AN INVESTIGATION OF THE GENETIC POLYMORPHISMS OF
N-ACETYL TRANSFERASE 2 IN HEALTHY
MALAYS, CHINESE AND INDIANS IN MALAYSIA AND IN TUBERCULOSIS PATIENTS ON
ISONIAZID
by
DR WAN NAZIRAH WAN YUSUF
Thesis submitted in fulfillment of the requirements for the
degree of Master of Science
August2006
ACKNOWLEDGEMENTS
First of
all.
I would like to express my heartfeltgratitude
to mysupervisor.
Rusli
Ismail. PharmD,
who never gave up on me. Isincerely appreciate
hisnever
ending advice, support, encouragement
andshowing
me thelight
when Ionly
sawdarkness. 1 thank him for hispatience
inreading
mythesis,
hisprecious
non-exhaustive scientific and technical advice.I would like to
acknowledge
theMinistry
ofScience, Technology
and Innovation for the researchgrant
that madepossible
thisstudy,
the Dean of School ofMedical
Sciences, USM,
INFORMM Director and Head ofDepartment
ofPharmacology,
School of Medical Sciences forlending support
andproviding
research facilities. I would also like to thank Dr Tan Sao Choon for
providing
meAct-INH for my HPLC and Dr Teh
Lay
Kek for hertechnical advice.I would like to thank members of the
Pharmacogenetics
ResearchGroup
fortheir
support during
the ups and downs ofmy research. 1 thank Nurfadhlina for her neverending support,
advice and discussions. I thank DrGan Siew Hua and Zuriati forcoaching
me with my first peRexperiments.
I thank SitiRomaino,
Khairi and Aziz forthe advicethey
gave toimprove
my PCRtechniques during
my methoddevelopments.
I would also like to thank Azaha(formerly
a research assistant atINFORMM)
forthe HPLClearning experience
and his
patience
inteaching
me. 1 would also like to thank Yasotha and Lee WeeLeng
for the many discussions we hadtogether.
I would like to thank En Wan Zainal for all the
help
that he gave me to ensure mytimely
thesis submission. I also thank all thefollowing
individuals fortheir invaluablesupport
andhelp:
Dr Hani Mohd Husin(TB/HIV Unit.
State HealthDepartment).
Dr Che Wan Aminuddin(HUSM),
staffs from TB clinicHUSM, HKB,
HPP and KKB KotaBharu.
DrWinKyi.
PuanMega
Herawati and EnLukmi
(Scientific Officer).
I would also thank mycollegues
DrRaju.
Dr Lau JenHou,
Dr Nik NorIzah,
Dr SitiArnrah,
Dr Aida Hanum and Fazni for theirsupport.
I am also indebted to all the volunteers and
patients
whoparticipated
in thisstudy.
Not
least.
I thank my husband for hisnever-ending support. patience
and forjust being
agood
listener and Iregister
aspecial
thank you to myparents,
mybrothers and sister and my children for their unconditional
support
andunderstanding.
TABLE OF CONTENT
Page Acknowledgements
Table of Contents iii
List ofTables vii
List of
Figures
ixList of Plates xi
List of Abbreviations xii
Abstrak xiv
Abstract xvii
Page
Chapter
1 Introduction and Review of Literature 11.1 Introduction 1
1.2 Literature review 7
1.2.1
Drug
Biotransformation 71.2.2
Pharmacogenetics
101.2.3
N-Acetyltransferases
141.2.4
N-Acetyltransferase
2 161.2.4.1 NAT2
Phenotype
and GeneticPolymorphisms
161.2.4.2 NAT2 and Other Diseases 20
1.2.5 Isoniazid
(INH)
211.2.6 Tuberculosis
(TB)
251.2.7 Mechanism of Resistance 27
1.3
Study Hypothesis
andObjectives'
29Chapter
2 AlleleSpecific
peRand NAT2Genotyping
2.1 Introduction 30
2.2 Materials and Methods 36
2.2.1 Chemicalsand
Reagents
362.2.2 Instruments Used for peR
Genotyping
and DNAExtractions 36
2.2.3 DNA extraction 40 2.2.3.1
Preparation
of Stock Solutions for DNAExtractions 40
2.2.3.2 DNA Extraction Method 42
2.2.3.3
Spectrophotometric
Detection of DNAConcentration and
Purity
432.2.3.4 Determination of DNA
Integrity
442.2.4
Development
of PCR Methods for the Determinationof NAT2
Polymorphisms
442.2.4.1 Primer
Design
452.2.4.2 Initial PCR Condition 52
2.2.4.3 PCR
Optimization
522.2.4.4 Final PCR Condition 57
2.2.5 Validation of the PCR Methods 63
2.2.5.1
Sequencing
632.2.5.2 Positive Control 63
2.2.5.3 Robustness 64
2.2.6 Gel
Electrophoresis
642.2.6.1
Preparation
of 6 XLoading Dye
642.2.6.2
Preparation
of 5X Tris-borate Buffer(TBE
64Buffer)
2.2.6.3
Preparation
of 1 X TBE Buffer 652.2.6.4
Preparation
ofAgarose
Gel 652.2.6.5 Gel
Image Capture
662.2.6.6
Interpretation
ofResults for GelElectrophoresis
662.3 Results 68
2.3.1 DNA Extraction 68
2.3.2
Genotyping
702.3.2.1 PCR
Optimizations
702.3.2.2 Final peR Conditions 77
2.3.2.3 Method Validation 88
2.4 Discussion 96
2.5 Conclusion 105
Chapter
3 GeneticPolymorph
isms of NAT2 in TB Patients andHealthy
Volunteers 1063.1 I ntroduction 106
3.2 Materials and Methods 109
3.2.1 TB Patients Enrolment 109
3.2.1.1 Inclusion Criteria 110
3.2.1.2 Exclusion Criteria 111
3.2.1.3 List of
Drugs
Known to Interfere with NAT2activity
1123.2.1.4
Study
Protocol 1153.2.2
Healthy
Volunteers Enrolment 1153.2.3
Sample Analysis
1153.2.4 Statistical Methods 116
3.3 Results 117
3.3.1
Demography
ofTB Patients 1173.3.2 NAT2 Allelic Variants
Among
TB Patients 1223.3.3 NAT2
Genotypes Among
TB Patients 1243.3.4
Demographic
Data ofHealthy
Volunteers 1273.3.5
Comparison
ofAllelic Variants betweenMalays,
Chinese and Indian
Healthy
Volunteers 1293.3.6
Comparison
ofGenotypes Among Malays,
Chineseand Indian
Healthy
Volunteers 1323.4 Discussion 139
3.5 Conclusion 146
Chapter
4Phenotyping
of TB Patients: A PilotStudy
1474.1 Introduction 147
4.2 Materials and Methods 152
4.2.1
Reagents,
Instruments andAnalysis
Condition 1524.2.2
Chromatographic Equipments
1544.2.3 Stock and
Working
Standard SolutionsPreparation
1564.2.4
Preparation
of INH and Act-INH for Calibrations 1564.2.5 H PLC Methods 158
4.2.5.1 Extraction Methods 158
4.2.5.2
Chromatographic Analysis
1604.2.6 Method Validation 161
4.2.6.1
Specificity
1614.2.6.2 Calibration Curve and
Linearity
1624.2.6.3 Precision and
Accuracy
1624.2.6.4
Recovery
1634.2.6.5 Limitof Detection
(LOD)
and LimitofQuantification
(LOQ)
1634.3 Results 163
4.3.1 HPLC Methods 163
4.3.2 Method Validation 169
4.3.2.1
Specificity
1694.3.2.2 Calibration Curve and
Linearity
1714.3.2.3 Precision and
Accuracy
1744.3.2.4
Recovery
1764.3.2.5 Limit of Detection
(LaD)
and LimitofQuantification
(LOQ)
1784.3.3 NAT2
Phenotype
1784.4 Discussion 188
4.5 Conclusion 195
Chapter
5 Discussion 196Chapter
6 Conclusion 202References 204
Appendices
Presentations
Arising
from this ThesisLIST OF TABLES
Page
Table 1.1 Factors that Influence
Pharmacology
11Table 2.1 Chemicals and
Reagents
Used in PCRGenotyping
37Table 2.2 Chemicals and
Reagents
Used in DNA Extraction 38Table 2.3 Instruments for PCR
Genotyping
39Table 2.4 Primer
Sequence,
Tm and Product Size for First PCR 47 Table 2.5 Reverse Primers with Common Forward Primer Used forSecond PCR with Tm and Product Size 48
Table 2.6 Forward Primers with Common Reverse Primer Used for
Second PCR with Tm and Product Size 49
Table 2.7
Summary
of Method for First PCR 59Table 2.8
Summary
of Methods for Second PCR 60Table 2.9 Estimated PCR Cost 95
Table 3.1 Characteristics ofthe
Study
Patients inGenotyping
andPhenotyping Study
119Table 3.2 Biochemical Test Results of Patients Included in the
Phenotyping
Studies 120Table 3.3 Site ofTB Infection 121
Table 3.4 Allele
Frequencies Among
TB Patients 123 Table 3.5 Observed andExpected Frequencies
with 95% CI of NAT2Genotype
for TB Patients 125Table 3.6
Demographic
Data ofHealthy
Volunteers 128Table 3.7
Comparison
of AllelicVariants of NAT2 amongMalays,
Chinese and Indians 130
Table 3.8 Observed
Genotype Frequency
amongMalays,
Chinese133 and Indians
Table 3.9 Allele
Frequencies
ofHealthy
Volunteers and TB PatientsAccording
to EthnicGroup
137Table 4.1
Examples
of HPLC Methods for the Determination ofIsoniazid and Metabolite/s 150
Table 4.2 Standards and
Reagents
forthe HPLC of INH and Act-INH 153Table 4.3
Instrumentation,
Parameters and Mobile Phase forthe 155 HPLC of INH and Act-INHTable 4.4
Preparation
of Calibrators for INH and Act-INH in Human157 Plasma
Table 4.5 Formula and Recommended Values for HPLC
Chromatogram
Parameters 166Table 4.6
Linearity
Data for Extracted INH 172Table 4.7
Linearity
Data for Extracted Act-INH 173 Table 4.8Precision, Accuracy
and Bias forthe Determination of INHand Act-INH in Human Plasma 175
Table 4.9
Recovery
Studiesfor INH and Act-INH 177LIST OF FIGURES
Page
Figure
1.1 INH MetabolismPathway
5Figure
1.2 The Fate ofDrugs
in the HumanBody
8Figure
1.3 Schematicview of the effects ofgenetic polymorphisms
ofbiotransforming
enzymes on metabolism of(pro)drugs
and 18(pro)toxins
Figure
2.1 Illustrations of the Flow of PCROptimization
to DetectVariations at 190
C>T,
341T>C,
499G>A,
803A>G and857
G>A,
Loci 55Figure
2.2Sequencing
Results 89Figure
2.3Chromatogram
ofSample
1 in Plate 2.19 94Figure
3.1 Flow Chart of TB Patients' Enrolment 113Figure
3.2 ObservedFrequencies
andPopulation Probability
Based onSample
with theirRespective
95% CI for TB Patients 126Figure
3.3Comparison
of Allelic Variants of NAT2 amongMalays,
Chinese and Indian from our
Study
and OtherPopulations
131Figure
3.4 ObservedFrequencies
andPopulation Probability
Based onSample
with theirRespective
95% CI forMalays
134Figure
3.5 ObservedFrequencies
andPopulation Probability
Based onSample
with theirRespective
95% CI for Chinese 135Figure
3.6 ObservedFrequencies
andPopulation Probability
Based onSample
with theirRespective
95% CI for Indians 136Figure
3.7Comparison
of AlleleFrequencies
for theMalaysian Population
between PresentStudy
and PreviousStudy
138 Done
by
Zhao etal.(1995)
Figure
4.1 Chemical Structures of INH and Act-INH 151Figure
4.2Chromatogram
of Extracted Blank Plasma 165Figure
4.3Chromatogram
of Un-extracted INH and Act-INH(Concentration
of 1 O�g/ml)
167Figure
4.4Chromatogram
of Extracted INH and Act-INH(Concentration
of 1O�g/ml)
168
Figure
4.5Chromatogram
ofSamples Spiked
withDrugs Commonly
Used in TB Patients 170
Figure
4.6 Plasma Concentration of Act-INH at4 hours in TB Patients 180Figure
4.7 In Plasma Concentration of INH at 4 hours in TB Patients 181Figure
4.8 INH Dose Versus INH Serum Concentration at4 Hours 182Figure
4.9 INH Dose Versus Act-INH Serum Concentration at 4 Hours 183Figure
INH Dose
against
MR 1844.10
Figure
INH
Dose,
MR to PredictedPhenotype
fromGenotype
1854.11
Figure
Probit Plot ofLog (Plasma MR)
of INH to Act-INH among 65186 4.12
Subjects
Figure
PredictedEnzyme Activity
Based onGenotype
toLog
4.13 Plasma MR
(INH
toAct-INH)
187LIST OF PLATES
Page
Plate 2.1 Gel
Electrophoresis Interpretation
67Plate 2.2 Gel
Electrophoresis
of DNA Extracted 69Plate 2.3
Single
ReactionsforVariation Detection at NAT 190 C>T,341
T>C,
499G>A,
803 A>G and 857G>A,
Loci 71 Plate 2.4Multiplex
PCR withEquimolar
Amountsof Primers 72Plate 2.5 Gel
Electrophoresis
Results of PrimerConcentration andMagnesium
ConcentrationAdjustment
73Plate 2.6 Effects of
Taq Polymerase
ConcentrationAdjustment
74Plate 2.7 Effects of
Annealing Temperature
onMultiplex
PCR 75Plate 2.8
Multiplex
PCRAmplifications Using
DifferentSamples
76Plate 2.9 Gel
Electrophoresis
ofFirst PCR 78Plate 2.10 Gel
Electrophoresis
Results for Detection ofVariations atNAT 190
C>T,
499 G>A and 857 G>A Loci 80Plate 2.11 Gel
Electrophoresis
Results for Detection of Variations atNAT 481
C>T,
and 759 C>T Loci 81Plate 2.12 Gel
Electrophoresis
Resultsfor Detection of Variations atNAT 845 A>C and 191 G>A Loci 82
Plate 2.13 Gel
Electrophoresis
Results for Detection ofVariations atNAT 590 G>A and 434 A>C Loci 83
Plate 2.14 Gel
Electrophoresis
Results for Detection of Variations atNAT 111 T>C Locus 84
Plate 2.15 Gel
Electrophoresis
Results for Detection of Variations atNAT 341 T>C Locus 85
Plate 2.16 Gel
Electrophoresis
Results for Detection of Variations atNAT 803 A>G Locus 86
Plate 2.17 Gel
Electrophoresis Containing
All the Second PCR for 187
Subject
Plate 2.18 Gel
Electrophoresis
for peR Performedby Participants
inthe First National
Colloquium
andWorkshop
inPharmacogenetics
91Plate 2.19 Detection of Variantat NAT 190 C>T Locus 93
List of Abbreviations
TB WHO HIV AIDS INH Act-INH NAT2 NAT2 NAT1 NATP SNP MDR-TB CYP2D6 CYP2C19 CYP3A4 CYP2E1 DNA SLE MTB PCR
PCR-RFLP
peR-ASO dNTP
Mili-Q water 1 X
EDTA TE TBE
Kel
- Tuberculosis
- World Health
Organizations
- Human
Immunodeficiency
Virus-
Acquired Immunodeficiency Syndrome
- Isoniazid
-
Acetylisoniazid
- Root
symbol
forN-acetyltransferase
2protein
or mRNA- Root
symbol
forN-acetyltransferase
2 gene orcDNA-
N-acetyltransferase
1 gene-
N-acetyltransferase pseudogene
-
Single
NucleotidePolymorphism
- Multi
Drug
Resistant Tuberculosis-
Cytochrome
P450 2D6subtype
-
Cytochrome
P450 2C 19subtype
-
Cytochrome
P450 3A4subtype
-
Cytochrome
P450 2E1subtype
-
Deoxyribonucleic
acid-
Systemic Lupus Erythematosus
-
Mycobacterium
Tuberculosis-
Polymerase
Chain Reaction-
Polymerase
Chain Reaction with RestrictionFragment Length Polymorph
isms-
Polymerase
Chain Reaction withAllele-Specific Oligonucleotide Assay
-
Deoxynucleoside Triphosphate
- Distilled and deionized water
- one time
-
Ethylenediamine-tetraacetic
acid- Tris-EDTA
- Tris-Borate
- Potassium Chloride
sec
min
-
Optical Density
- Basic Local
Alignment
Search Tool- National Centre for
Biotechnology
Information- distilled water
- double distilled water
- volts
- units
- base
pair
- wild
type
- mutant
-
melting temperature
-
High
PerformanceLiquid Chromatography
- Standard Deviation
-
interquartile
range- Confidence Interval
- undetermined
- failed
amplification
- Chi square
- microlitres
- milimolar
- rotations per minute
- Food and
Drug
Act- second
- minute 00
BLAST NCBI dH20 dDH20 V U
bp
wt mt Tm HPLC SD
iqr
el und FA X2
�I
mM rpm FDA
SATU KAJIAN POLIMORFISMA GENETIK N-ACETYLTRANSFERASE 2 DI KALANGAN
MELAYU,
CINA DAN INDIA YANG SIHAT DI MALAYSIA DAN DIKALANGAN PESAKIT TUBERKULOSIS YANG DIBERIKAN ISONIAZID
ABSTRAK
N-acetyltransferase merupakan
enzim yang ditemui dalamhepar,
ususkecil, pundi kencing,
paru-paru dan kulit. Iaberperanan
dalam metabolisme Fasa II untuk bahanasing yang mengandungi
amina aromatic ataukumpulan
hydrazine.
Ia bersifatpolimorfik genetik
yang disebabkanbeberapa
SNP.Substrat-substratnya
termasuk INH,pro-karsinogen
dankarsinogen.
Olehsebab itu, ia
berperanan
dalampatogenesis sesetengah
kanserdan dalamfarmakoterapi sesetengah penyakit,
contoh yangpaling penting
adalahtuberkulosis.
Objektif kajian
ini adalah untukmenyelidik jenis
dan frekuensipolimorfisme
NAT2
dikalangan tiga kumpulan
etnikpenting
diMalaysia
dan dikalangan pesakit
TB untuk membantu meramalpengaruhnya
ke atas kadarcepat
metabolisme INH.Sukarelawan sihat
Melayu,
Cina dan India telahdipilih daripada kalangan penderma
darah dan darah mereka diambil untuktujuan
menentukangenotip
NAT2. Pesakit yang baru
didiagnoskan dengan
TB telahjuga dipilih.
Darahuntuk
ujian genotip
danfenotip
diambil 4jam selepas pengambilan
INH dikalangan pesakit
yang dirawatdengan
INH.Ujian genotip
dilakukanmenggunakan
kaedah "nestedallele-specific multiplex
PCR" danujian fenotip
dilakukan
dengan mengukur
INH dan Act-INHplasma menggunakan
HPLC.Di
kalangan
sukarelawansihat,
frekuensi untukNAT2*4, NAT2*5, NAT2*6,
NAT2*7 dan NAT2*12 untuk 212
Melayu,
172 Cina dan 175 India adalahmasing-masingnya 43.4%, 10.6%,25.5%,
16.3% dan 4.3%dikalangan Melayu;
64.0%,3.2%,16.3%,12.2%
dan 0.3%dikalangan Cina;
dan22.6%,30.6%, 30.9%,6.9%
dan 3.4%dikalangan
India. Jenis dan frekuensi untuk allel NAT2dikalangan pesakit
T8 adalahNAT2*4, NAT2*5, NAT2*6,
NAT2*7 dan NAT2*12pada kadar47.4%, 14.0%,21.2%,12.9%
dan 2.3%masing-masingnya.
Genotip paling
biasa adalahNAT2*41*4, NAT2*41*7,
NAT2*41*5 dan NAT2*61*6 yangmempunyai
frekuensimasing-masingnya 25%, 18.9%,
15.2% dan 15.2%.Tiada
perbezaan signifikan
darisegi
frekuensi alleldikalangan pesakit
TB dansukarelawan sehat.
Bagi
62pesakit
yangmenjalani ujian fenotip, kepekatan
INH berkisar
daripada
0.31ke 4.17IJg/ml
danbagi
Act-INHdaripada
0.01 ke2.48
IJg/ml. Terdapat
tren untuk nisbah metabolik untukmeningkat dengan genotip
yang meramalkan aktiviti lebih lemah.Hubungan
di antaragenotip dengan
MR adalah walaubagaimanapun kurang
sempurna.Kami merumuskan bahawa kami telah
berjaya
membentuk kaedah-kaedah analisa yang telahdiaplikasikan
ke ataspeserta kajian
untukmengkaji
polimorfisme genetik NAT2, kedua-duanya pada tahap
molekul dan biokimia.Kedua-duanya
kaedah"allele-specific
PCR" dan HPLC yang kami bentuk adalahasli, sensitif, spesifik
danpraktikal
untukdigunakan
dalamkajian
populasi polimorfisme genetik
NAT2 dan untukdiaplikasikan
dalam keadaan klinikal.Kajian
kamimenunjukkan
NAT2 adalahpolimorfik dikalangan penduduk
Malaysia.
Polimorfisme ini adalahheterogenus dengan perbezaan
etnik yang ketara di antaratiga kumpulan
etnik utama. Namundemikian,
kamimendapati
yanghubungan
di antaragenotip
dan MR adalah tidak sempurna dankajian
lanjut diperlukan
untuk melihathubungan
yang lebih baik demipemahaman
lebih
mantap mengenai
peranannya dalamfarmakoterapi
tuberkulosismenggunakan
isoniazid.AN INVESTIGATION OF THE GENETIC POLYMORPHISMS OF N·
ACETYLTRANSFERASE 2 IN HEALTHY
MALAYS,
CHINESE AND INDIANSIN MALAYSIA AND IN TUBERCULOSIS PATIENTS ON ISONIAZID
ABSTRACT
N-acetyltransferases
are enzymes found in theliver,
the smallintestines, urinary bladder, lungs
and skin.They
mediate Phase II metabolism ofxenobiotics
containing
an aromatic amine or ahydrazine
group.They
aregenetically polymorphic
with severalimportant
SNP's. Their substrates includeINH, pro-carcinogens
andcarcinogens. They
therefore haveimportance
in thepathogenesis
ofsome cancers and in thepharmacotherapy
ofsomediseases, notably
tuberculosis.The
objective
ofourstudy
is toinvestigate
thetypes
andfrequencies
ofNAT2
polymorphisms
in the threemajor
ethnic groups inMalaysia
and among TBpatients
to forecast their influence on the rate of metabolism of INH.Malay,
Chinese and Indianhealthy
volunteers were recruited from blood donation drives and their blood was taken for NAT2genotyping. Newly diagnosed
TBpatients
were also recruited. Blood forgenotyping
andphenotyping
were collected at 4 hours after INHingestion
inpatients
who weretreated with INH.
Genotyping
was doneusing
nested allelespecific multiplex
peR methods andphenotyping by measuring plasma
INH and Act-INH on the HPLC.Among healthy volunteers,
thefrequencies
forNAT2*4, NAT2*5, NAT2*6,
NAT2*7 and NAT2*12 in the 212Malays,
172 Chinese and 175 Indians were43.4%, 10.6%,25.5%,16.3%
and 4.3%respectively
amongMalays; 64.0%, 3.2%,16.3%,12.2%
and 0.3% amongChinese;
and22.6%,30.6%,30.9%,
6.9% and 3.4% among Indians. Thetypes
andfrequencies
for NAT2 alleles in TBpatients
wereNAT2*4, NAT2*5, NAT2*6,
NAT2*7 and NAT2*12 at47.4%,
14.0%,21.2%,
12.9% and 2.3%respectively.
The most commongenotypes
were
NAT2*4/*4, NAT2*41*7,
NAT2*4/*5 and NAT2*6/*6 with thefrequencies
of25%, 18.9%,
15.2% and 15.2%respectively.
There was nosignificant
differencein allele
frequencies
of TBpatients
andhealthy
volunteers. For the 62patients phenotyped,
INH concentrationsranged
from 0.31 to 4.17j.Jg/ml
and for Act-INH concentration from 0.01 to 2.48j.Jg/ml.
There was a trend forthe metabolicratios to increase with
genotypes
thatpredicted
pooreractivity.
Correlation ofgenotype
to MR was howeverimperfect.
We conclude that we have
successfully developed analytical
methods thatwere
successfully applied
in oursubjects
tostudy
thegenetic polymorphism
ofNAT2,
both at the molecular and biochemical levels. Both ourallele-specific
PCR and HPLC methods we
developed
werenovel, sensitive, specific
andpractical
for use inpopulation
studies of NAT2polymorphism
and forapplications
in the clinicalsettings.
Ourstudy
revealed that NAT2 ispolymorphic
in our
Malaysian population.
Thepolymorphism
isheterogenous
with clearethnic differences for the three
major
ethnic groups studied. We however found that the correlation betweengenotype
and metabolic ratio wasimperfect
andfurther studies were needed to better define the
relationship
for animproved
understanding
ofits role in thepharmacotherapy
of tuberculosis with isoniazid.Chapter 1
Introduction and Review of Literature
1.1 Introduction
N-acetyltransferases
are enzymes found in thecytosol
of liver and the small intestines.They
are also found in smaller amounts inurinary bladder, lungs
and skin(Kawakubo
andOhkido, 1998). They
are involved in Phase II metabolism.N-acetylation
is themajor
route ofbiotransformation for xenobioticscontaining
an aromatic amine(R-NH2)
or ahydrazine
group(R-NH-NH2>,
whichare converted to aromatic amides
(R-NH-COCH3)
andhydrazides (R-NH-NH
COCH3) respectively. N-acetylation
masks the amine with a non-ionizable groupso that many
N-acetylated
metabolites are less water-soluble than theparent compounds. However, N-acetylation
of certain xenobiotics such as INHconverts its intermediates into more water-soluble derivatives thus facilitates their
urinary
excretion.NAT2 is associated with increased
susceptibility
todevelop
certaincancers when
exposed
to certaincarcinogen
orprocarcinogen
such asarylamine
orheterocyclic
amines which can be found indye substances,
well done meat andcigarette
smoke. Fastacetylators
forinstance,
are athigh
risk todevelop
colonic cancer whenexposed
to certainprocarcinogens (Gil
andLechner, 1998). Conversely,
slowacetylators
has beensuggested
to conferincreased risk of bladdercancers when
exposed
to certaincarcinogens (Marcus
Although
NAT2 mayplaya
role inenvironmentally
induced diseases like cancers, itsimportance
inpharmacotherapy
hasprobably
attracted moreattention. In
pharmacotherapy,
a veryimportant
substrate of NAT2 is Isoniazid(I NH),
aprimary drug
for tuberculosis(T8)
treatment(Petri, 2001).
It is also theonly drug
used in TBprophylaxis (Kinzig-Schippers
elaI., 2005).
It isparticularly
valued for its
efficacy
intreating TB, preventing
the emergence ofdrug-resistant organisms
and low cost(Jindani
elai., 2003).
INH has aunique property
ascompared
to other anti-T8drugs
where it has the mostpotent early
bactericidalactivity especially during
the first 2days
oftreatment ascompared
to other antiTB
drugs
such asrifampicin
andstreptomycin (Jindani
etai., 2003).
It also hasthe
ability
topenetrate
well into caseousmaterial, pleural,
ascetic fluids andmeninges (Petri, 2001)
ascompared
tostreptomycin,
sitesfrequently
affectedby
the infection.The
importance
ofINH cannot beoveremphasized. Although
TB is anancient disease the incidence ofwhich declined
significantly
with theintroduction of anti-TS medications in 1940's and
1950's,
it isre-emerging.
Theglobal
burden ofTS is nowgrowing
in many areas of theworld,
fuelledby
HIV/AIDS
infections, (Iyawoo, 2004). Immigration
from endemicneighboring countries,
increase in urbanmigrations
anddrug
abuse also contribute to the increased incidence of TS. The disease is notonly
associated withmorbidity
and
mortality.
It hits hardest theworking-age population,
thereforecontributing
to a loss of economic
productivity.
World Health
Organizations (WHO)
estimated about 9 million newTBcases and 1.7 million TB deaths in the year 2004 alone
(WHO, 2006).
Some 80% were in Sub-Saharan Africa andAsia,
coincident with the HIVpandemic.
In2004,
12.4 % of11,727
HIV/AIDSpatients
werepositive
for TB and 27% of84,947
TBpatients
were HIVpositive
in 41 countries(WHO, 2006).
HIV/AIDScauses
patients
to become more vulnerableto turnMycobacterium
Tuberculosis(MTB)
infection to active TB and more prone todevelop
active TB at exposure.With its increased co-occurrence with
HIV/AIDS.
it is alsoexpected
thatthe incidence of TB with resistant strains to increase.
Globally,
theproportion
ofTB caused
by drug
resistant strains isincreasing (Junien
etal., 2000).
IN2004,
the incidence of resistant strains was about 1% to INH and 0.1% to
multiple drugs (Iyawoo, 2004).
Thepercentages
may rise unlessappropriate
measuresare taken to
prevent
it.Multi-drug
resistant TB(MDR-TB)
is avirulent,
mutatedtype
of TB that is much more difficult to treat. Itsspread
is often acceleratedby
HIV infections.
Worldwide,
the rate of MDR-TB in the year 2000 was estimated at about 3.1 % or more than aquarter
of a million cases,although
very few of these werediagnosed
and treated.Treatmentfor MDR-TB costs 100 times more and
curability
cannot beensured. Frieden el al.
(1996) reported
that In New YorkCity
from 1990 to 1993there were
8,021
TB cases and 13% weremulti-drug
resistant(MDR). Thirty
five
percent
of the MDR strains were of the same strain resistant to INH at low concentrations(0.2 mg/dL
and 1.0mg/dL)
butsusceptible
to INH athigher
concentrations
(more
than 5mg/dL) (Frieden
etal.•1996). Drug
resistantTS,
particularly
disease causedby mycobacteria
strains which are resistant to INH andrifampicin (2
mostactivedrugs),
is much harderto treat and is often fatal(Frieden
elai., 1996). They
alsorequire
morepotent
second linedrugs
whichare
costly
and associated with more side effects.In
Malaysia,
the incidence of TB and its death rate arethehighest
among communicable diseases. About 10% of TB cases notified inMalaysia
werehowever detected among
immigrant population
who were fromhigh
burdenneighboring
countries(Iyawoo, 2004).
The incidence isincreasing.
In 1985there were
10,569
TB cases, of which6,682
wereinfectious,
in 199312,075
cases of T8 were
reported
with6,954 being
infectious and in 2000 there were15,057
TB cases with8,156 being
infectious(MOH, 2001)
INH
undergoes
metabolism in the liver(Figure 1.1). N-acetyltransferase
2(NAT2)
converts INH toacetylisoniazid (Act-INH).
NAT2 enzyme ispolymorphic
and is coded
by
the NAT2 gene(Hein, 2002)
that has several knownSingle
Nucleotide
Polymorphisms (SNP's).
Todate,
13 SNP's have beendescribed, leading
to more than 29 allelic variations in the NAT2 gene. The effects of these variations on the enzymeactivity
can begrouped
into 3categories:
the socalled
"fast",
"intermediate" and slowacetylator phenotypes.
Slowacetylators
metabolize INH at a rate much slower than that among fast
acetylators.
As aconsequent,
Chen el al.(2006)
found a 35-fold inter individual differences in INH concentrations whenthey
administered300mg
INH to 46 individuals.OOH II I
N C -N-
NH2
Pyruvic hydrazone
INH
a-Ketoglutaric hydrazone
O H H O
]J
III
C-N-N -c -el-h
conjugation
*acetylation
Act-INH
Monoacetylhyd
razinel
·acetylationDiacetylhydrazine
Isonicotinic acid
l
Isonicotinyl glycine
Figure
1.1 INH MetabolismPathway, adapted
from Weber and Hein(1979)
• indicate involvementof NAT2 foracetylationAn
important
feature with NAT2polymorphism
amongpopulations
lies in the factthat,
on the average more Asians are fastacetylator phenotypes
compared
to Caucasians.Thus,
90% ofJapanese
are fastacetylators
of INHbut 40 to 70% ofCaucasians are slow
acetylators (Chen
eta/., 2006).
Thecurrent
practice
ofgiving
INH doses based on Caucasianrequirement
toAsianpatients
is thereforeinherently
flawed. Some strains ofmycobacteria
areresistant to INH at lower concentrations but are
susceptible
athigher
concentration. As
suggested by
Freiden etal.(1996)
there is thus ahigher possibility
for thedevelopment
of INH-resistant strains among fastacetylator
Asian
patients,
asthey
areexpected
to have lower INH concentrations ifgiven
dosesdesigned
togive adequate
concentrations in Caucasianpatients.
Another
problem
withacetylation polymorphisms
for INH metabolism isdevelopment
ofsideeffects inpatients
who are slowacetylators.
Since slowacetylators
metabolize INH at slowerrate,
there aretendency
of thedrug
toaccumulate in the
body.
These accumulations may lead to side effects such asperipheral neuropathy, drug-induced hepatitis,
and seizures. The side effects may lead topatients' non-compliance
to thedrug
which may later contribute todevelopment
of resistance strains and it also reducespatients' quality
of life.The
study
ofpharmacogenetics
willhopefully improve
theefficacy
andsafety
ofthe
already long existing drug,
INH and assist theproblem
ofnon-compliance
due to side effects. This we
hope
will alsohelp
inpreventing morbidity
andmortality
in T8patients.
This thereforesuggests
a need for further studies to determine theoptimum dosage
for INH among Asians and to determine its influence on outcomes of INHtherapy
for TB.1.2 Literature Review
1.2.1
Drug
biotransformationOnce a
drug
isadministered,
it is absorbed and distributed to its site of action where it interacts withtargets
such asreceptors
and enzymes,undergoes
metabolism and is excreted(Figure 1.2).
Because of the need fordrugs
to interact with lifecomponents, drugs
areusually hydrophobic
and this makes itdifficultfor thebody
to eliminate them as eliminationusually requires
water
solubility.
Metabolismusually
convertsdrugs
to metabolites that are more watersoluble(Sweeney
andBromilow, 2006)
and are thus moreeasily
excreted. Some other
drugs however,
do not have an inherentpharmacologic activity
andrequires
"activation". Metabolism can also convert these"prod rugs"
into
therapeutically
activecompounds.
Via the samemechanism,
metabolism may even result in formations of toxic metabolites from entities thatarepharmacologically
active or inactive.Drug
metabolism cangenerally
be classified as Phase I reactions(oxidation, reduction, hydrolysis)
and Phase II reactions(acetylation,
glucoronidation,
sulfation andmethylation).
Phase II mayprecede
Phase I andoccurs without
prior oxidation,
reduction orhydrolysis
if there arepolar
substrates
(Sweeney
andBromilow, 2006). Both,
mostoften,
convertrelatively
lipid
solubledrugs
intorelatively
morewater-soluble metabolites.�Xl�;�;:-' �.:.'
.}�I-�
1-...._ot-·.�_.I_·;
I'�:.:.i.�:,..·:��._.
Figure
1.2 The Fate ofDrugs
in the HumanBody
The
principal
organ ofdrug
metabolism is the liver.However,
every tissue has someability
to metabolizedrugs.
Other tissues thatdisplay
considerable
activity
include thegastrointestinal
tract,lungs,
skin and thekidneys. Following
oraladministration,
mostdrugs
are absorbed intact from thesmall intestine and are
transported,
first via theportal system
to the liverwherethey undergo
extensive metabolism known as the first pass metabolism.Intestinal metabolism may also contribute to first pass metabolism for certain
orally
administereddrugs
which are moreextensively
metabolized in the intestine than in the liver. Such is theexample
withnifedipine,
adrug
thatundergoes
metabolismby CYP3A4,
an enzyme found inlarge quantities
in thegastro-intestinal
tracts. The first pass effect maygreatly
limit thebioavailability
of
orally
administereddrugs.
It is not
only drugs
thatundergoes
metabolism. Otherforeign
chemicalsor xenobiotics include man-made chemicals and nature's creations. Such are
industrial
chemicals, pesticides, pollutants, pyrolysis products
in cookedfood, alkaloids, secondary plant
metabolites and toxinsproduced by molds, plants
and animals are also
subjected
to metabolism. Also included is the conversion of procarcinogens
tocarcinogens
or non-activecompounds
tocarcinogenic compounds
in thebody.
The environmental substances humans are
exposed
to are notonly
metabolized. A number of them are known to affect the
activity
of liver enzymesinvolved in
drug
metabolism. These substances include certainfood,
medications,
recreational substances such asalcohol,
tobacco andpollutants
found in the household and the
atmosphere.
Other than liver enzymes, several factors are also known to influence the metabolisms of xenobiotics. These include age, sex,hereditary
andgenetic factors,
diseasestates, dietary
andnutritional status, hormonal
changes
in thebody
andactivity
of liver enzymes(Sweeney
andBromilow, 2006).
1.2.2
Pharmacogenetics
In the
1950's,
anesthetists who gavepatients succinylcholine
observedthat some
patients
went intolife-threatening respiratory
arrests on theoperating
tables. Itwas
similarly
observed that somepatients given
INH for TBdeveloped peripheral neuropathy.
Thus variable response todrug therapy
became ofconcern. Beta-blockers are ineffective in one third of
patients. Antidepressants
do not work in half the
people taking
them.Therapeutic
doses for warfarin in agiven patient
can cause severebleeding
in another.Why
does onepatient
suffers an adverse reaction and others don't?Why
does aparticular drug
workswell for one
patient yet
have little or no effect on otherpatients?
Table 1.1 Factors that Influence
Pharmacology
INTRINSIC
I
EXTRINSIC I
I
I I
-
Genetic Physiologicalandpathologicalconditions Environmental
I i
I
I
Age(children-elderly)I
Gender I Climate
I
Height
L�h'
PoIlu,io,Bodyweight
I LiverKidney Culture
I
Cardiovascular functions Socioeconomicfactors EducationalstatusI I
LanguageI
--
ADME Receptor sensitivity
I
Race
I
I MedicalpracticeI
, DiseasedefinitionlDiagnosticTherapeutic
I approach
! Drugcompliance
L-
Geneticpolymorphismof thedrug I
metabolism I
I
-_
-_----_-_
Geneticdiseases Diseases Regulatorypractice/GCP
,
Methodology/Endpoints
�--_ --
I
SmokingAlcohol FoodhabitsStress
11
The answer lies in the individual variations of human in
drug
response.Human
variability
indrug
response has been associated with several factors which can be divided intophysiological
and environmentalfactor (Table 1.1).
Physiological factors
include age,gender, ethnicity
andbody weight
andenvironmental factors include
dietary intake,
concomitantdrug
administration and exposure to certain chemicals(Koo
andLee, 2006).
Genetic variation isincreasingly recognized
as animportant
factor in thevariability
ofdrug
response. Individuals' functional variants caused
by
SNPs in genesencoding drug metabolizing enzymes, transporters,
ion channels anddrug receptors
areassociated with inter-individual and interethnic variation in
drug
response,genetic
variations in these genesplaya
role ininfluencing
theefficacy
andtoxicity
of medications(Koo
andLee, 2006).
It is now known that muchindividuality
indrug
response is inherited. The clinicalconsequences range
frompatient
discomfortthrough
serious clinical illness to the occasionalfatality (Wolf
et
al., 2000).
Thegenetically
determinedvariability
indrug
response defines the research area known aspharmacogenetics (Wolf
etal., 2000).
Pharmacogenetics
has been defined as thestudy
ofheredity
andresponse to
drugs (Koo
andLee, 2006).
The aim ofpharmacogenetics
is toaid physicians
in theprescription
of theappropriate
doseof
theright
medicine to aperson in an
attempt
to attain maximumefficacy
and minimumtoxicity
based ongenetic
tests(Koo
andLee, 2006).
In thefuture, individuals
who inherit the enzymedeficiency
may benefit fromappropriately adjusted
dosesof
theaffected
drugs
based ongenetic
tests. It is agrowing discipline with great
potential
ofimproving
humanhealth-care,
in termsof understanding individual
drug
responses, adversedrug
reactions associated withgenetic
so thatmedicine could be tailored
accordingly
toprevent
side effects and thusreducing
cost of
therapy
andhospitalization. Pharmacogenetics
can alsoprovide
information about
genetic
characteristics of a disease which could be used toimprove drug design
andimprove efficacy
andsafety
ofexisting drugs.
Infuture, pharmacogenetics
mayhelp
in the determination of risk ofdiseasebased on the identification of
susceptibility
geneearly
in life and thus measures can be taken to avoid the disease.Pharmacogenetics
isimportant
when thedrugs prescribed
have narrowtherapeutic
indexes and the metabolismpolymorphic.
It is alsoimportant
that when newdrugs
aredeveloped,
pharmacogenetic
variations are knownearly
in thedevelopmental stage
so asto avoid unnecessary costs of
drug
misadventures due togenetic
traits.Pharmacogenetics
is not a newdiscipline
but its progress has been slow.The
concept originated
from clinical observations that somepatients
had veryhigh
orvery lowplasma
orurinary drug
concentrations followedby
realization that the biochemical traitsleading
to this variation were inherited. The term wascoined in 1959
by Vogel
to describe thestudy
ofgenetically
determinedvariations in
drug
response(Smits
etaI., 2004.
Eichelbaum andEvert, 1996).
Overthe
past
25 yearshowever, pharmacogenetics
hasprogressed rapidly especially
in relation to thepharmacogenetics
ofcytochrome
P450(Smits
elaI., 2004).
The
applications
ofapharmacogenetics approach
totherapeutics
ingeneral
clinicalpractice
is still far frombeing
achievedtoday owing
to variousconstraints,
such as limitedaccessibility
oftechnology, inadequate knowledge, ambiguity
of the role of variants and ethical concerns(Koo
andLee, 2006).
Sofar, pharmacogenetic testing
iscurrently
used inonly
at a limited number ofteaching hospitals
andspecialist
academic centers. It iscurrently
mostadvanced in the Scandinavian countries
(Wolf
etal..2000).
The mostwidely accepted application
ofpharmacogenetic testing
is the use of CYP2D6genotyping
to aid individual dose selection fordrugs
used to treatpsychiatric
illness. In
Malaysia,
nopharmacogenetic
tests are availableroutinely currently.
1.2.3
N-acetyltransferases
N-acetyltransferases
are enzymes found in thecytosol
of liver and the small intestines.They
are also found in smaller amounts inurinary bladder, lungs
and skin(Kawakubo
andOhkido, 1998). They
are involved in Phase II metabolism.N-acetylation
is themajor
route of biotransformation for xenobioticscontaining
an aromatic amine(R-NH2)
or ahydrazine
group(R-NH-NH2),
whichare converted to aromatic amides
(R-NH-COCH3)
andhydrazides (R-NH-NH
COCH3) respectively. N-acetylation
masks the amine with a non-ionizable groupso that many
N-acetylated
metabolites are less water-soluble than theparent compounds. However, N-acetylation
of certain xenobiotics such as INH converts its intermediates into more water-soluble derivatives thus facilitates theirurinary
excretion.N-acetyltransferases
are codedby
theN-acetyltransferase
gene(NA n
located on chromosome 8 at locus