643
The integration of microarray information development process Scott Inthe
Braxton*
and Tod Bedilion?
past year, microarray technologies
stage. Microarrays
being used for genome-wide
expression
polymorphism
screening
large nuniher
have moved
beyond the proof-of-principle large-scale
in the drug
si\,ely
are now
csprcssion
monitoring,
of
and mapping, and for
of probes
p:irallcl
ci”“ntific~ltion.
niolccular
biology
sc:llin,q technologies.
the evaluation of drug candidates. Addresses Syntenl Inc., 6519 Dumbarton Circle, Fremont, CA 94555, USA
IIIIO\VS ;I rcse:ircher
‘:e-mail:
[email protected]
tcncc ofniiiltipl~
‘e-mall:
[email protected]
sinj$e
Current
Opinion
in Biotechnology
1998,
of
hlicroarrays
step
to nic;lsurc
EST
information
is ciirrcntly
RA SNP
single
nucleotide
high-density
arc
oligonllcleotitlcs
‘1%~ pharmaceutical
scqiicnti:ill~
intiustr)
is bcinfi
the incrc:iaecl cost ofqztting
profitabilit);
the number
aping. dccreasc dc\-clopnient dccrc:ise nitics.
the Liilurc ‘I‘licre
dc\~clopnicnts lcnis l:or
thy
arc dcvcl-
clecrc~sc clinical
costs,
riitc. and de\,elop better drug opportu-
ha1.e hccn
;I
in rcccnt )ears
csamplc. the cuplosion an unprcccdcnted
for drug development. prlt \crccning
I>ct\vccn
and rcduccd
drug companies
of drugs
timr,
nnnil,er
of
technological
that ha\,c sol\,cd some proI,-
in the driig dc\ clopnient
produced
scjuee/.ed
;I drug to market,
maintain
~1ill need to incrc:isc
funnel.
but created others.
of genomic number
inforn~ation
of potential
\\‘ithin
in medical diag-
used
nianagcincnt
of patients.
has
Ius reduced
and IIOW ultr:l-tl’l’PLS
the tinic to screen \,alidated targctc
and
in
:icti\,c
Ilk,4
hybridization
iisc.
One
s)-nthcsizcd masked
dircctl~
photolabile
[ 1.11. the other, IISCS long l)Nr\ 3rd
by IY:K,
[Si].
‘Ike
short his
gcnc chips
cIsc\\ here [&I?]. stanci;trdizing dticiblc focuses
chcniistq
t)pically
substrate
gcncr-
using robotics
of microarray
and
and rc\.icwcd cxtcnsi\-cl? are being made in
g each tcchnolojiv
assays [13-1.5.16”].
ircliahlc
on the utility
using
:id\mces
and clii:intif!-in
:intl
on :i substrate
history
clcscribcd
Significant
short
fragments.
technological Bern
tech-
of
nuclcotidc
on ;i suitable
printed
ma!-
consists
ofniicroarra~-
into repro‘i’his
information
rc\ic\\
in the driig
de\~elopnicnt process.
targets
‘I‘hc dc\~elopment of high-through-
(H’I’I’S).
\vill I,c
Microarray technology ‘Ii\.0 prini:ir)-
polymorphism
Introduction
‘Ii)
of 1 iable drug
drug toxicit);
tag
nologies
drug rc\‘cnncs.
;I
(;enc
being iised to hc1p 1 al-
to help in the sclcction
and for the clinical
esis-
c:irryorit
of conditions.
unti to p-edict potmtial
nostic tests
expressed sequence rheumatoid arthritis
‘I’his
csprcssion
to probe for thr
for thousands
the nc\-t dec~ide. niicroarra!-s
Abbreviations
mKNX
or e\entiiall~
diagnosis
c Current
669
the
gene niut;itions.
candidates.
0958-I
no\xl engineering-interisi~.~ that t~sed to be done
with
http://biomednet.com/elecref/0958166900900643 Ltd ISSN
gene
the po\vcr
H~hridizations
idate drug targets.
Biology
or
combine
10,000 gcncs simultaneo~isly,
c\-prcssion
9:643-649
‘I’hcb- pro\,ide niassequrncing
can no\v be done 10,000 at 3 time.
one-Lit-3-time Ic\zl
arc attached.
h~,bridization-based
find potential
lead
Genetic analysis Recent applications analysis
support
in
the
the effort
arca of Lirray-hascd
to derix
practical
genetic
inforniation
htit has produced an c\-plosion of c01~~p0111~ds for the cntirc drux disco\xr) process, from mapping discase genes to stratifying patient populations in clinical to c\xluatc for dc\-clopnient. I:inally, many dnigs ;irc onl! defining allele-specific therapeutics. fractionall? cffccti\ c. or effecti\ e in only certain s11l~p0p11- trials. :incl ultiniatel~ lations and positi\c clinical outconic ma)- not Ix possihlc Genome-wide mapping \\.ithout siihscttinfi the population.
compo~~~idc,
\I’inzclcr
\I;in) steps in dtq de\~clopmcnt ;irc incft‘icient :rnd ne\\ nicthocls riced to Ix cmplo~cd that ;irc miich niorc prcdicti\.c of the cffccts of drilxs on humans. ‘l‘hcsc nicthods riced
nrc)
to md
he
rclati\-cl!
incrpcnsi\.e
(compared
deployable cad? in driif
to tlrug
kiil-
yclist
CT o/.
using
inap of the entire niiiltidrng
of the effects (icnctic
analysis
sti-atifying and
on cells,
is us&l
patients
3rc cspccted sion
of drugs for
are a poIvci+ul tissues.
for mapping cffccti\e
to be the dominant
or whole disease
treatment.
four
are small
t\~o-dimcnsioi~~li
genes and for cxprcs-
de\ elopnient.
surfaces
was then iised
l0c11s. ‘I’lie authors
Iv idcntificd
:ipplicd
confirming
gcncs. and localizing
kno\Vn
of mapping
3 high
in
resolution to map II the new
the loca-
the prcviousl>
gcnc to a 57 kh region that LV;IS subsequent-
II? ;I c;indid;itc
;ippro;ich
and dclction
anulysis.
animLlls.
\licroarrays
tcchnolog>-
gcnctic :inaI> sis in pharmace~itical
hlicroarra!s
nic;isurc
the cast
generated
map to a set of fi\.c Ioci. siniultancousl~ rinkno\\-n fifth
(;lolxil cl~angcs in jiene expression
‘Ilie!
genome which
rcsist:ince
tion of the
dc~~clopnicnt.
[ 17’1 dcnionstr;itc
oligo arrqs.
to ~7hich 3
Single nucleotide I’ol~niorj’hisiii has :ilso
polymorphisms
disco\.cr)
(typically
and chips
screening
found broad applic:ition
approach of c:it:iloging phisins
and
with
using
and assayin :: indi\.idunl
sinfilc
niicleotide
niicroarra)-s
the niorc
directed polynior-
pol~inorphisiiis
644
Pharmaceutical
Figure
biotechnology
1
(4
tcca
ram
THP.1 Control
(d)
loa
10332
1OuOrn
THP-1+ PM?!
63)
10
1w
lam
lum
lm!m
Thp.1 Control Current Opinion
Expression monitoring for 10,000 genes in a model of inflammation. (a) THP-1 cells were differentiated to a macrophage-like state with PMA for 48 hours. (b) Several genes characteristic of neutrophils disappear (cathepsin G, monocyte chemoattractant protein [MCPl] receptor, GCSF receptor), and macrophage-associated genes are upregulated (osteopontin, IL1 -/3, IL6, CD-I 4). (c) Subsequent stimulation with lipopolysaccharide (LPS) for four hours produced
a
I”
Eiwtechnology
profound change in gene expression patterns. (d) Several cytokines including SCYAP, MIPl-0, LD78, IL6, and MCPl are highly upregulated. In addition, the drug target of NSAlDs, prostaglandin G/H synthase, is highly upregulated. Ten of the top 23 upregulated genes are ESTs. The reproducibility of the assay is demonstrated in (e) where the same sample is hybridized against itself; 99% of the elements gave differential expression values < +/- 1.4.fold.
The integration of microarray information in the drug development process Braxton and BedIllon
(SNPs]). oligo
the
Initial
implemcntlitions
arrays covering mitochondrial
membrane
ha\,e
of the HI\‘-1 genome
segments gcnome
conductance
included
[l].
the
regulator
cystic
gene
fibrosis
645
Figure 2
short
[1X], trkms-
[ 191, and the beta
globin gcnc [ZO]. Hacia ul N/. [21] describe a refined method using tvwcolor competiti\-e hybridization to scan the 3.45 kb cxon 11 of the RR(X1 gene. ‘I’he high information density and ability to scan for nerv polo-morphislns v,irh
these
arrays
is particularly
important
in allelicall>
genes. such 3s 13R(Al. whew heterogcneows expected I0 be extcnsi\,e and unpredictable. ‘1%~ next step to extend many genes nndcrtaking
is nicely described
SW
screening
variation
and analysis
\
Tamoxifen
is
across
illustrated b)- the large collaborati\,e I~\- \I’ang @ l/l. [22’]. ‘I’his massi1.e
effort scanned almost 17,000 sequence tagged sites (Z/3 of \rAiich \\ere expressed secluence tags [WI’s]) across a total of 2 \Ib of sequence, and required 1-D unique fabrications of short oligo microarrays. Because of assav scnsiti\,ity and complexity constraints in the human genomc, probes were gcncrated from pools of IY:R products requiring specific primers for each of the 17,000 sequences snnqed across each of sc\zn indi\ iduals. ‘I’he rcsnlt turned up approximately 3000 SNP candidates. ‘I‘he survev information ;1 dedicated genotyping arr+ for.2 test subsct
\\‘a~ reduced to of .5.58 SNPs.
(:oniplimentary mapping utility is predicted for the method of genomic mismatch scanning (GhlS). GhlS selects rhc population of fragments that are identical b)- descent among members of a pedigree or lvirhin a population by a process of solution hybridization and enzymatic selection of heteroduplex-hybrids containing no mismatches. High resolution mapping information is derived from labeling and hyhridization to high densit); microarrays if there is ;I sufficient number of mapped and ordered clones. I:irst de\,eloped in the Iess complex )-cast genome [23,21], current refinements show promising hybrid enrichment in human samples [25,X], vhich could facilitate disease gene mapping [27-311 and genome-wide scanning for relevant allelic \wiation \+,here large pre-cataloged
sets of SNPs do not already
exist.
‘I’he potential value of these approaches incited rhc current expansion of commercial efforts and alliances based on col&ring and typing polymorphism information. Studies and statistical approaches using SNP and polymorphism data are becoming more sophisticated [32-341. Array-based methods clearly add needed leverage, but because of the current limitations on sensitivity, throughput, and accurac); the most effective formats probably remain to be developed.
Expression analysis Small arrays to large arrays to time-course studies Heller et a/. [3.5] provide the first example of profiling genes involved in disease progression using small 5%cI1NA microarrays, which include genes previousI) implicated in this process in the literature. In a model of inflammation, cytokines and chemokines were upregulatcd as expected. Comparison of primary chondrocytes and
Ethinylestradiol Current Op~monI” Biotechnology
Cladistic representation of Inflammation. U937
for different steroid treatments in a model cells were differentiated with 100 nM phorbol
mynlstlc acid (PMA) for 48 hours, followed by the combination of lipopolysaccharide (LPS) (10 ng/ml) and TNF-c( (0.1 ng/ml) for 24 hours with or without
one of 10 steroids.
Differential
expression
Information was generated using 10,000 gene microarrays. To compare the relatedness of different steroid treatments, a distance matrix was generated differentially experiments. the publically using
expressed Clustering avallable
Drawtree.
Inflammation hydrocortisone)
from the correlation
Philip
package.
The four steroids
(fluocinolone, gave quite
by the tight clustering
coefficients
for genes
by greater than threefold in any one of the was calculated using the Kitch program In The diagram
commonly
dexamethasone, stmllar expression
was drawn
used to treat prednisone, patterns,
and as shown
above.
s)-no\ iocytes from human rheumaroid arthritis (RA) tissue gave remarkably similar profiles upon srimulation \vith ‘I’NP and 11,-l, thus demonstrating the utility of primary cell culture as a model for authentic human disease samples. (:omparati\,e analysis of R.4 and inflammatory bowel disease revealed both qualitative similarities, underlying the similar inflammatory nature of both diseases, and distinct differences, representing inflammaGon in intlammarorl;
the more subdued level of bowel disease. ‘l’he repro-
ducibility of this assay and the underlying biology is demonstrated by the fact that samples from se\zral Ii.4 patients gave similar results. as did rcpcat samples from the same patient. DeRisi ectrl. [ 1.51used larger microarrays containing a mixture of known and anonymous genes to identif! the genes on chromosome 6 responsible for tumor suppression. Probes were derived from the 1YACC-903 melanoma cell line and ir’s non-tumorigenic counterpart IJACC-903(+6) suppressed b) addition of a normal chromosome 6. Of the 870 unique genes arrayed, 1.7% were downregulated and 7.3% were uprcgulated in rhe non-tumorogenic strain as compared to the melanoma cell line. In each case, Northern analysis verified the microarray rcsuhs. ‘I’he authors speculate that the specific genes that change their expression and camsc tumor suppression are candidates for therapeutic intervention.
646
Pharmaceutical biotechnology
Figure 3 Expression profile for several drugs and one Non-specific activator
15
Lead candtdate
Optimized
lead
Known
toxin
Best drug
toxin. HepG2
cells were treated with a variety of
agents, and the expression using a 10,000
(a)
(b)
(d
Cd)
In each treatment
(e)
represents
the target gene: 5-, 4-, respectlvely.
proflle IS captured
gene microarray. The first gene the upregulatlon
12.,14.,
To slmpllfy the representation,
genes with a dlfferentlal expression than twofold up- or down-regulated In addition to upregulating deacylating
of
15.fold only
of greater are shown.
the target, a histone
agent control (a) caused a variety of
genes to be turned on and off. (b) The lead candidate
only caused fourfold upregulation
of
the target. (c) Medlclnal chemistry produced compound which upregulated the target by 1 P-fold, and was consldered candldate
for development.
to be an excellent Microarray analysts
revealed that several unexpected signlflcant
changes
a
genes had
Cd)The
In expression.
expresslon
profile matched closely to the pattern
generated
by a known toxic agent. The cellular
toxlclty of the optimized lead was vertfted using an in vitro assay. Medicinal chemistry efforts, starting with a different lead compound,
Gene index Current Op,n,on ,n B,atechnology
;\n:tlyzing ,qencs
esperinicnrs cliallcngcs
on
the
microarra!s
in\,estigator
10.000
recruit
other
out
tlndcr
uviind
hcding.
from
and espind rhc information set for wcn the niosI well de\ eloped systcnis. I.sing such arrays in model ofintlamm~ltio~~. ‘I’HI’-1 cells (a monoc~tic ccl1 line) ucrc diffcrcnriatcd I0 ;I macroptiajic-lilcc state \vith phorrhc
lamp’
street
the 3
I~01 niyristic acid (I’hl.Ii) ~intl then actiutcd I\ ith 13 (:ocks. (; I’ortcr, lil~o~~ol~sacch~iritlc (S Braxton, .I Scilhanicr. iinpul~lished data). Ikspitc the well-explored mxiin of classic infl:ininiation moclels, se\xxrl l> follmving
tibroblasts
not
authors
siniilar
of three
response distinct
sccrctc
applied
to
pitwrns of the
gents
through
tinic
to
resol~cd
inro
he
‘I’hc
first
of transcription response.’
;I series
of
:inal\-zc
an algorirhm
richness
phases.
in csprcssion
‘reprojiramming
feasible
expression ‘I’hc
10,000
healing
by chxijics as the
is
commllnicatioii).
\\otind image
it
so the
Ixiscd
gcncs
phase.
third
in
rhc
tilxd)lasts
In addition
dvnamic
rcsunx e
rcniodclin~
their
of
prolitkition
in
;111
~iind cktentling
verifying
pukis work on gcncs inwl\cd in w011ncl haling, the\ found a nunilxx of gcncs and parhv ays u host role in 1, oiin;l healing \\‘;I\ iincyxcrccl, but casity rationalid. ‘l’his i5 ;I proniincnt indicarion that microarray will pro\ iclc ddirional ~~~~l~~al~lc inforniation foi- e\en \\-cl]-charactcri/.cd svsum5. In addition, :I \xr! large set of nox~l gcncs \\ crc found I0 Ix diffcrcntially Iregiilatcd during the \\oiind-healing rcsponsc.
:is iman\ of die iinkiio~~~ii genes clusrcr \I itli uell-kno\\n patterns pro\idc the tii-st hints :il)our hwncs, their expression their
fiinction.
‘1%~ :it)ility
scs about
the
qqxo;ich
to functiond
of a
tiinction
art: three analyiis
‘I’tiere
list
‘I’he
I0 generate
more
no\ cl bs’l
\\,ill
assignnicnt
of
na-row allo\\.
no\ cI
h! pothc-
2 s;\‘swni;itic
I- Ixxause
\vcrc also altcrcd
general
of the entire
and abour
can Ix
the silwtion
site
inacri\ ad
might
of the mniendws
Additionally
the authors
the
step
againsr
will
u,hich
ix
midi
types
~ipproxh
rhese complcn regiilaumy
\\as used
:IS the basis for iteratiw and biological
c\,clin-dependent
sulxet
of the
I0 die drug nutniutuil.
is ;I
‘I’his
or
us):
cell
can
the
lx
used
dru g candidates
closely
I [sing a
kinmc-2.
analog
directed chemical librm
resulting
in potent inhibitors
High-density
proniisc
hetwecn
can Ix
oursel\xs
uprcgillate S 13raxton,
a particular unpublished
sion
of an optinii~ed
profile
discmwing
from
fact confirmed pounds
lx
Icad
compo~~~ici
and disco\wcd
in
\I ho were
~wuld \I I,earncd, llic cxpresfo
(I:igLirc
drug
a stud)
that
esprcssion
3). they
umuld protxiblv
on mother
candi-
data \I ith
niolcculc
conipoi~nds
ia ~~+/n analwis.
efforts
Ixxter
profiles.
(I’ Bawcrlc. 13~ comparing
able to infer that the conipound da clopnient
I>rugs of lhc
ar ‘liil;lrik.
;I small
receptor data).
mxic
nieusured.
rcalizcd
and scienrists
in
of
fingerprint
different
ken
using
profile
3s a ‘gold standard’
niicroarr;i~
has
inmxxtecl
fingerprints
cliniination
:ind, thcrcforc.
intcgraring
decisions
acri\xz
antiscnsc
esprcssion
match the expression
of
de\~elopnicnr
‘I’hc gene
deletion.
stratcgics.
rranscript
casts,
standal-d \vill bc more specific
‘l’hc
functions.
\vcrc
bc toxic, :I
‘I’hc\ then f~Auseci their srructural
;I much better
drug
class of conicandidate.
and
of integrating proccss.
approach, a purine
synrhesis
asa!;
method to
nct\\orks by dclction
into the drug discovers chcniistr)
arc possible.
one poRmtial
an example
nicclicin:~l
that it is
depdi of~:~“o”i”-\\,icle
Chips and drugs CT 01. [37’] demonstrated
(;ray
of
iniportdnt
uncharacter-
of anatyx5
gtmes.
rrditional
pro-
niorc straightfor\~ard
c‘obligator)
dominant-ncjiliti\,~
null-acti\,ity
that niosI
a\-ailable tiata-
prmidc
o\.Cr-;iCti~;ilio11 of mo rqylamy
analvsis
yeast
case, the
match that of the
I>)- ;i \ arictv of nicthods:
replaccnicnt.
data
100 of these g:cncs
in an)- of die pilblicly
data that rhcse
the
this
ml>- ;I minor
in the gcnctic
for targets that do not sm
rcprcssion.
p:ith\v:iy.
in the gaps in padi\\a\s. Note
niicroarra~
two
prot~lciii \vhcn die proposed drug targcr is essential.
In these
of one ,qene is cm&
information
niicroarra~
i~nra\cI
the
that the expression
~\ould closcl>
I~nfortiinatcl?;
ribo/.ynies.
‘I’hesc
to assign f~inction to thcsc pre\ iouslv
izccl gcncs, and fill
In
gcncs that changed in response
translation
As ncarl! e\wy yeast gcnc is represcnrcd on these amy. in theory all p;ith\fys ;irc‘ reprcscnted. In practice. man! gcncs do nor ) et ha\ c ;I function assigned. and mm) pathuays ha\c holes in them. ‘I’his is echoed in die fact that ;‘i’i”-o~irnatcl~ halfofthc differentially regulated genes ha\.e
txixs.
that
3 tcmpcratilre-sciIsiti\.~
dates than those that ha\,c ~astl)
do no1 ha\ c a honiolo~
not
inhibitors.
kinasc,
kinasc-2.
‘I’hc\ espectcd
drug treatnicn~s. all-cycle nient
(UcZXp
essential,
1~as used.
For
challcngc rhc dogma that there is one key. rawlimiting
no nanic
of~encs
kinasc
\I ith cells differently.
of c!clin-depcndclit
pirh\\2\
patterns.
ncarl) e\.cry gene in the known glycolytic
c~ample.
ib the xx
similar
to niodcl the cffccts of a pcrfcct drug. (;ra) c~tc//. [.i7’] compmxi the cspression profile of their drugs in yeast
One hops with
two
arc interacting
of
\virh about
captured.
7.5% of the 6200 )‘cast jicnes
Imets.
rhc
file of the gcnctic niutanr
(,I N/. [lb’]
expression
In an cfhrr
gcnc
the gycarest contrit~i~tion in die array fictd.
Going genome
1:ult)
bcmeen
expression
die
conipo~~nds. I:or in cuprcssion was easy to
the chnge
\\‘hat is more intcrcsring
compounds
mutant I)cliisi
gcncs,
in common (knc
alter-ed
t,v more than tnwfold.
with knon n drugs and powntial
knou
I\ ill niakc
acri\,c conipo~~nds
‘I\\m of thcsc
647
process Braxton and Bedilion
oligonw
‘Ii) make this approxh robust. large-scale gene esprcssion datahscs for the interacrion of chemical compounds and cells arc essential. Ihtabascs are important hcciuse the\ fxiliute interprctarion of coniplcs patterns and relationships
in large-scale
the most profiles
gcnc expression
ob\Aous databases induced
and for all
I~ood
‘I’he expression
will
I>>- a large \ aricty and IIrug profile
expcrinienm.
‘Ike
of
bc the gene expression of knou n roxic
Administration
agents
appro\ ed drugs.
of ;I drug candidate
can then
ix
648
Pharmaceutical
compared
biotechnology
to expression
uncover
potential
databases
to measure
efficacy
and
expression
broadly
analysis
applicable
ment
process.
is the first new technology
for many
Expression
of the gene analysis
interaction
tissues, cacy
expression
will serve
essential
Global
for treating
patients
and toxicity),
benefit apply
expression
population clearly
and genetic
be unethical
(:onversely,
some diseases
is not
In practice,
as they
ments.
some
genetic
‘I’he
treatment ‘I’hc
patients
to choose
inaccessible mutation, phenotyping an entirely
the
genomic to global
IO.
Marshall A, Hodgson J: DNA chips: an array of possibilities. Nat Biotechnol 1998, 16:27-31,
11.
Schena M, Heller RA, Theriault TP, Konrad K, Lachenmeler E, Davis RW: Microarrays: biotechnology’s discovery platform for functional genomics. Trends Biotechnol 1998, 16:301-306.
12.
Ramsay G: DNA chips: state-of-the 16:40-44.
13.
Wodlcka L, Dong H, Mittmann M, Ho MH, Lockhart DJ: Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat Biotechnol 1997, 15:1359-i 367.
14.
Lockhart DJ, Dong H, Byrne MC, Follettle MT, Gallo MV, Chee MS, MIttmann M, Wang C, Kobayashl M, Horton H, Brown EL: Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 1996, 14:1675-l 680.
15.
DeRisi J, Penland L, Brown PO, Blttner ML, Meltzer PS, Ray M, Chen ‘f, Su YA, Trent JM: Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet 1996, 14:457-460.
systematic
of time,
paradigm
they
and effccti\,e
based
exploitation
a
on
tests measure-
is the ability from
the thcra-
diagnostic
on more objective
expression,
are
to restore cycles.
patients of
to treat
of previousI) gcnomic
in effect
point
extending
Icvel. L%‘eare on the verge of
for treating
References and recommended
human
massivley parallel genomics. Soence
gene
art. Nat Rote&no/
1998,
over
it could take years
segregated
information: gent:
drug treat-
one therap);
As we understand
makeup
of microarrays
to the molecular ntw
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on
to one drug, and if it
period
invention
to be based
promise
using
9.
microarrays.
gain
the cost sav-
have many potential
we have always
phenotype.
allowed
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with Qene expression
the it will
is sure to put pressure
drug. In some casts,
bet\vccn
the
to segregate
py, wc will have ;I much better opportunity patient to health without iterative treatment
some
8.
how to
non-responders,
to hit upon the right drug treatment. relationship
Fodor SP: DNA sequencing 1997, 277:393-395.
risks (side
we understand
non-responders,
reason
within
to another
be
bc used only when
are usuc~lly assigned
effcctivc
switched
7.
effi-
uill
tests.
with no objective Patients
for
about
certain
information
only responders
appropriate
another.
Schena M: Genome analysis Bioessays 1996, 18:427-443.
and cells,
but incur all the risk. In addition,
ings for treating
6.
effectively.
versus
to treat
of dis-
information
the risks. When
developing
mcnts,
should
the
marker
information
more
into responders
no benefit
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new drug targets.
involves
drugs
outweighs
allow
compounds
genetic
As the use of pharmaceuticals effwts
5.
to bc
develop-
component
as a surrogate
chemical
and will yield
toxicity.
drug will
of promising
between
or humans and
in the
microarrays
ease and the identification the
steps
High-density
measurement
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toxic interactions.
Conclusion Gene
4.
disease.
reading
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in the drug
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in
36. ..
Weinstein JN, Myers TG, O’Connor PM, Friend SH, Fornace AJJ, Kohn KW, Fojo T, Bates SE, Rubinstein LV, Anderson NL et al.: An information-intensive approach to the molecular pharmacology of cancer. Science 1997, 275:343-349. -.. The NU has screened more than 60,000 compounds against 60 well-characterized tumor cell lines. This paper tries to make sense of the vast amount of data, and various Interesting patterns emerge. Tumor cells with similar molecular lesions respond to similar drugs. Clustering information IS useful for determination of the mechanism of actlon of a new compound. Multidlmenslonal structure-activity relationship (SAR) informatlon from this set of data will be applied to large chemical Ilbraries, and better anti-cancer drugs are more likely to be found. 37. .
Gray NS, Wodicka L, Thunnissen AM, Norman TC, Kwon S, Esplnoza FH, Morgan DO, Barnes G, Leclerc S, Meijer L et al.: Exploiting chemical libraries, structure, and genomics in the search for kinase inhibitors. Science 1998, 281:533-538. The authors measured the gene expression changes in yeast induced by several inhibitors of the kinase Cdc28p. Although several genes changed In common for these treatments, more than half of the mRNA changes were distinct. Gene expression monitoring suggests that these compounds inhibit the target to different degrees, or that other targets are also affected. Comparison of the gene expression pattern of drug treatment to yeast with a temperaturesensitive mutation In Cdc28p should have yielded similar patterns, but did not on the whole. These results were confounded by incomplete gene inactivation and the bevy of changes associated with heat shock and cell cycle arrest. The approach outlined here should be more practical when a drug interacts with only one target, and the target can be specifically ablated.
