2

3

One-size fits all …??

4Adverse Drug Reactions

5

Pharmacogenomics and its

significance

Devi Lekshmi S

2013-11-192

Department of Plant

Biotechnology

Major Advisor,

Dr. P A Nazeem

6

OutlinePharmacogenomics

Genes and enzymes involved in drug

metabolism

Variants and SNPs

Role of bioinformatics in pharmacogenomics

Clinical significance of pharmacogenomics

Personalized medicine

Benefits and challenges

Significance in plants

Conclusion

Pharmacogenomics :

pharmacology +

genomics

How genetic variation

influences drug action

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Pharmacogenomics

8

…pharmacogenomics

Different platforms

Human Genome Project (2001-2003)

International HapMap Project (2003)

1000 Genomes Project (2010 onwards))

(Carr et al., 2014)

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Pharmacogenetics (Friedrich Vogel) often used

interchangeably with pharmacogenomics

Pharmacogenetics focus on single drug-gene

interaction

Pharmacogenomics- a more genome-wide association

approach incorporating genomics and epigenetics

Pharmacogenetics and

pharmacogenomics

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Genes involved in drug metabolism

PK genes and PD genes

Pharmacokinetics (PK)

- “what the body does to the drug”

Pharmacodynamics (PD)

- “what the drug does to the body”

PK genes encode proteins involved in

ADME of drug

(Altman et al., 2012)

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Fate of drug in a human body

Enzymes involved in drug metabolism

• Cytochrome P450

enzymes (<20)

Clinical drugs metabolized by

one or more cytochrome P450

enzymes

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(Ma and Lu, 2011)

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Cytochrome P450 enzymes

a) CYP2D6

Metabolism of 20-25% of marketed drugs

Polymorphism best studied

Drugs: antidepressants, antipsychotics

b) CYP2C19

More than 20 polymorphism reported

Eg: CYP2C19*2, *3

Drugs: antiulcerative, anticonvulsant

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c) CYP3A4/5

Most abundant

Seen in human liver

Metabolism of more than 50% of drugs

20 variants identified

Eg: CYP3A4*16, CYP3A4*2CYP3A4*7

…cytochrome P450 enzymes

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Polymorphism of drug transporters

1. ABCB1 genes

Encode P-glycoprotein : transporter

protein

SNP C3435T occurs most frequently

Effects metabolism of drug statin

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…polymorphism of drug transporters

2. ABCG2 genes

Breast Cancer Resistance Protein (BCRP)

Polymorphism adversely affect disposition of

anticancerous drugs

Eg: Rosuvastatin

(Hesselink et al., 2003)

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How variants formed ?

SNP and addition, deletion, duplication of

nucleotide bases

Single nucleotide polymorphism - most common

variation

14 million SNP identified in human genome

60,000 SNPs are located in the coding region

Certain SNPs associated with drug efficacy

(Alwi, 2005)

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SNP and drug efficacy

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…SNP and drug efficacy

Statin- highly effective in reducing risk of

cardiovascular and cerebrovascular events

MDR1 gene helps in metabolism of drug

50 SNP were reported

3 main SNPs C3435T, G2677T/A, C1236T

Reduced bioavailability of statins

(Babu et al., 2012)

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Role of

bioinformatics in

pharmacogenomics

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Role of bioinformatics

Interdisciplinary field – develop methods and

tools for understanding biological data

Reduces time to interpret the data

Many bioinformatic tools and databases to help

pharmacogenomics

(Satendra et al., 2010)

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Bioinformatic tools and databases

Retrieval of data from databases

(Uniprot Knowledge Database )

Multiple sequence alignment using clustalW2

server

- To identify the identical, similar and different

regions in the sequences

- To generate phylogenetic tree

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ClustalW2

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Basic Local Alignment Search Tool (BLAST)

• Widely used for searching regions of similarity

between biological sequence

To compute the potential effects of SNP on RNA

structure use SNPfold

PolyPhen tool used for assessment of variants-

• Predict the functional effects of aminoacid changes

using 3D statistical models

…bioinformatic tools and databases

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…bioinformatic tools and databases

Pharmacogenomics Knowledge Base

(PharmGKB)

Information about variants

Interpret evidence behind each variant

Genes in which variants found

Variants influencing the drug

<http://www.pharmgkb.org>

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PharmGKB data base

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Clinical significance of

pharmacogenomics

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Warfarin:

significant problems for humans

Company director died- brain

hemorrhage

Warfarin effect: cause of the

death

(Brutlag, 2014)

David Belk, July 2,

2008

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Significance in cardiology

Anti thrombotic drugs : warfarin and clopidogrel

Oral coumarin anticoagulants (OCAS)

Enzymes influence OCAS dose response

1. CYP2C9- metabolizes OCAS

2. VKORC1- target for two drugs

(Ventola, 2011)

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…significance in cardiology

CYP2C9*2 and *3 variants inhibit the metabolism of

OCAS

VKORC1 – 1639G >A influences pharmacodynamic

response to coumarins

Improper metabolism- ADR

FDA – optimized drug dose for patients identified

with above variants either one or both

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Oncology

Human epidermal growth factor receptor 2

HER+3 variant - high level of HER2

Over expression – breast cancer

HER2 expression variability- Trastuzamb

treatment

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Diagnostics in pharmacogenomics

Highly accurate diagnostic tests are

available

First diagnostic- BRAC1: Myriad genetics

(1997)

Use high throughput technologies

(Daniel et al., 2014)

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Biomarker Disease Drug Assay

Kit

Technology

HER2 gene

amplification

Breast

cancer

Trastuzumab SPOT-

Light

HER2

CISH

CYP2C19

variants+

Depressi

on

Atomoxetine Roche

Amplichip

CYP450

test

FISH

Invitro diagnostic tests by FDA

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Biomarker Indication Drug Assay Kit Technology

EGFR

protein

expression

Colorectal

cancer

Cetuximab

`

EGFR

pharmDx

IHC

KRAS

mutation

Colorectal

cancer

Cetuximb Therascreen Real-time

PCR

…invitro diagnostic tests by FDA

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Personalized

medicine

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Personalized medicine

(Verma, 2012)

Prescription of drugs based on patients genetic

profile

Reduce speculation in drug prescription

Increases the confidence of both physicians and

patients

Every patient is different, we need to

individualize every patients therapy

Lung cancer

Victor- lung cancer (2010)

Too advanced stage for

radiation

Genetic mutation- ALK gene

ALK- Anaplastic Lymphoma

Kinase

37(www.uchospitals.edu/specialties/cancer/patient-

stories /victor-lung)

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… lung cancer

Discovered EML4-Alk gene in 2007

Pfizer, the company developed drug to block gene

Drug: Gizotinib

Prescribed dosage

CAT result: shrunken tumour and not producing

any new growth spots

Angelina Jolie Effect

On February 16, 2013 Jolie

underwent double mastectomy

Family tree warranted

genetic testing for BRCA

mutation

Found out 87% of risk in

developing cancer

Mastectomy lowered this risk

to under 5%

39(www.breast-cancer-research.com/content/16/5/442)

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…Angelina Jolie Effect

Mutation in BRCA1 and BRCA2 shows 45 to

90% chance to develop breast cancer

Jolie’s announcement in media, increased

number of women preferred for testing

A positive celebrity effect- Angelina Jolie Effect

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Benefits of

pharmacogenomics

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Benefits

Identification of diseases related to genes and specific

drugs- more drug specific cure

Categorizing of human diseases at genome level

Can adopt primary and secondary preventive

measures

Maximal patient care and minimum ADR

4343434343

Challenges in

clinical practice

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1. Ethical issues

Privacy of the study subjects

- Individuals

- Family

May not be affordable for a common man

- Developing countries

- Subsidized by government

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2. Legal issues

What is the legal liability if the genetic data is

lost ?

How much the doctor is obliged to inform the

person?

What is the legal issue for job discrimination?

(Bansal et al., 2005)

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Pharmacogenomics

in plants

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Significance in plants

Pharmacogenomic enzymes: significant role in plants

Plants are exposed to toxic compounds

Eg: Herbicides, insecticides and pollutants

Detoxification: P450 enzymes and ABC transporters

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Detoxification by plants

Plant CYP enzyme Herbicide

(Substrate)

H. tuberosus CYP76B1 Phenylureas

Soybean CYP71A10 Phenylureas

Tobacco CYP81B2,

CYP71A11

Chlortoluron

(Kumar et al., 2012)

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Phytoremediation

Using transgenic plants for herbicide metabolism

Uses cytochrome P450 genes from plants and

human

Transgenic rice encoding human genes

- CYP1A1, CYP2B6, CYP2C19

Showed more tolerance to atrazine and diuron

A promising field in near future

(Kawahigashi, 2009)

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Conclusion

A boon for medical fraternity

Unravels the genetic basis of individual

variability in drug response

Not well studied and exploited in plants

Right drug, in right dose for the

right patient at right time

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