Open LectureOn Genomics, l\4etabolomics, Proteomics :

Perspectives for the Future

by o.L.Jnrv. Prot. Mag Dr. citnrher K. Bonn

ilgn !r..td'12irutir.i,. .

^

t*

o.univ. Prof. Mag. Dr. Grinther K. BonnCurriculum Vitae

Etenentaty Schaat tn6btuck

stLdy at chenrstry at the Leap.td Ftanzens Unileciq at lvshruckreache,ship Enn n chenishy.n!t Physrcs

Gaduatan "M6tet at Natuat sciuces'rhess at the hstitute af RadiachenDesz.tatian at Gttcase, calabrase and Cettutase'

cantact Assisbnt at the tnstitute tot Rattiachenistty

UnilesityAssis|an|aLlhe]nsr|ule|a|

Radiachenist y univeEity af tnnsbtrck

H a b i t it ata n ta I an a tla i 6 t c h e n kL.y

v)s.P,atessat at fale unirc'sity, De

Ensin New Haveh. cr usA, Ptal Cnba HaN.t\

nk aw*d ,Asttsbnt Pntessat'

F n Prctaat lat Analtlicat Chenistty

at Johannes'Kepteruniletsrty af Lin2, ALshia anti

Head at Depadnent at the Depannent af Analtticat Chenis@ Jahannes

FLttPrctessot Iat AmttlrQl Chenist.t tnsrtob af aharyh.t chenBhy andR a di a ch q i s[-y Leop D t tt F d n ze sHead ot the tnsttui€ ot Anatyticat chffirsLry antt RadiochemisLty

Menbet at th. Arstnan scienF FaLndanan (FwF)

Ptesi.ient af lhe BLteau tat tnbtnatonat R$earch and rechnataw

viE Ptes af the Austian Cauncit tot science antt Lpdhnotasy Devetapnon\

vce Ptes al the B.atd or ke Medcat Uhiv.tstly ot Innsbtuck

rnsrirure or Ana ytidar chefrisrry and Rad odhefrislry

unvereryor nnsbruck lnnra n s2a

sep€€lion science, new maieria s idr s€pa€tion science, developmenl of .ndcning techniqustor app i€lions n Oenomi6, proioom e and melabo omics

(1) Capilary Eleclrcphorcs s ol SDall M o ecules and lons

P Jan ik, G. Bonn, vcH, N.w Ydk 1993

(2) Ana }1ical chenislry or carbohydraies

G. Bdn, H. Sch.a, thiene, Studsatl, 1997

Hara* Medal Award - 2003

M€mbeFhip in Edibdal loards

chomarogEphia

Curcnt Medicina Chen stycur€nl Ana yt ca chem stry

Joumal of c homaioq €phio sc €nds

LC-GC Eurcpe

Guest Edilo.J.um.l ol ChrcmalosEphy

Bioana ytcal Reviews

Genomics - Metabolomics - ProteomicsPersDectives for ihe Future

C,W. Huck, M- Rainer, R. Bakrylnstitule ofAna !t€lChem stry andnnrain 52a, 6020 Innsbruck, Austria

G.K. BonnRrd o(hem slry, Leopo d.Franzens Univer5iiy,

"om 6' is a genera ce anli ens neer n9 for ana yz ^g

p mleome, mera bolome exp.essome an d in te.aclom€ Th€ .lea of lrac nO pole ntial b oma,ke corom 6 s goiiing deep€. in ilsapp.cdhesand becominslasl

a.€arily.HowevertissflanajorchaenoetopnpointbomarkeBoutorcompexsampres(e.9boiruids)and adoplthen for c

^r€rdiaonosis prognos s andrhe€peu

need ror h gh y erficienr appmaches ro hand e rhe probrems assoc aled w rh sampte p€parar on,sepa€lidn and idenlificaton or booqica speces Many newy emeEed technoosies meetthe basc requ remenls. Maior tocus has io be p aced on lhe dev€loanalta lechdques in ihe ierd of ife scences, usng hgh pedomance s nsle, and murlldimensiona sopakrion and 6ffch e exracrion {sPE) quid

chomatosraphy (HPLC)o. capirrary dedrcphtrs s (cE)coupled b ma$ spectromel.y (Ms).

an d up a nd doM {es ulalion domains beiwee tr d seased an d conlrol sa mpl6s.

The systomalc acquisilion of informalion €levani lo genon6s, qene

and ihen lunctons a^d ts qlobaland compreh€nsiveanay3s, ofren €fered Ioassenomicsandprcieofrics isarundamenta conrdbutDnolanayt*lchemisrrylotheprosre$ofrcsearchin

'Omics s a s€ne€ltem fofa b@ad d scp ne ofscience and engineednq

lor analyzing ihe intoractons of boogica mo€curar.omponents inincudelenome, pmleome, nelabo

ped or morc .ccuEreyd asnosins and teaiins d sease willsoon become a rea ry The posl.senomics e.a has b.oughtwilh t ever ncreas ngdemandsto obserue andcharaclers€ vaiations wiihin bio ogi€lsystems

e genohic (senefunciion),protrdmic (prolen resuarion)andth€ frebbo omic Gmar mo ecura we shr mdabo b) evers (Fisue r ) n rbe ro ow ns chaprereIrr€ndividuaievelsarediscussedindelairincrudnsasummaryorlhemoslapproprialeanaLyrdlIechniqu€s lor canying oul dera €d invesligaroN allhe@da n reve s.

a

Fidure 1 obsedrror ot biologrcat svstens is canad auL at the s

,,;,".-, ". .",;:. :". , ."

",t' * 0.,j.' . ,",,]t*. " '

ne tr3t step an the lans rcatt t' udestan'tna t)'ns ceiis

iome ProFdr 'n

2003 contnues I

* *",,"t. *p,*,-. "t *. :!zed d sease preventon

r sks for one or more or the najor c

I o,.."" "qao'd4'?'4BoqP'o'."'."''"'"lhefumroNolhceqeres.andi;;,;;";," """,.".;",, ",,.'."r

.' .,,.; -""-^ ". ntaeeoomic phenomena

"."" .". , ;.:;.;; o-"- oo 4' atdd o

;" " " ", , "-" "",:., " ",""

" ".ii" "i",0,,, """-"^ ",her seierc nake up rhE appoac

i;"i " .;,. """.' "" ",

,,, ,"","' , "

;?;""""' ; ,;* - "" ,"."' -*" ' '*u -"*,

**"pi.o"..",n q;:;;.";:";,";.".

", *" t *""t* lo**" ,l rhe sen mr re*adr enends r'om qene d sFVery ro is

";;;;;" '"* * ';* -o *

6

;;..J

sene runcrion and sludles nlo rhe morecuar mechanisns ofdrseaso.bas€d daqnoss 3nd rsk prDlectodevelopm€nt are a I made poss ble by lhe crcss'cun ng naiure or rfre qenetE and senomcsstrareg es Msna€ssofsenomics ene rherapy rcpbducrves€nom c, qenel'c dalabark systemalcs and phamacogenomds

f andysisis'he micme€ylasoknoamyorDNAchp) A micrcarcy usla yconssls or triodsands or DN

oe.es laken rrom ce s underspe.e of a I ass or praslc s d0 soluro

n sear.hes for a marh nslary moe.uiar recosiirion benve€i

ron mn be measuredbytrreinlensiyhe geie s mpodadt lornwhch I was ana ysed

i;

sep!dualhaqaduplexDNA|'agn'rn!s0n|jupafoaIy|j'.ndUdnscac.tunn an.l a naraxthl. paty(s1yrene/.llvrnftbenzene) c.prttary

Proleomics is lhe study or the fun Tremendous prcgress

are n seneralng rarce{.ale data sels ror prcte n prole n

The lem pmleome was firsl co ned to des$rbe rfre sel of poteins encoded by rhe g-anone

orcle n 'sofomsafd

modrcarions. rhe nrer.ci'ons behveen them ihe

cs wo! d notbe Poss be willrour rb

7

I

Itre rh.lasks ofpmt€om.s can u

rhe huoe bd stashfiotuard chaieises nia y facfq lhe qenone proleds un k€ rhe {aLab e

wilh iG aneidanr enabiig te.hnDo

vasr dvnamic €n9e (more ihan

106 fod fo, p.ore n abrndance aone) a p elhora of pon taGraio

!!h le prcleomcs t bydelnion expecled royeld dneclboroq.a isqhG an orthesedirrcu tes

rcnde. any conprehensve prcteom6 orcled an inrrdenlv mtmdalnq aid ofien humbing

thods nusl be capable ol identrvns an.r qlaniJvns bdrr

proreom c le.hno qries loday

qud.hrcmatoqraphy (Lcl .oflbn ometrv (Msl r,ls w be

saidquadfybdr'ihe tud prob is and pept d€s produ.ed

by enzymarc prcleii d qesr on

perfofmance mass spedrcnelere .cyc olrcn resonsn.e lFr cR) and qusdrupore tme ofilshl lo roF)mss speclronelere Dara

casses of Ms based apprcaches(2DE) ro cpnde mmp* pro'en

and enzymalca y dgesG{r io produce peprdes rhat .an be

n zarioi (MALD ) comb rcd wrh a

ys ds prole ns rhat rebin slrucl!rare possib ry or deredns orher I

Ne iqu d crronaloq.aphy(Lc)sep nizalioi(EslMsrofiheeplLdes or PrDrc is nracr prcte is orpeprdes 9eneraled ffom

enzymarc dseioi ol p'ole nsare ana yzed bv d €Lta..u'ate massn

mass spe.l,omerr/ (Ms/Ms) roaches NlSrMs snavss can

cs 1or rheorci.al MsiMS

spectrl lo denify prorens Proreome anayses musl be qGn

efra nrY so lhal ror€xample 'hang

mav l,e derem ied confi'lenlrv

ced bv Boni aid h sworki9sroupforp6le n proi n! s

qra0h. pre.oidenraroiTOFMS nvesrisaiDr From

lEprn.ipe depi.le.] n F gure 3 i.slrr,.ia'oreddcs9iorrheMELDIcairelmatera.ons'srinsol€q polvh vc dv metha"v 3ie

co-d viiybenzene IGMAIDVB)) ceLu ose s .a c60 i! reren. eic de valzed w lri 'rfierenr

iumlioia t* (MAc. affiiily rereEed phase erc lb_rsh ouf the aia!1e of nrercslwlh hsh

I

The

a

,c

Of MELD

0"

d. . trno n. ri'r,7e ooc

,a.iFigute 3 rhe PinciPt-P af MELDT

rcd spectos.op c INrRS)delecron s lermed as ME RS

n speclrcscopy frrs approach rias

sliab€ lo, rhe anays s or hi<rh. and ow densiry poprcleins in hunnrra€d mag nq speckos.opy ben

record represeniarve maqes ofsa uccessru y apo ed for lhe

screeniiq ot differenr foms 3nd slaoes ol cancer n tssue samples

. non nv:sive rlre rissue sanpreol nleresr can be used lobe ludhe

Pflnciples of the meosurement j

I

f ihe geione aid is 'rerned

as lhe

or sma mDecuaf weight compomds (mdaboibt pr4ed n

a .e or o4anism wh ch Ffr.paome s arqe (s cerev'siae

apprcxmaley 600 nelabo 16) . p:nr knqdom up lo 200000 merabo i€s

siqn rcanlry owe, numbes rof d lrerent spe.ies and aia yssorrhe hL

er.l metabo tes dere.ted

lEnsdiptone. the nelaboome 's

more dve6e in chen.a and phys.lhe acerva,atons studies of rh€ meraboome ii.ude trre aiaysL.ora wd€ ranqe or.hem E spedies.lrom ow moe.ula' we grilporairo hAh no ecu ar *elht 0oar s u.osdes non polar lpi.ls ai.r

th. aiarylica le.hn.oq es emp.ye M€raboom.s (and spe. f.a y

meiabonomi.sl sdennedasthen ldilgrealed metabo ies

Non tarcered snayses oreidoqei,on based manner and a(er miiina sampe preparatoi arqe nunbeG

d apprcad (r0 30 mn mavss loesl obiecrves n.fterhe dedfcdion of bom e6 (medra dssmst re are.r io hea rhy K dFsed sbbs (or

$m*sfrl d,uq fGmed on) rL4elaboric b ochemsrs have arsuabry been dons metaboomics

son nvesrigarn9 Pau igs

coined nlhe leeosbyo ver s 6 D B and Basanz F (ree8l

tssues 2 Sepa€lon oJ thc aiaLyles.caPirarY eect Phores s. s a so

used 3 Dere.ron or rhe anaLyles lorowinq seFraron by chromrosI denifElion and qranlili.aloi ofrhe aia /rca The pfepararon or

.lependenl on lhe meraboom.s stategy emproyed

ovef n ie orde6 or msntude (PM mM)

sses orsepa€ton of r..lteled merabo relsrfiom the ercess

samp e mat'x (n. udine olher melabodet

cas.hr.nalogrePhY iGcl Peformcwth Msdete.loi p.ovdes an excB eitsysremlDr performinq qLoba merabo . prof ii9 To dale

GC.MS has arcey beei used io obb n merabo rc orclie rrom panbn.ud ns man The ri9h

rcsoi!iion or Gc..omb ned wirh lrre MS dere.ron (usnq e lher e ecton mpa.r lE )or chem.aion zar on (c ) prcrdb a qood slad ns poiil ror denlrcarion or pu

Pracl.a mlaion orGc based mcnaryzed dre.tv dle 1o rhetr

porarryaid ack orvo athy IhsmeUceVarab|yandosses

l0

n As !]ifcad€nhsn.ement n lrre

enlor m!ldlmensona cc usua rydernbed 4 Gc:Gc (or

.ompreheisLve Gcl The adva.iaqes orGC Ms and pa cu arv GCrGc Ms 'ncude

verv hiqh

tYor rerar ve Y. rcbuslLC.MS has re

e d rccilY ile.led ftorheLcs mioa preteatmeni (prolei precpilatonl LCIiS saso9b0ut. has 3 reasonabre dyiamc G

poleila lor boma,ker idenrifi.alotr n qenera s.paralons ror LC MS have been.edomedrion lEs ) n bllh Pos( ve

ES and nesarve Es

to rs high chromatosraplr. rcsou

one or the ea{rhq te.hnoog es u

pro.esses for more rsn 30 yeaiavs s lo hep decpher

hat sPoctaracqu sion s re arive Y

riYey alge sampe szes (-500 !L) Ho\@v€r wh rhe.ecenr

ntodu.rion or hgher re d masneG le00 MHz) .ryosenicarly.ooed probes (rh3r incease signa

by a facrof !r 3l an{r sma vollde minoDmb€s 160 !L)

elabo tes can be d€recrcd ( i vivol

b r00 merabo rc ( n vto) n.Bnain boru{rs

or.ancer thrculh lhe aPP .3toi oq Y.omL.s PhosPhooroleomics or

and bDdy ilr ds curienry rh. aoa

.ompdeds n rlr4e inpres les prote.s or merabo ret.ai tunhe'

nttv ihat s obl€clivev mcas rcd aocess or phamacoog. resp.nse o a

luie:.'nG endpoii A

pr.d cl c i.al benert 1or rram or ack or bencrr.r Mrm)

tl

bas€d on ep den arog c.lherapeulbioma*ers as s uros ate clinica L measu €s, d€ lect ear y b o og ica responses alter d ru g t€almdntfor anaryz nq dtuI safdly and eary efi @cy of new drugs Biomadcc c

and daqnoslic uses For inslance. onc€ the disease semanagemeni ofdiseas€

one can 6e b omdere io srraqwirh blomarkes eads ro discrim naron ofa bea thy sbie lrcm 6ady asymplonatid slase of rbe

c. td nduslry: PhannDgenanic Data subni*ian eoas)a "va d bona*el s one'ihal s measurcd n an anarrca Gsi sydem w h wellesiabish€dperfo.mance characrerislics 2nd fo ewo*orbodyofevide^derh ar e dc dares the physioroq ca , iotico ogicar pharmacoo9ca orc n€lsisnl€nce ol the tesi

r is difierenlial€d "for wh ch rhere

nry The "pmbable vaid bioma*e. may not have r€adhad

el because th€ data e ucldar ns ils ssnifican@ nay have

bee. deverop€d frcm wiih n a sns be lor pub D sDrutiny lnp clions in modern bio ogy and nedicine. Fiom prcqnancy

lor d asnosiics an.l predictoc of re ure in prcrou^d ways Tlreded ota rroma*erdepend on how ( win be empoyed.

X@---ii;\xr@...------./

rhe cha€ctd6ttcs (sqedrc Y ah'thaw it ||itt be enpl.yetl fat ctinicat

Fiswe 5 Wa flow ft hbnikciphnarys%sitvity) an t euatiti* denanded or a

F

'12

toso.a ed prof ins merhods whc edlorarangeorma eGtrnqenl

'lifie€nt al on and

absilercassrcalionorpaiientqrcups(rtr4amde lrrosewlhcanerandrhosewihoul) rhisrrasePos t ve or rcgalNe

Bnt eves Mo$ npo'lanlly I iss wL €ad loberertherapesaswe

oncedis.overed ih€sebiomadeE iud nsd aQnosngdisease

biomaders in 3 re atvely eracenl manne,

'I caicer research

lenomics e0i9enomLca.

and bo nrorharcs. Receni advances in hish ihroughp0t omics

ted'nooges have p'ovded new oopodunlly n (he molecu af anaysunpre.edenredsPeedanddelaiis TomG rechnoroqes vides ciuelor sene regu alion and seneknockdown lo, .an.ef managemenl The approva ot Manmaprrnl and Oncorype DX ndicatas

rhar mu tp ex diagnosic ma,ker s

micrcRNAsin hum.n Encers lras opened a new pase rorcancerrcs€arche6 Some rherapeurcurienf y underoo'.9 k€en

mpodaii roe n cancer bona*er d

poteomeds*se eaionshps provide a mean ror coniectvly analysis Fluorcscenl dyepand cviom 6 The hqle

y murlipa,ameter singe ce low o. s de based cttometryce popularions cance s

a so an dea fied oraoolicaton ror m

Fisrre6 tt h env'sined thal .nrcs technaLagtes witteahance aLt un

sisnaties al drseases on both qu

ta, hishty efticient apprca.hes ta th enpte ptepaQtian

G.n'te*ty. vtkbititt Epndrcturt)ty.. ) i.tertiticatidh lsensitvrtv quaftihcdion, ) an't dakevatuatian (dab nanssenent ard )nlee,atan)

l3

The nover"dmcs" lechnoroqes hav en cers a he gene,vanscrpr prorein meraboire,andlhen riera.lionn€Mo (teve i.*arex pou ndin s lhe d rus mecha n ism-or+dlion, idenlitin q advece efiecrs n un ex pecred nt€.acr on.valldating curenl druo larsers, speen ng up he d s@very of now tarcers expto ng porenr aapp €lronsror nov€rltuss and enabuns lhe lmnstaron from bench io b€dside (Fisu.€ 6). rhelierd is movinq rast, specia z€d lechniqu€s are beins devetoped ro inre

toqy (hr pJlw. rie benpub. co trJp rcd ucts/ p rcducr

Narure senetcs (hhpr vw naiurc con4, Genome Research (hrp://qenome.csh poQ4. Gen omics (hiip/lvw etsev e Lcom/wps/f

^d4ou m a desq pr on NS home/6223 33/

desc,iptontdescripron), Geneiics a^d Genomt6 (hrpj rM.sprif,sercom/tfe+scences/g€nerc+%26+genomics?scwtD=1 10036-0{ 0)

A.E Gunmachei FS Corins. N EngrJ Med,2003 349. 996.

J. Ber Narure,2004 429 .4s3 1156

D.Aue*ach S Thaniny, M. O Nongeraid

M. Bogyo and J H Huey, cun op n chem

!!.s franmck s L.wuandPsrreh pbreomc,

c N Pet€r N. Hegr M Rain€. R Bakry J pa ua

s aqlar Prcreomc 2002 2,6r1

P'oeon6,rD swl,1F \16-tune?cRETRY:1&SRETRY=o), Journa or Proreome Research (hllp //pubs acs ors/iomar/iprobt, Mo4urarand celurarprcteom 6 onp/ rw mDpon n€ ors/)

proIeomss: tarse sca e proreii denlfcarion by r!vo.no ac d anatlsts Biotechnoogy 1.4,61.65 (1se6).

. Faue6ren,M. Naiam-u-Haq, M Rane( L Trcj6r, R.Baky, N HtdayarApritita,csreche( C.w.lludk l-1 Krocke. G. Barisch,A Guhman and G.K. Bonn, J Am Soc.MassSpecrom 2005,17, 1203

FS Co n5 E.D Green AE Gurlna(h-ai Guyer Na'rre 2001 422,335

c H Pener N rres, R Bakry G.K Bonn A. Rilsch,

D S W shan, cuirenr P.oqress in mmputariona merabotom cs.2007

s G oivelM K winson D.B Ke andEBaganz Trends B orechnot 1993.16,

c G. H. a. R Good.crc,]\retabotc PrcJitins: is Roe in Bioma*erDiscovery and G€neFuncl on Anarysis KruwerAca,lemcPubtishe6 London 2003

R Goodac€. S VadyanarM^, w B Dunn G. G. Hariigan and D BB)Dtecnno., 20a4, 22, 24 5 252

J. Fo6rer, r.Famri P Fu B o. PatssonandJ. Ntetsen GenomeRes 2003.13.214

r: o. Fiehn comp.Funct.Genomics.2001,2 155-163.

,i B. LahneiJ M. Gons, M Mahmoudlan E L Smith, K' S Abid'E E Rose6 M L

cueinol J. F. Harper, J M wa|d L. Mclnryre. J schroed'r and D' E salt Nat'

Biolechnol.. 2003, 21, 121s-1221

r' c.A.Daykin,PJ.D Fonll, s c. Connor, J C LddonandJ K Nicho$n A'a'Bioch€m., 2002, 304 220 230

. J L.Glffn,cunopln Ched Biol 2003,7 643 3s4

:r D.M,wikonandA.L Auringame Bochem Blophvs R$ Commun 56(1974) p 323

15