precision medicine and drug...

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/


andDrug Response

• Introduction• Pharmacogenetics• Pharmacogenomics• Pharmaco-omics• Conclusions

Application of “omic” science to study variation in drug response phenotypes.

Critical component of Precision Medicine.


andDrug Response

Evolution ofPharmacogenetics-Pharmaco-omics

Pharmacogenetics(candidate genes)

Pharmacogenomics(genome-wide studies)

Pharmaco-omics(Multiple “omics”)

Goals• Avoid adverse drug reactions• Maximize drug efficacy• Select responsive patients• Drugs as molecular probes


andDrug Response


andDrug Response


Julie Axelrod

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

DBH and COMTSib-Sib Correlations

DBH COMT

Science 181: 943-45, 1973 Nature 242: 490-491, 1974

R=0.57P

Plasma DHB Pedigrees

Am J Hum Genet. 1975 Sep; 27(5): 573–585

COMTFrequency Distribution

Thermal Stability and Genotype

Lachman et al, Pharmacogenetics 6:243-50, 1996

COMT Polymorphisms – 1947 Publications by 2017

©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


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


andDrug Response


SSRIPharmacogenomics

and Pharmaco-omics

Variation in SSRI Therapeutic Outcomesand

SSRIs as Molecular Probesfor MDD Molecular Mechanisms


Mayo-NIH PGRN SSRIPharmaco-omics Research Program

Pharmacometabolomics Pharmacogenomics

Replication

Discovery StudyMayo PGRN SSRI

Clinical Trial

STAR*D PGRN ISPC

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

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


SevereSymptoms


Very SevereSymptoms


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.

Citalopram Biotransformation

Ji, et al. Brit J. Clin. Pharmacology. 78.2, 373-383, 2014

Citalopram Pharmacokinetic GWAS

Ji, et al. Brit J. Clin. Pharmacology. 78.2, 373-383, 2014

CYP2C19 CYP2D6

MDD and SSRIPharmacogenomics

GoalsBiomarkers for

SSRI Pharmacokineticsand

SSRI Pharmacodynamicsand

SSRI Mechanisms

SSRI ResponsePharmacogenomic GWAS

Lack of Replication• Possible explanation- phenotypic

heterogeneity• Possible approach- use

pharmacometabolomics to inform genomics


andDrug Response



MetabolomicsInformed PGx

Genomics

Transcriptomics

Proteomics

Metabolomics

Clinical Phenotypes

LCECA Metabolomics

Mayo PGRN Citalopram-Escitalopram

Clinical Trial

• 918 patient samples (290 subjects, 3 timepoints)

• 37 LCECA metabolites assayed• Dr. Wayne Matson, Bedford, MA

Challenges

Plasma Pharmacometabolomics

• Merging metabolomics and genome-wide genomics

• Relationship of peripheral metabolites to CNS function

Pharmacometabolomics Informed Pharmacogenomics

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

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.


Serotonin-Kynurenine Balanceand

Major Depressive Disorder

L-Tryptophan

Serotonin

(SerotoninNeurotransmission)

Kynurenine

(GlutamateNeurotransmission)

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


Baseline Serotonin Concentrations by ERICH3 and TSPAN5 SNP Genotypes


ERICH3 and TSPAN5 Locus Zoom Plots


TSPAN5 GTEx Tissue ExpressionR

PKM

ERICH3 GTEx Tissue ExpressionR

PKM

TSPAN5 SNPs are cis-eQTLs


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


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


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


Culture Media Serotonin ERICH3 and TSPAN5 KD and OE

SerotoninConcentration

KD and OEEfficiency

SK-N-BE(2) Neuroblastoma Cells

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


Sheet1

PGRN-AMPSISPCSTAR*D

rs11580409 (ERICH3)0.160.0220.041

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

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

Baseline Plasma KYN GWAS

Baseline Plasma Kynurenine

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

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

DEFB1 and KYN Pathway Functional Genomics in Monocytic Cells

K/TTRPKYN

IDO1 TDO2

AHR and KYN Pathway Functional Genomics in HepaRG Cells

C

AHR and KYN Pathway Functional Genomics in U87 MG Cells

CBA


andDrug Response


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

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.”

GoalUnderstanding the

causes of MDD and the mechanisms of drugs

used to treat MDD.

Beyond the Genome

Mayo Pharmacogenomics Laboratories - 2016

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

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