13/09/2014(

1(

The$ciliary$proteome$

Mar,jn(Huynen(

Centre(for(Molecular(and(Biomolecular(Informa,cs(Radboud(Ins,tute(of(Molecular(Life(Sciences(

(

Human ciliated tissues in movement, sensing and signalling

Inner ear: Stereocilia function in hearing and balance

Cerebral cavities, Bronchia & Fallopian tubes

Retina: Cones and Rods

Sperm cells

The$non0mo1le/$primary$cilium$as$a$signaling$hub$

•  MechanoD,(ChemoD,(Thermosensa,on(•  Sonic(Hedgehog(signaling(•  Non(canonical(WNT(signaling(

•  Effec,ve(as(cellular(antenna(•  Large(specialized(membrane(surface(•  Ac,ve(transport((IFT)(•  Selec,ve(ga,ng(of(receptors(at(the(base((synapse)(

Fluid$flow$detec1on$by$cilia$regulates$proper$development$of$nephric$ducts$

Nephric(duct(Thome(et(al.(2007(Nat.(Cell.(Biol.(

Zang(et(al.(2004(Physiology(

13/09/2014(

2(

Cilia$in$renal$disease$

•  Autosomal(polycys,c(kidney(disease((APKD)(•  Nephronophthisis((medullary(cys,c(kidney(disease)(•  Kidney(func,on(affected(in(mul,Dsyndromic(ciliopathies(

•  BardetDBiedl,(Joubert,(Meckel,(Senoir(Loken,(…(

NPHP( APKD(

“A(systems(biology(approach(to(dissect(cilia(func,on((and(its(disrup,on(in(human(gene,c(disease”(

Systems$biology$of$the$cilium$ Large$scale$data$acquisi1on$for$the$predic1on$of$new$cilium$genes$

•  ProteinDprotein(interac,ons(•  Tandem(Affinity(Purifica,onDMS(•  Stable(isotope(labeling(by(amino(acids(in(cell(culture(•  YeastD2DHybrid(

•  Bioinforma,cs(•  CoDevolu,on(•  Microarray(metaDanalysis((systems(coDexpression)(

•  Func,onal(screens(•  Genome(wide(siRNA(on(ciliogenesis(•  Comprehensive(drug(panel(screen(on(ciliogenesis(

13/09/2014(

3(

Data$gathering$and$organiza1on$Predic1ng$new$cilium$proteins$by$comparing$genomes$

Gold$Standard$&$Nega1ve$set$

Extracellular$

Co0expression,$exploi1ng$>$1600$experiments,$35K$arrays$

13/09/2014(

4(

How$can$we$integrate$mul1ple$datasets?$

Proteomics(data(

Gene,c(data(Published(data(

Expression(data( Evolu,onary(data(

?(

A$Bayesian$classifier$to$iden1fy$novel$ciliary$genes$

Proteomics(data(

Gene,c(data(Published(datasets(

Expression(data( Evolu,onary(data(

Bayesian$integra1on$of$mul1ple$observa1ons$

•  n(is(the(number(of(datasets(considered(•  fi$=(dataset(i$•  P(fi|T)(=(probability(that(a(gene(is(reported(by(dataset(i(given(it(is(a(known(ciliary(gene(

(

GeneScore = log2PCiliumP~Cilium

!

"#

$

%&

Pr ior! "## $##

+ log2i=1

n

∑P fi T( )P fi F( )!

"##

$

%&&

log(a ⋅b) = log(a)+ log(b)

13/09/2014(

5(

Bayesian$integra1on;$$

$dis1nguishing$between$ciliary$vs.$non0ciliary$genes$Ranking$poten1al$ciliary$genes$

18(

Ciliary(Predicted(NonDciliary(

FRD(cutoff(at(25%:(405(genes(of(which(283(unknown(to(be(ciliary(

Experimental$valida1on$

•  72(genes(of(the(283(will(be(tested(((25%(FDR)(•  C.$elegans:(roaming(and(dyeDfilling(essays((phenotype)(•  Zebrafish:(morpholino,(CRISPR((phenotype)(•  Immunofluorescence(in(human(ciliated(cell(lines((localiza,on)(

•  35(tested(so(far(•  25(show(ciliary(phenotype(and/or(cilia(localiza,on((FDR(29%)(

N2 control

oscp-1

Roaming$assay$screen$in$C.#elegans#

Julie(Kennedy,(Blacque(lab(University(College(Dublin(

13/09/2014(

6(

C.#elegans#dye0filling$assay$N

2 co

ntro

l dy

s-1(

eg33

) /d

ystro

phi (

DM

D)

dys-

1(cx

18)

/dys

troph

in (D

MD

)

mag

i-1(g

k657

) /M

AG

I2

R10

F2.5

(gk7

48)

/OS

CP

1 R

10F2

.5(g

k699

) /O

SC

P1

Immunofluorescence$in$human$respiratory$cells$

Gerry(Dougherty,(Omran(lab((Wespälische(WilhelmsDUniversität(Münster(

Immunofluorescence$in$hTERT0RPE1$(re1na)$

Erik(de(Vrieze,(Kremer(lab(Radboudumc(

Analyzing$pa1ent$exome$sequence$data$

•  Premise:(•  Causal(genes(in(ciliopathy(pa,ents(perform(a(func,on(in(the(cilium(

•  They(are(“ciliary(genes”(•  And(“behave(like”(other(ciliary(genes(

•  Our(Bayesian(classifier(is(a(probabilis,c(model(or(descrip,on(of(“ciliary(genes”(based(on(a(collec,on(of(experimental(and(bioinforma,cs(data(

•  Genes(found(mutated(in(pa,ents(and(which(are(classified(as(“ciliary”(are(prime(candidates(

13/09/2014(

7(

Predic1ng$causal$genes$in$JBTS$pa1ents$

Five(pa,ents(with(JBTS(of(unknown(cause(and(no(family(history(

Marijn(Stokman,(Nephrology(dept.(UMC(Utrecht(

Filtering$and$ranking$of$causal$muta1ons$

Acknowledgements$•  Radboudumc(

•  John(van(Dam(•  Robin(van(der(Lee(•  Radek(Scklarczyk(

•  Ronald(Roepman(•  Dorus(Mans(•  Minh(Nguyen(

•  Hannie(Kremer(•  Erik(de(Vrieze(

(•  UCD(

•  Oliver(Blacque(•  Julie(Kennedy(

•  UCL(•  Phil(Beales(•  Victor(Hernandez(•  Miriam(Schmidts(

•  Kouncil(WP1(•  Marijn(Stokman(•  Kirsten(Renkema(•  M.R.(Lilien(•  Heleen(Arts(•  M.M.(Oud(•  Ies(Nijman(•  H.Y.(Kroes(•  N.(Geijsen(•  E.(Cuppen(•  Rachel(Giles(•  Nine(Knoers(

•  WWU(•  Heymut(Omran(•  Gerry(Dougherty(

•  UTUB(•  Marius(Ueffing(•  Karsten(Boldt(•  Yves(Texier(

•  TIGEM(•  Brunella(Franco(

•  LIMM(•  Colin(Johnson(•  Kasia(Szymanska(•  Gabrielle(Wheway(

•  Duke(•  Erica(Davis(

•  SYS(IT(•  Grischa(Toedt((EMBL)(•  Qianhao(Lu((UHEI)(•  Konstan,nos(Koutroumpas((UEVE)(•  Jeroen(van(Reeuwijk((RUNMC)(