0.097 0.159 PurineSalicylic Acid -0.082 0.163 Phenylalanine
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Baseline Plasma KYN GWAS
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Baseline Plasma KYN GWAS
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Baseline Plasma Kynurenine
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36 AA; 3.9 KDa
DEFB1: Beta-Defensin 1
Nat Rev Microbiol. 2006 Jul;4(7):529-36.
Nature 2011 Jan 20;469(7330):309-10
(LPS)
• Constitutively expressed in epithelial cells;
• Functions in anaerobic environment.
Oxidized Reduced
DEFB1 (shown in purple) Antimicrobial Peptides
DEFB1 Function
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DEFB1 SNP Association with Severity of MDD Symptoms
QIDS-SC
SNP Gene p Value Beta p Value Beta
rs2702877 DEFB1 1.74E-04 0.9422 1.25E-05 1.5987
Mayo-PGRN AMPS
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DEFB1 and KYN Pathway Functional Genomics in Monocytic Cells
K/TTRPKYN
IDO1 TDO2
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AHR and KYN Pathway Functional Genomics in HepaRG Cells
C
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AHR and KYN Pathway Functional Genomics in U87 MG Cells
CBA
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Pharmacogenetics to Pharmaco-omicsPrecision Medicine
andDrug Response
• Introduction• Pharmacogenetics• Pharmacogenomics• Pharmaco-omics• Conclusions
-
Mayo-UIUC-NSF Center for Computational
Biotechnology and Genomic Medicine (CCBGM)
Predictive Algorithm -SSRI ResponseMen• QIDS: 72%• HAMD: 68%
Women• QIDS: 80%• HAMD: 95.8%
Using both Clinical Symptoms and Metabolomics
Arjun Athreya
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April 29, 2013“In a few weeks the APA will release…DSM-5. Unlike our definitions of ischemic heart disease, lymphoma or AIDS, the DSM diagnoses are based on a consensus about clusters of clinical symptoms, not any objective laboratory measure. Patients with mental illness deserve better.”
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GoalUnderstanding the
causes of MDD and the mechanisms of drugs
used to treat MDD.
Beyond the Genome
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Mayo Pharmacogenomics Laboratories - 2016
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We shall not cease from explorationAnd the end of all our exploring
Will be to arrive where we started And know the place for the first time.
T.S. Eliot“Four Quartets”
Slide Number 1Slide Number 2Slide Number 3Slide Number 4Slide Number 5Slide Number 6Julie AxelrodSlide Number 8Slide Number 9Slide Number 10Slide Number 11Slide Number 12Slide Number 13Slide Number 14Slide Number 15Slide Number 16Slide Number 17Slide Number 18Slide Number 19Slide Number 20Slide Number 21Slide Number 22Slide Number 23Slide Number 24Slide Number 25Slide Number 26Slide Number 27Slide Number 28Slide Number 29Slide Number 30Slide Number 31Pharmacometabolomics Informed PharmacogenomicsPlasma Serotonin and Change in Plasma Serotonin were Associated with SSRI Clinical ResponsePlasma Serotonin Concentrations�After SSRI TherapySerotonin-Kynurenine Balance�and�Major Depressive DisorderSlide Number 36Baseline Serotonin Concentrations by ERICH3 and TSPAN5 SNP GenotypesERICH3 and TSPAN5 Locus Zoom PlotsSlide Number 39Slide Number 40TSPAN5 SNPs are cis-eQTLsSlide Number 42Slide Number 43Slide Number 44Slide Number 45ERICH3 SNPs and Clinical Outcomes in SSRI GWASSlide Number 47Association of HAMD Scores with �Baseline Metabolite ConcentrationsBaseline Plasma KYN GWASBaseline Plasma KYN GWASBaseline Plasma KynurenineSlide Number 52DEFB1 SNP Association with Severity of MDD SymptomsDEFB1 and KYN Pathway Functional Genomics in Monocytic CellsAHR and KYN Pathway Functional Genomics in HepaRG CellsAHR and KYN Pathway Functional Genomics in U87 MG CellsSlide Number 57Slide Number 58Slide Number 59Slide Number 60Slide Number 61Slide Number 62