ARLTS1
and P os a e Cance Risk - Analysis o Exp ession
and Regula ion
Sanna Sil anen
1
, Daniel Fische
2
, Tommi Ran ape o
1
, Vi pi Lai inen
1
, John Pa ick Mpindi
3
,
Olli Kallioniemi
3
, Tiina Wahl o s
1
, Johanna Schleu ke
1,4
*
1Ins i u e o Biomedical Technology/BioMediTech, Uni e si y o Tampe e and Fimlab Labo a o ies, Tampe e, Finland, 2School o Heal h Sciences, Uni e si y o Tampe e,
Tampe e, Finland, 3Ins i u e o Molecula Medicine (FIMM), Uni e si y o Helsinki, Helsinki, Finland, 4Depa men o Medical Biochemis y and Gene ics, Ins i u e o
Biomedicine, Uni e si y o Tu ku, Tu ku, Finland
Abs ac
P os a e cance (PCa) is a he e ogeneous ai o which se e al suscep ibili y loci ha e been implica ed by genome-wide
linkage and associa ion s udies. The genomic egion 13q14 is equen ly dele ed in umou issues o bo h spo adic and
amilial PCa pa ien s and is consequen ly ecognised as a possible locus o umou supp esso gene(s). Dele ions o his
egion ha e been ound in many o he cance s. Recen ly, we showed ha homozygous ca ie s o he T442C a ian o he
ARLTS1 gene (ADP- ibosyla ion ac o -like umou supp esso p o ein 1 o ARL11, loca ed a 13q14) a e associa ed wi h an
inc eased isk o bo h unselec ed and amilial PCa. Fu he mo e, he a ian T442C was obse ed in g ea e equency
among malignan issue samples, PCa cell lines and xenog a s, suppo ing i s ole in PCa umou igenesis. In his s udy, 84
PCa cases and 15 con ols we e analysed o ARLTS1 exp ession s a us in blood-de i ed RNA. A s a is ically signi ican
(p = 0.0037) dec ease o ARLTS1 exp ession in PCa cases was de ec ed. Regula ion o ARLTS1 exp ession was analysed wi h
eQTL (exp ession quan i a i e ai loci) me hods. Al oge he ou een signi ican cis-eQTLs a ec ing he ARLTS1 exp ession
le el we e ound. In addi ion, epis a ic in e ac ions o ARLTS1 genomic a ian s wi h genes in ol ed in immune sys em
p ocesses we e p edic ed wi h he MDR p og am. In conclusion, his s udy u he suppo s he ole o ARLTS1 as a umou
supp esso gene and e eals ha he exp ession is egula ed h ough a ian s localised in egula o y egions.
Ci a ion: Sil anen S, Fische D, Ran ape o T, Lai inen V, Mpindi JP, e al. (2013) ARLTS1 and P os a e Cance Risk - Analysis o Exp ession and Regula ion. PLoS
ONE 8(8): e72040. doi:10.1371/jou nal.pone.0072040
Edi o : Amanda Ewa Toland, Ohio S a e Uni e si y Medical Cen e , Uni ed S a es o Ame ica
Recei ed Ap il 4, 2013; Accep ed July 3, 2013; Published Augus 5, 2013
Copy igh : ß2013 Sil anen e al. This is an open-access a icle dis ibu ed unde he e ms o he C ea i e Commons A ibu ion License, which pe mi s
un es ic ed use, dis ibu ion, and ep oduc ion in any medium, p o ided he o iginal au ho and sou ce a e c edi ed.
Funding: This wo k was suppo ed by he Tampe e G adua e P og am in Biomedicine and Bio echnology sala y and O ion-Fa mos Resea ch Founda ion g an o
S.S. and by he Sig id Juselius Founda ion, he Academy o Finland (251074), he Finnish Cance O ganisa ions, and he Compe i i e Resea ch Funding o he
Pi kanmaa Hospi al Dis ic (9N069) g an s o J.S. The unde s had no ole in s udy design, da a collec ion and analysis, decision o publish, o p epa a ion o he
manusc ip .
Compe ing In e es s: The au ho s ha e decla ed ha no compe ing in e es s exis .
* E-mail: Johanna.Schleu k[email p o ec ed]
In oduc ion
P os a e cance (PCa) is a he e ogeneous ai , and i is he mos
common malignancy among men in wes e n coun ies, including
Finland. I is a mul i ac o ial disease, and de ini i e isk ac o s
include age, e hnic o igin and amily his o y. In Finland, he
incidence o PCa is 89.4/100,000, and in 2010, 4697 new p os a e
cance cases we e diagnosed (h p://www.cance . i/
syopa ekis e i/en/). Despi e ex ensi e esea ch o e he las
decade, he e iological isk ac o s and genes ha cause gene ic
suscep ibili y emain la gely unknown. This lack o knowledge has
hampe ed e ec i e cance p e en ion and de elopmen o be e
ea men s.
Mu a ions in he known high-pene ance PCa p edisposi ion
genes explain only a small ac ion o PCa cases. A polygenic
model o amilial agg ega ion o cance has been p oposed whe e
se e al low-pene ance alleles may ha e a mul iplica i e and/o
modi ying e ec . One low-pene an candida e gene is ARLTS1
(ARL11), ADP- ibosyla ion ac o like umou supp esso p o ein
1, a pu a i e umou -supp esso gene on ch omosome 13q14,
which has been shown o unc ion in many human cance s [1–5].
ARLTS1 is a membe o he ADP- ibosyla ion ac o amily ha
plays a ole in apop o ic signalling. The same ch omosomal a ea
on 13q has been indica ed in a mul i-cen e genome-wide linkage
s udy in amilies wi h a leas i e a ec ed membe s [6]. In ano he
ecen s udy, he immedia e adjacen egion 13q13 showed a
sugges i e linkage o PCa, wi h a HLOD.1.9 [7]. In addi ion, he
locus 13q14 is among he mos equen ly dele ed ch omosomal
egions in soma ic umou issues in bo h unselec ed and
he edi a y p os a e cance s [8,9], sugges ing ha ARLTS1 could
be a a ge o bo h ge mline and soma ic mu a ions. We
p e iously epo ed a signi ican associa ion o ARLTS1 T442C
( s3803185) homozygo e ca ie s wi h PCa [10]. This isk
geno ype was also associa ed wi h dec eased ARLTS1 exp ession
in he lymphoblas oid cell line samples o PCa pa ien s, and
ARLTS1 co-exp ession signa u es om da a mining e ealed ha
ARLTS1 exp ession was s ongly associa ed wi h immune sys em
p ocesses. These p ocesses a e o in e es because a link be ween
ch onic in lamma ion and PCa p og ession has been epea edly
p oposed, and mul iple genes ac ing in in lamma o y pa hways
ha e been linked o PCa suscep ibili y [11–13].
Complex diseases, such as cance , a e caused by a combina ion
o mul iple gene ic in e ac ions and en i onmen al ac o s, which
a e ha d o de ec and link o each o he . To de e mine ue causal
associa ions using s a is ical me hods and pheno ype in o ma ion,
i is ad isable o o ganise indi idual ma ke s in o g oups acco ding
PLOS ONE | www.plosone.o g 1 Augus 2013 | Volume 8 | Issue 8 | e72040
o meaning ul biological c i e ia, such as in lamma ion. By
composing a ian se s, i is possible o educe he numbe o
hypo heses being es ed, which allows he associa ion be ween a
genomic ea u e and a pheno ype o be mo e easily de ec ed.
Epis asis in geno ype le el is de ined as he in e ac ion among
mul iple genes o loci, and his join gene ic e ec may be he
ac o behind ‘‘missing he i abili y’’, a phenomenon linked o he
unexplained po ion o he edi a y cance suscep ibili y, which is
obse ed in PCa. The genome-wide exp ession quan i a i e ai
loci, eQTL, analysis is a me hod o s udying epis asis in complex
ai s ha is able o de ec associa ions be ween geno ypic and
exp ession da a. The eQTL analysis is a widely used app oach o
gain insigh in o he ole o single nucleo ide polymo phisms
(SNPs) a ec ing ansc ip le els.
In his s udy, we in es iga ed he mechanisms behind he
p e iously obse ed associa ion o ARLTS1 and PCa by ocusing
on inding gene/exp ession in e ac ions ha dispose pa ien s o
PCa, including in e ac ions in ol ing he ARLTS1 gene. To
u he in es iga e he ARLTS1 exp ession di e ences seen
p e iously in umo samples, p os a e cance and lymphoblas oid
cell lines [10], we pe o med unc ional eQTL analysis om whole
blood de i ed o al RNA om PCa pa ien s. The p e iously
epo ed ARLTS1 co-exp ession wi h immune sys em p ocesses
[10] was es ed by MDR analysis. To ou knowledge, his is he
i s s udy epo ing he indings o ARLTS1 in e ac ing a ian s
and p os a e cance eQTLs a he 13q14 egion.
Ma e ials and Me hods
S udy popula ion
All he samples we e o Finnish o igin. The iden i ica ion and
collec ion o he Finnish HPC amilies has been desc ibed
elsewhe e [14]. The amilial samples analysed in his s udy had
a leas wo a ec ed i s o second deg ee ela i es. Al oge he ,
102 p os a e cance cases and 33 heal hy male amily membe s
belonging o 31 amilies we e ini ially aken in o he s udy
popula ion. The clinical cha ac e is ics o he amilial pa ien s used
in RNA sequencing (n = 84) a e e e ed o in Table 1. A e age
age a diagnosis was 63.0 y.
Pa ien in o ma ion and samples we e ob ained wi h ull w i en
in o med consen . The s udy was pe o med unde app op ia e
esea ch pe missions om he E hics Commi ees o he Tampe e
Uni e si y Hospi al, Finland, as well as he Minis y o Social
A ai s and Heal h in Finland.
Genome-wide SNP Geno yping
Genome-wide SNP geno yping was pe o med using he
HumanOmniExp ess BeadChip mic oa ay (Illumina, Inc., San
Diego, CA, USA) by he Technology Cen e, Ins i u e o
Molecula Medicine Finland (FIMM), Uni e si y o Helsinki.
This a ay co e s mo e han 700,000 ma ke s wi h an a e age
spacing o 4 kb ac oss he en i e genome.
DNA Sequencing
The ARLTS1 a ian s a us o he PCa pa ien s used in Illumina
geno yping was examined by di ec sequencing. Sequencing was
pe o med in an Applied Biosys ems 3130xl Gene ic Analyze (Li e
Technologies Co po a ion, Ca lsbad, CA, USA) acco ding o he
manu ac u e ’s ins uc ions. P ime s and PCR condi ions used in
he mu a ion sc eening a e a ailable upon eques .
RNA Ex ac ion and sequencing
To al RNA was ex ac ed om 84 PCa cases and 15 heal hy
male ela i es. All subjec s belonged o he 31 Finnish HPC
amilies men ioned abo e. To al RNA was pu i ied om whole
blood collec ed in PAXgeneHBlood RNA Tubes (P eAnaly iX
GmbH, Swi ze land/Qiagen/BD) using he MagMAX
TM
o
S abilized Blood Tubes RNA Isola ion Ki (AmbionH/Li e
Technologies, Ca lsbad, CA, USA) and he PAXgene Blood
miRNA Ki (P eAnaly iX GmbH, Swi ze land/Qiagen/BD). The
RNA quali y was assessed using he Agilen 2100 Bioanalyze and
he Agilen RNA 6000 Nano Ki (Agilen Technologies, San a
Cla a, CA, USA).
Lib a y p epa a ion, a ge en ichmen and massi ely pa allel
pai ed-end sequencing o exp essed ansc ip s was pe o med by
Beijing Genomics Ins i u e (BGI Hong Kong Co., L d., Tai Po,
Hong Kong) using Illumina HiSeq2000 echnology (Illumina Inc.,
San Diego, CA, USA).
eQTL analysis
To ob ain ARLTS1 exp ession alues, i s , he eads om RNA
sequencing we e aligned wi h opha 2 using hg19 as he e e ence
genome [15]. The aw ead coun o ARLTS1 was calcula ed
using HTseq, and ead coun s we e ans o med o no malised
exp ession alues using DESeq (www-hube .embl.de/use s/
ande s/HTSeq/, [16]). The linea eg ession model implemen ed
in PLINK was used o de ec ansc ip speci ic a ian s.
Associa ions in cis we e delinea ed by a 1 Mb window ups eam
o downs eam o he ARLTS1 SNP s9526582, as mos o he cis-
eQTLs a e loca ed wi hin o close o he gene o in e es [17]. In
addi ion, we applied a new me hod based on p obabilis ic indices
o es o eQTL. The new me hod is a non-pa ame ic di ec ional
es (simila o he well-known Jonckhee e-Te ps a es ), imple-
men ed in ou R-Package Gene icTools ha is a ailable on he
Comp ehensi e R A chi e Ne wo k (h p://c an. -p ojec .o g/
package = Gene icTools), and a package desc ip ion is unde
Table 1. Clinicopa hologic indings a diagnosis o he PCa
pa ien s used in RNA sequencing (n = 84).
n(%)
Age a diagnosis
,65 yea s 48 (57.1)
$65 yea s 35 (41.7)
S age
T s age
T1 (clinically unde ec able) 31 (36.9)
T2–T4 (clinically de ec able) 48 (57.1)
M s age
M0 (no e idence o me as asis) 53 (63.1)
M1 (bone me as asis) 0 (0)
MX (bone me as asis canno be
assessed)
27 (32.1)
PSA alue
,20 ng/ml 60 (71.4)
$20 ng/ml 14 (16.7)
G ade
Gleason sco e
,7 44 (52.4)
7 10 (11.9)
.7 0 (0)
doi:10.1371/jou nal.pone.0072040. 001
Exp ession and Regula ion o ARLTS1 wi h PCa
PLOS ONE | www.plosone.o g 2 Augus 2013 | Volume 8 | Issue 8 | e72040
de elopmen (unpublished da a). P- alues we e calcula ed using
pe mu a ion es s and we e adjus ed o mul iple es ing by
applying he Benjamini-Hochbe g co ec ion. We also calcula ed
o each es size ain [0,0.1] he a io o he amoun o expec ed
es ejec ions and he amoun o obse ed ejec ions. The a o
which he a io o hese wo alues was maximal, we chose also as
an op imal es size.
Gene exp ession da ase
All mic oa ay gene exp ession da a on cell lines (n = 1445)
included in hese analyses a e publicly a ailable ia he Gene
Exp ession Omnibus (GEO) (h p://www.ncbi.nlm.nih.go /geo/,
accession numbe s; GSE36133, GSE7127, GSE8332, GSE10843,
GSE10890, GSE12777, GSE15455, GSE18773, GSE20126,
GSE21654 and GSE24795) and GSK Cance Cell Line Genomic
P o iling Da a (h ps://cabig.nci.nih.go / ools/
caA ay_GSKda a) (2008) [18] (GlaxoSmi hKline). The bulk o
he gene exp ession da a was acqui ed om he Cance Cell Line
Encyclopedia (CCLE) (GSE36133) [19]. We used samples om
he mos ecen and widely ci ed A yme ix mic oa ay pla o m,
HGU133_plus 2.0, o pe o m hese analyses.
Gene exp ession da a No malisa ion
Gene exp ession da a no malisa ion was pe o med om he
aw CEL iles using he A oma A yme ix (Ve sion 1.3.0) R
package (h p://www.a oma-p ojec .o g) based on cus om CDF
iles ( e sion 16) ound a h p://b aina ay.mbni.med.umich.edu
[20]. We p ocessed exp ession o 19,003 dis inc genes. All
compu a ions we e pe o med in he R s a is ical en i onmen ,
employing he BioConduc o sui e o packages.
Co-exp ession analysis o ARLTS1.The co-exp ession
analysis me hod was desc ibed p e iously [10]. The me a cell line
da a (n = 1445) o igina ed om o e 48 human ana omical pa s.
A co ela ion alue .0.30 and a p- alue ,0.05 we e used as
de e minan s o a s a is ically signi ican associa ion. We pe -
o med mul iple es co ec ions using Benjamini Hochbe g and
Bon e oni me hods. We decided o use he Benjamini Hochbe g
(BH) me hod o selec ing signi ican ly co-exp essed genes because
i was mode a ely s ic a calling a gene pai co ela ion a alse
posi i e.
In silico unc ionali y p edic ion
RegulomeDB (h p:// egulome.s an o d.edu/) and HaploReg
(h p://www.b oadins i u e.o g/mammals/haplo eg/haplo eg.
php) [21,22] da abases we e used o u he elucida e he ole o
eQTLs in gene egula ion. RegulomeDB allows he ea u es o
DNA and egula o y elemen s o non-coding egions o be
assessed, and HaploReg is a ool o de eloping mechanis ic
hypo heses o he impac o candida e egula o y non-coding
a ian s on clinical pheno ypes and no mal a ia ion.
MDR analysis
The mul i ac o dimensionali y educ ion (MDR) p og am is
publicly a ailable om he in e ne (www.epis asis.o g). We used
e sion 2.0_be a_8.4 o examine gene-gene in e ac ions. MDR
de ec s in e ac ions in ela i ely small sample sizes. MDR is a non-
pa ame ic, model- ee da a mining app oach cons uc i e
induc ion algo i hm ha ans o ms he high-dimensional da a
in o one-dimensional a iables by pooling geno ypes in o high and
low isk g oups based on he a io o cases o con ols ha ha e he
geno ype in ques ion [23]. MDR selec s one gene ic model (a one,
wo, h ee o ou s age locus) ha mos success ully p edic s he
pheno ype o disease s a us, e.g., cance . Da a a e hen di ided
in o en equal pa s o pe o m a 10- old c oss- alida ion. The
model c ea es a aining se (9/10 o he da a) and es ing se (1/10
da a) o e alua e he p edic ion abili y. The p ocedu e epea s his
p o ocol en imes and calcula es he c oss- alida ion consis ency
(CVC). CVC depic s he numbe o imes ha pa icula model is
chosen as he bes one o hose en in e als. F om he MDR
esul s sec ion, es ing balanced accu acy (TBA) shows how many
ins ances a e co ec ly classi ied. The ARLTS1 geno ypes om 102
PCa cases and 33 con ols we e combined wi h he GWAS da a o
700,000 SNPs.
Selec ion o genes and SNPs o MDR
The genes unc ioning in immune sys em p ocesses and
in lamma ion pa hways we e selec ed om a p e iously published
comp ehensi e collec ion made by Loza MJ e al. [24] because
MDR is no able o un da a se s o housands o SNPs wi hin
easonable ime limi s. In sho , he SNPs selec ed included hose
in ol ed in apop osis, cy okine signalling, Toll-like ecep o
signalling, leukocy e signalling, complemen , adhesion and na u al
kille cell signalling. We also an MDR wi h a subse o genes
ga he ed om ou p e ious ARLTS1 co-exp ession s udies (e.g.,
wel e genes wi hin B-cell ecep o [BCR] signalling pa hway).
The o al amoun o SNPs was 12,011 o which 4,764 we e ound
in ou Illumina Human OmniExp ess GWAS da a.
Resul s
RNA exp ession
The ARLTS1 RNA exp ession le els we e analysed om o al
RNA o 84 PCa cases and 15 con ols. A signi ican dec ease o he
ARLTS1 exp ession le el in PCa cases was de ec ed (p = 0.0037,
Fig. 1). This is in conco dance wi h ou p e ious esul s om cell
line, benign p os a ic hype plasia (BPH) and umou specimen
RNA exp ession da a [10].
eQTL analysis
To iden i y possible cis-ac ing gene ic a ian s associa ed wi h
ARLTS1 ansc ip le els, we pe o med an eQTL analysis wi hin
a special a ea o he 13q14 egion. By a linea eg ession model
(PLINK), we we e able o de ec 5 eSNPs a ec ing ARLTS1
exp ession (Table 2). When he calcula ion window was dimin-
ished om 1 Mb o 200 kb, only one SNP, s7997377, emained.
Wi h he di ec ional es pe o med by he R-Package analysis
ool, 11 s a is ically signi ican eSNPs we e ound (Table 2), and
wo we e in conco dance wi h he PLINK linea eg ession model
Figu e 1. Rela i e
ARLTS1
RNA exp ession om PCa pa ien s
and heal hy con ols. Rela i e ARLTS1 RNA exp ession was de e -
mined by RNA sequencing analysis. Columns ep esen means o
indi iduals; ba s ep esen SD.
doi:10.1371/jou nal.pone.0072040.g001
Exp ession and Regula ion o ARLTS1 wi h PCa
PLOS ONE | www.plosone.o g 3 Augus 2013 | Volume 8 | Issue 8 | e72040
esul s. Fo bo h es p ocedu es a es size o 0.01 was chosen. The
eSNPs ound by he di ec ional es we e loca ed mainly in non-
coding egions (Table 2). The genomic loca ions o he eSNPs
ound in he 13q14 egion a e isualised in Figu e 2. Al oge he ,
468 genomic a ian s wi hin he 1 Mb egion o igina ing om
ARLTS1 SNP s9526582 we e es ed by a linea eg ession model
and di ec ional es .
A e adjus ing o mul iple es ing, a FDR o 39% in he linea
model and app oxima ely 32% in he di ec ional es has o be
accep ed o keep he signi ican es esul s om he ma ginal p-
alues. Fo a mo e common FDR le el o 10% one signi ican
eSNP om he di ec ional es emained signi ican ( s9568354).
When we conside ed he a io o expec ed and obse ed signi ican
es s, a maximum a io o a= 0.011 in di ec ional es was
iden i ied. Fo ha aapp oxima ely 2.5 imes mo e signi ican es
esul s appea ed han expec ed. Hence, we epo also he abo e
men ioned non-adjus ed p- alues o a signi icance le el 0.01.
Wi h linea eg ession model, he amoun o obse ed signi ican
es s ma ched he amoun o expec ed es ejec ions unde he null
hypo hesis.
The associa ion o he eSNP geno ypes wi h he ARLTS1
exp ession le el was calcula ed. A s a is ically signi ican co ela-
ion was na u ally obse ed be ween all he 14 SNPs and ARLTS1
ansc ip le els. The eSNP geno ype - ARLTS1 exp ession
associa ion box plo s a e depic ed in Figu e 3.
The unc ionali y and possible ansc ip ional egula o y e ec
o he 14 eSNPs wi hin genes ound by eQTL was e alua ed using
ENCODE-da a in he RegulomeDB and HaploReg da abases.
Al oge he nine o he ou een eQTLs a e epo ed in
RegulomeDB. The indings in he GM12878 lymphoblas oid cell
line a e emphasized below because his cell line esembles he
issue ype om which he RNA sequencing da a was e ie ed.
The mos subs an ial e idence o he egula ion o ARLTS1 was
ound o SNP s2532975. I s egula o y ole is suppo ed by i s
loca ion in a egula o y ac i e egion. Acco ding o he Chip-Seq
da a om he GM12878 cell line, s2532975 esides in a BATF
(basic leucine zippe ansc ip ion ac o ) binding si e. In addi ion,
using posi ion weigh ma ix (PWM) ma ching, a CDC5 (cell cycle
se ine/ h eonine-p o ein kinase) binding mo i has been iden i ied
ha spans he genomic posi ion o his a ian . Fu he mo e, a
p omyelocy ic leukemia zinc inge (PLZF) mo i is epo ed in
HaploReg. As epo ed by HaploReg, CDC5 binding e iciency
dec eases while PLZF binding inc eases. Addi ionally, he
ch oma in s a e in he egion su ounding s2532975 migh adop
weak enhance cha ac e is ics. This p edic ion is u he s eng h-
ened by he p esence o wo his one ma ks in his egion,
H3k4me1 and H3k4me2, iden i ied in he GM12878 cells.
Ano he possible candida e o ARLTS1 egula ion is s9562905.
In a Chip-Seq s udy, a POLA2 binding si e was iden i ied in a
human emb yonic s em cell line, H1-hESC, in he egion
su ounding s9562905. HaploReg p edic s ac i e enhance
cha ac e is ics in he ch oma in su ounding s9562905 in he
lymphoblas oid GM12878 cells, simila o s2532975. This
in e p e a ion is suppo ed by he p esence o wo enhance
Figu e 2. Schema ic diag am showing he genomic loca ions o eSNPs ga he ed by eQTL analysis in PCa pa ien s. The gene symbols
a e as ollows: CYSLTR2 (cys einyl leuko iene ecep o 2), FNCD3A ( ib onec in ype III domain con aining 3A), MLNR (mo ilin ecep o ), CDADC1
(cy idine and dCMP deaminase domain con aining 1), CAB39L (calcium binding p o ein 39-like), SETDB2 (SET domain, bi u ca ed 2/CLLD8), PHF11 (PHD
inge p o ein 11/NY-REN-34 an igen), RCBTB1 ( egula o o ch omosome condensa ion [RCC1] and BTB [POZ] domain con aining p o ein 1/CLLD7),
ARLTS1 (/ARL11, ADP- ibosyla ion ac o -like 11), EBPL (emopamil binding p o ein-like), KPNA3 (ka yophe in alpha 3, impo in alpha 4), SPRYD7 (SPRY
domain con aining 7/C13o 1, ch omosome open eading ame 1), MIR3613 (mic oRNA 3613), TRIM13 ( ipa i e mo i con aining 13), KCNRG
(po assium channel egula o ), MIR-15A and MIR16-1 (mic oRNA genes 15a and 16-1) and DLEU2 (dele ed in lymphocy ic leukemia 2).
doi:10.1371/jou nal.pone.0072040.g002
Exp ession and Regula ion o ARLTS1 wi h PCa
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associa ed his one ma ks, H3k4me1 and H3k4me2. In addi ion, a
FAIRE-sequencing s udy conduc ed o he GM12878 cells also
implies ha his egion is in an open ch oma in s a e and is
he e o e likely o ha e egula o y ac i i y.
The a ian s s1543513, s7997737 and s9568354 sha e
simila ch oma in s uc u al ea u es in he GM12878 cells.
Acco ding o HaploReg, he ch oma in s a e associa es wi h he
weakly ansc ibed egion. This p edic ion is con i med by he
elonga ion o his one ma k H3k36me3 in he su ounding egions
o he a ian s s1543513, s7997737 and s9568354. Acco ding o
RegulomeDB, s1543513 is loca ed wi hin he I x3 and I x6
mo i s. Howe e , in HaploReg, he p esence o hese mo i s is no
epo ed. Simila ly, he ansc ip ion ac o binding mo i o AIRE
(au oimmune egula o ) is epo ed o s1262781 in RegulomeDB
bu no in HaploReg. A MZF1 (myeloid zinc inge 1) mo i
su ounding s7997737 is epo ed in bo h da abases. HaploReg
epo s a nega i e LOD sco e di e ence o s7997737, which can
be in e p e ed as lowe ed binding e iciency o MZF. Compa ed o
he h ee a ian s men ioned abo e, s9568232 sha es simila
cha ac e is ics ega ding i s ch oma in s a e. Acco ding o
HaploReg, his ch oma in s a e is ela ed o elonga ed ansc ip-
ion.
The a ian s s2075610 and s1262774 a e loca ed wi hin
egions mos likely unde he con ol o epigene ic egula ion by
he polycomb-g oup p o eins in he GM12878 cells. In addi ion,
DNase-Seq s udies pe o med o se e al cell lines indica e an
open ch oma in s a e su ounding s2075610. Howe e , wo
ep essed s a e ch oma in his one ma ks, H3k27me3 and
H3k9me3, ha e also been iden i ied. Va ian s1262774 is no
epo ed in he RegulomeDB.
The emaining a ian s a e loca ed in he e och oma in egions,
acco ding o HaploReg. Fo s7995192, s2580189 and
s1262781, his p edic ion is u he con i med by he p esence
o H3k27me3. In addi ion, ano he ep essi e s a e associa ed
his one ma k, namely H3k9me3, is p esen in he s7995192 and
s2580189 egions. Al hough he e is e idence o ep essed s a e
ch oma in, RegulomeDB epo s ha ansc ip ion ac o binding
mo i s do in ac span he genomic posi ions o s2580189 and
s1262781.
Two mo i s o XBP-1 (X-box binding p o ein 1) and ATF6
(ac i a ing ansc ip ion ac o 6) span he egion o s1262781,
acco ding o RegulomeDB. HaploReg con i ms he p esence o
XBP-1 and ATF6 mo i s and an addi ional mo i o SOX-17
(SRY [sex de e mining egion Y] box 17). HaploReg epo s lowe
p edic ed binding e iciencies o XBP-1 and ATF6 and a sligh ly
inc eased binding e iciency o SOX-17.
RegulomeDB epo s a ZNF143 (zinc inge p o ein 143) mo i
in he egion su ounding SNP s2580189. Howe e , HaploReg
does no epo he p esence o his mo i . Taken oge he , he
esul s ga he ed om RegulomeDB and HaploReg indica e ha
he ARLTS1 eQTLs a e loca ed wi hin egula o y a eas o he
13q14 egion.
Co-exp ession analysis
The GeneSapiens mRNA exp ession da abase da a, including
ARLTS1 exp ession, om 1445 cell lines (48 cance sub ypes) and
p os a e cance umou s was a ailable o in e ac ion s udies.
Al oge he 1381 genes wi h co ela ion alue .0.30 and p- alue
,0.05 was ound o be posi i ely co ela ing wi h he ARLTS1
gene. Using DAVID GO unc ional clus e ing, (h p://da id.abcc.
nci c .go / ools.jsp) [25,26] a s ong associa ion wi h nucleus and
zinc- inge p o ein p ocesses was illus a ed when all he genes
posi i ely co ela ing wi h ARLTS1 exp ession (n = 36) in he PCa
cell line coho we e aken in o accoun (wi h a mo e s ingen
co ela ion alue .0.50). The g oup o nuclea p ocesses (nucleus,
in acellula o ganelles, ansc ip ion and DNA-binding) was
en iched when da a o PCa cell lines was s udied. The en ichmen
sco e was 13.49 wi h a p- alue 1.1E-32. The adjus ed Benjamin
sco e was 5.1E-30, and he clus e o zinc- inge binding p o eins
e ealed a p- alue o 9.0E-22. The same phenomenon was
Table 2. Ch omosomal egion 13q14 isk a ian s (eSNPs) associa ed wi h di e en ial ARLTS1 exp ession.
SNP Gene Posi ion Allele1 Allele2 P- alue Adjus ed P- alue
Linea eg ession model
RS1886014 N/A 49321044 A G 0,007 0,369
RS7997737 SETDB2 50033188 G A 0,006 0,322
RS7337547 N/A 50443527 C A 0,008 0,384
RS7995192 N/A 50782599 G A 0,008 0,331
RS2532975 N/A 50945011 G A 0,005 0,322
Di ec ional es
RS2075610 MLNR 49795705 G A 0,010 0,322
RS7997737 SETDB2 50033188 G A 0,008 0,322
RS1543513 SETDB2 50034684 A C 0,007 0,322
RS9568232 PHF11 50089844 A G 0,000 0,322
RS9562905 N/A 50210212 A C 0,008 0,322
RS9568354 SPRYD7 50487993 A G 0,002 0,000
RS2580189 N/A 50806640 A G 0,009 0,322
RS2532975 N/A 50945011 G A 0,001 0,322
RS1262781 N/A 51066171 A G 0,010 0,322
RS1262774 N/A 51068896 A G 0,006 0,322
RS17074618 N/A 51153475 A G 0,006 0,322
doi:10.1371/jou nal.pone.0072040. 002
Exp ession and Regula ion o ARLTS1 wi h PCa
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Exp ession and Regula ion o ARLTS1 wi h PCa
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obse ed wi hin he whole da a o cell lines (me a coho ) wi h
genes showing a co ela ion alue .0.30. ARLTS1 co-exp ession
genes (wi h co ela ion alue .0.50) om he me a cell line da a
e ealed a ca ego y o immune sys em p ocesses (B-/T-cell
ac i a ion, leukocy e/lymphocy e di e en ia ion and ac i a ion),
wi h an en ichmen sco e o 2.94 (p- alue 5.57E-7, adjus ed
Benjamin sco e 2.9E-5).
ARLTS1 co-exp ession da a o genes nega i ely co ela ed o
ARLTS1 iden i ied a s ong gene on ology o glycop o ein and
plasma memb ane p o ein genes in PCa cell lines (n = 2722,
co ela ion alue,20.50, en ichmen sco e 52.13, p- alue 3.4E-
72 and 38.35, p- alue 7.9E-32, espec i ely). Wi hin he nega i ely
co ela ing genes, a clus e o immunoglobulin domain con aining
p o eins ha bou ed an en ichmen sco e o 12.23 wi h a p- alue o
5.4E-24. The GO e m ‘‘cy okine ac i i y’’ e ealed an en ich-
men sco e o 10.43 wi h a p- alue o 6.5E-10 wi hin nega i ely
co ela ing genes. In addi ion o he esul o ARLTS1 nega i ely
co ela ing genes, we also iden i ied clus e s o G-p o ein coupled
ecep o s and cell-cell signalling.
Top i e posi i ely and nega i ely ARLTS1 co ela ing genes in
cell line da a a e p esen ed in Table 3 (uppe panel). Addi ionally,
esul s o he ARLTS1 co-exp ession wi h genes (SETDB2, PHF11,
SPRYD7, MLNR) ha ha bo ed eSNPs a e p esen ed in he lowe
pa o he Table 3, om he co-exp ession analysis pe o med in
he me a cell line, p os a e cell line da a and p os a e umo da a.
The exp ession o ARLTS1 was posi i ely co ela ed wi h he
exp ession o SETBD2, in bo h he whole da a o cell lines (me a
cell line coho ) (co ela ion alue 0.64, p- alue 0.000) and in he
Figu e 3. Co ela ion o he di e en geno ype g oups o eSNPs o
ARLTS1
RNA exp ession le els. A, s2075610; B, s7997737; C,
s1543513; D, s9568232; E, s9568354; F, s1886014; G, s7337547; H, s7995192; I, s9562905; J, s2580189; K, s2532975; L, s1262781; M, s1262774
and N, s17074618.
doi:10.1371/jou nal.pone.0072040.g003
Table 3. ARLTS1 Co-exp ession signa u es om umo specimens and cell lines.
Gene Co ela ion alue P- alue Samples (n) p al_co ec ed* p al_co ec ed#
Top i e genes
Co-exp ession in me a cell line da a
Posi i e co ela ion
BTK 0,69 0 2818 0 0
GPR18 0,66 0 2818 0 0
CXo 21 0,66 0 2818 0 0
P2RY8 0,66 0 2818 0 0
PIK3CG 0,65 0 2818 0 0
Nega i e co ela ion
NCKAP1 20,62 1,69E-295 2818 3,22E-291 7,70E-295
CDC42BPB 20,59 1,64E-263 2818 3,11E-259 7,43E-263
GIPC1 20,57 1,10E-239 2818 2,10E-235 5,01E-239
PTMS 20,53 2,68E-208 2818 5,09E-204 1,22E-207
KIAA0284 20,53 1,04E-203 2818 1,97E-199 4,71E-203
Genes ha bo ing eSNPs
Co-exp ession in me a cell line da a
MLNR 20,15 1,35E-16 2818 2,57E-12 2,96E-16
PHF11
0,44 0,000 2818 0,000 0,000
SETDB2
0,64 0,000 2818 0,000 0,000
SPRYD7 0,28 0,000 2818 0,000 0,000
Co-exp ession in PCa cell lines
MLNR
2
0,35 0,0352 36 1 0,081
PHF11 0,09 0,608 36 1 0,704
SETDB2
0,61 9,01E-05 36 1 0,001
SPRYD7 0,17 0,336 36 1 0,451
Co-exp ession in p os a e umo samples
MLNR 0,03 0,821 75 1 0,934
PHF11 20,07 0,576 75 1 0,806
SETDB2 20,07 0,547 75 1 0,788
SPRYD7
2
0,34 0,003 75 1 0,045
*Bon e oni co ec ion.
#
Benjamini Hohchbe g mul iple es ing co ec ion.
doi:10.1371/jou nal.pone.0072040. 003
Exp ession and Regula ion o ARLTS1 wi h PCa
PLOS ONE | www.plosone.o g 7 Augus 2013 | Volume 8 | Issue 8 | e72040
speci ic PCa cell lines (co ela ion alue 0.61, p- alue 0.00009)
(Table 3). Exp ession o he PHF11 gene was posi i ely co ela ed
wi h ARLTS1 exp ession in he me a cell line da a (co ela ion
alue 0.44, p- alue 0.000). Exp ession o MLNR and SPRYD7 was
nega i ely co ela ed wi h ARLTS1 exp ession. ARLTS1 and
MLNR had a co ela ion alue o 20.35 (p- alue 0.04) in PCa
cell lines, and ARLTS1 and SPRYD7 had a co ela ion alue o
20.34 (p- alue 0.003) in p os a e umou specimens (Table 3).
The s ong nega i e co ela ion o ARLTS1 and SPRYD7
exp ession le els was also alida ed in ou ansc ip ome da a o
84 PCa cases and 15 con ols.
MDR analysis
By di ec sequencing, we we e able o de ec six ARLTS1
a ian s a he same amplicon om PCa pa ien s included in he
Illumina geno yping (n = 135). All he a ian s we e p e iously
known ( s117251022, s3803186, s147120792, s3803185,
s138452698 and G446A [T p149S op]). To elucida e he
geno ypic ARLTS1 in e ac ions we used mul i ac o dimensionali y
educ ion (MDR). Gene-gene in e ac ion s a us be ween ARLTS1
and genes unc ioning in immune sys em p ocesses wi hin 102 PCa
cases and 33 con ols was calcula ed, bu we we e no able o ind
any s a is ically signi ican ARLTS1 in e ac ions in his s udy
coho (da a no shown).
Discussion
ARLTS1 is a cance -p edisposing gene wi h p o en umou
supp esso p ope ies. Howe e , e y li le e idence on unc ion,
especially on pa hways, is cu en ly a ailable. In his s udy, we
we e able o e i y down egula ed ARLTS1 exp ession in he
blood-de i ed RNA o PCa pa ien samples, demons a ing o he
i s ime he e ec o ge mline al e a ion on ARLTS1 exp ession
le els. Tumou supp esso unc ion o he ARLTS1 gene has been
p e iously p o en by Calin GA e al., who ound ha ansduc ion
o ull-leng h ARLTS1 o A549 cells in Nu/Nu mice dec eased
umou g ow h when compa ed o emp y ec o [1]. The abili y o
ARLTS1 o supp ess umou o ma ion in p eclinical models has
also been obse ed wi h o a ian [27] and lung cance cells [28].
Howe e , hese esul s a e based on soma ic mu a ions in
cance ous cell lines, whe eas ou esul e eals a no el exp ession
di e ence a he ge mline le el, suppo ing he ole o ARLTS1 as a
umou supp esso gene. In he u u e, hese ypes o indings
could be used o enable sc eening and de ec ion o a - isk pa ien s
e en be o e clinical diagnoses.
We ha e p e iously geno yped ARLTS1 a ian s in p os a e,
b eas and colo ec al cance [29] and p oduced a p os a e cance
ollow-up s udy [10]. In he i s s udy [29], we epo ed a
s a is ically signi ican associa ion wi h ARLTS1 a ian s T442C,
G194T and p os a e cance isk. Howe e , a e adjus ing o
mul iple es ing, none o he esul s we e signi ican . In he ollow-
up s udy wi h la ge sample size, we epo ed a s a is ically
signi ican associa ion wi h T442C a ian and p os a e cance isk
[10]. We epo ed also a dec eased o los ARLTS1 RNA o
p o ein exp ession in clinical p os a e umo s, p os a e cance cell
lines and xenog a s, suppo ing he ole o ARLTS1 as a umo
supp esso gene. Thus, he e is no con lic be ween he p e ious
publica ions and his s udy ha is con i ming he umo supp esso
ole o ARLTS1.
He e, 14 eSNPs loca ed a he 13q14 egion we e shown o
signi ican ly in luence ARLTS1 ansc ip le els in PCa pa ien s.
The eQTL analysis was pe o med wi h wo me hods, a linea
model app oach and a di ec ional es . One ad an age o ou
di ec ional es me hod o e he commonly used linea model
app oach is i s obus ness agains ou lie s and he weake model
assump ions. In he linea model app oach, he exp ession alues
o he di e en geno ype g oups a e conside ed o ollow he same
no mal dis ibu ion up o a loca ion shi pa ame e . I he loca ion
shi pa ame e is no equal o ze o, i gene a es a es ing p oblem.
The di ec ional es only assumes ha he di e en exp ession
alues ollow ce ain dis ibu ion unc ions, so a es ing p oblem
only occu s i he dis ibu ions o he geno ype g oups a e
s ochas ically o de ed.
In e es ingly, 5 o he eSNPs a e loca ed wi hin he p o ein-
coding genes SETDB2,PHF11,SPRYD7 and MLNR. Two eQTLs
we e posi ioned in he SETDB2 (SET domain, bi u ca ed 2) gene,
also known as he CLLD8 (ch onic lymphocy ic leukemia dele ion
egion gene 8 p o ein) gene, which unc ions mainly in epigene ic
egula ion [30]. The PHF11 gene, ano he hi o he eSNPs, is a
posi i e egula o o Th1- ype cy okine gene exp ession h ough
nuclea ac o kappa B, (NF-kB) [30,31]. The hi d eSNP gene,
SPRYD7, (SPRY domain con aining 7/ch omosome 13 open
eading ame 1 [C13o 1]) also known as ch onic lymphocy ic
dele ion egion gene 6 p o ein, (CLLD6) [32], is p oposed o ha e a
umou supp esso unc ion because i has been de ec ed o be
down egula ed in B-CLL pa ien s [33]. The SPRY/B30.2 p o ein
domain occu s in a a ie y o cellula p o eins, media es p o ein-
p o ein in e ac ions and nega i ely egula es cy okine ac i i ies
[34,35]. The ou h eSNP gene, MLNR/MTLR1, (G-p o ein-
coupled ecep o 38, GPR38) is a membe o he G-p o ein
coupled ecep o 1 amily and is iden i ied as he mo ilin ecep o
[36]. The ound eSNPs we e no a ec ing he exp ession o he
gene hey esided in, sugges ing he ole o hese eSNPs as speci ic
egula o s a ge ing ARLTS1 exp ession. Howe e , no explici
conclusions abou he ac ual causal in e ac ion be ween hese
a ian s and ARLTS1 can be made wi hou u he unc ional
alida ion. The eQTL esul ga he ed in his s udy was om a
ela i ely small sample se in which analyses encompassed 1 Mb
up- and downs eam o he ARLTS1 gene. Thus, u he alida ion
in la ge sample se s and genomic a eas a e wa an ed. Howe e ,
in ou esul s, one eSNP emained signi ican e en a e
adjus men s o mul iple es ing. Those adjus men s a e in ica e
in he case o eQTL analysis and s udies wi h small sample sizes
o en su e om a low de ec ion a e a e mul iple es ing
adjus men [37]. One possible s a egy o deal wi h his is o accep
a ela i ely high FDR o he sake o la e alida ion in a la ge
popula ion. He e, no po en ial candida e eSNPs we e excluded
om u he s udies because he awi h la ges a io be ween
obse ed and ejec ed es s was conside ed as op imal es size.
Lymphoblas oid cell lines (LCLs) a e widely used in eQTL
s udies because hey a e an easily accessible sou ce o pa ien
samples o a single cell ype. Pa icula ly wi h p os a e cance , he
umou specimens o mul iple oci a e ha d o collec in la ge
amoun s making i di icul o eliably de ec disease-associa ed
ai s. By using p os a e cance specimens, i is possible o ind
issue-speci ic gene ic e ec s, bu he use o lymphoblas oid cell
lines o whole blood o amilial p os a e cance pa ien s enables
one o de ec he possible he i able ge mline di e ences which may
con ibu e o p os a e cance suscep ibili y. I has been a gued ha
SNP- ansc ip app oaches using LCLs o small sample se s a e
unde powe ed [38], bu many s udies ha e been able o ind
o e lapping eQTLs in cell lines and p ima y issues [39–41]. Ou
inding o he eSNP in he SPRYD7 gene was endo sed in he co-
exp ession da a, in which he ARLTS1 exp ession le els we e
signi ican ly co ela ed wi h SPRYD7 exp ession, and in he
p os a e umou specimens (Table 3). Addi ionally, in he da a
om he ENCODE conso ium, he signi icance and usage o
LCLs a e jus i ied because he lymphoblas oid cell line (GM12878)
Exp ession and Regula ion o ARLTS1 wi h PCa
PLOS ONE | www.plosone.o g 8 Augus 2013 | Volume 8 | Issue 8 | e72040
is one o he h ee cell lines in he highe p io i y Tie 1 coho
[42].
The e may be a join e ec be ween he 13q14 genes. Fo
example, one la ge ansc ip a ian ha consis s o mo e han
one gene has been p oposed wi h SETDB2 and PHF11 [30]. Ve y
li le is known abou he in e ac ions in his a ea, pa icula ly he
genomic collabo a o s o he ARLTS1 gene. A ecen s udy
iden i ied cellula e inoic acid binding p o ein 2 (CRABP2) and
phosphoglyce a e mu ase 1 (PGAM1) as no el ARLTS1-binding
p o eins using he in- ame cDNA lib a y echnique [43]. These
p o eins we e no obse ed in he exp ession o geno ype le el o
ou da a, so u he s udies a e needed o elucida e he ac ual
ARLTS1 in e ac ing genes and p o eins.
Conside ing he in e ac ions be ween ARLTS1 and in lamma-
ion pa hway genes, i was ou hypo hesis ha ARLTS1 would
ha e in e ac ions wi h in lamma o y genes, as ch onic in lamma-
ion has been p oposed as a p os a e cance isk ac o . Wi h MDR
analysis, we aimed o in es iga e he p e iously obse ed ARLTS1
connec ion wi h immune sys em p ocesses [10]. Ano he aim was
o es he hypo hesis o genes unc ioning in in lamma ion
p ocesses a ec ing p os a e cance isk. Howe e , we ailed o
subs an ia e ou hypo hesis, and s a is ically signi ican associa ion
be ween ARLTS1 T442C SNP and he in lamma o y/immune
sys em SNPs was no ound wi hin he 700,000 SNPs analysed.
Fo he analysis, we ex ac ed dis inc SNP g oups om 4,764
ma ke s ound om ou da a o 700,000 a ian s in o al. One
possible eason o he nega i e esul s may be he ela i ely
limi ed sample se o 135 cases and con ols because we we e no
able o gene alise he esul s o he es da a. We we e also
conce ned abou o e i ing he da a wi h MDR.
Ou p e iously ound associa ion be ween ARLTS1 T442C and
p os a e cance isk may be caused by he in e ac ion ne wo k o
di e en SNPs in he 13q14 egion. Va ian T442C may be
included in a e y a e haploblock, o he e may s ill be a missing
a ian because he egion has been connec ed o o he cance s in
addi ion o PCa.
In conclusion, in his s udy we ha e shown ha he ARLTS1
exp ession le el is in luenced by changes in ge mline exp ession
le els and ha he ARLTS1 gene is a quan i a i e ai locus o 14
eSNPs in he 13q14 egion. Thus, ou esul s indica e a mo e
complica ed ne wo k o changes ha inc ease PCa isk han
me ely one gene ic a ian in ARLTS1.
Acknowledgmen s
We hank all o he pa ien s who pa icipa ed in ou s udy and acknowledge
he con ibu ion o Riina Liikala and Rii a Vaala uo o echnical
assis ance.
Au ho Con ibu ions
Concei ed and designed he expe imen s: SS TW DF JPM JS. Pe o med
he expe imen s: SS VL DF JPM TR. Analyzed he da a: SS DF TR JPM.
Con ibu ed eagen s/ma e ials/analysis ools: JS OK. W o e he pape :
SS TW JS.
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PLOS ONE | www.plosone.o g 9 Augus 2013 | Volume 8 | Issue 8 | e72040