1
Scien i ic RepoR s | 6:25671 | DOI: 10.1038/s ep25671
www.na u e.com/scien i ic epo s
Gene ic Rela ionship be ween
Schizoph enia and Nico ine
Dependence
Jingchun Chen1,*, Sil iu-Alin Bacanu2,3,*, Hui Yu4, Zhongming Zhao4, Peilin Jia4,
Kenne h S. Kendle 2,3, Hen y R. K anzle 5, Joel Gele n e 6, Lindsay Fa e 7, Camelia Minica8,
Rene Pool8, Yu i Milaneschi9, Do e I. Boomsma8, B enda W. J. H. Penninx8,
Rachel F. Tyndale10, Jenni e J. Wa e11, Jacqueline M. Vink12,13, Jaakko Kap io14,15,16,
Ma cus Muna ò11,17 , Xiangning Chen1,18, Co inine me a-analysis g oup & FTND
me a-analysis g oup
I is well known ha mos schizoph enia pa ien s smoke ciga e es. The e a e di e en hypo heses
pos ula ing he unde lying mechanisms o his como bidi y. We used summa y s a is ics om la ge
me a-analyses o plasma co inine concen a ion (COT), Fage s öm es o nico ine dependence
(FTND) and schizoph enia o examine he gene ic ela ionship be ween hese ai s. We ound ha
schizoph enia isk sco es calcula ed a P- alue h esholds o 5 × 10−3 and la ge p edic ed FTND
and ciga e es smoked pe day (CPD), sugges ing ha genes mos signi ican ly associa ed wi h
schizoph enia we e no associa ed wi h FTND/CPD, consis en wi h he sel -medica ion hypo hesis.
The COT isk sco es p edic ed schizoph enia diagnosis a P- alues o 5 × 10−3 and smalle , implying
ha genes mos signi ican ly associa ed wi h COT we e associa ed wi h schizoph enia. These esul s
implica ed ha schizoph enia and FTND/CPD/COT sha ed some gene ic liabili y. Based on his sha ed
liabili y, we iden i ied mul iple long non-coding RNAs and RNA binding p o ein genes (DA376252,
BX089737, LOC101927273, LINC01029, LOC101928622, HY157071, DA902558, RBFOX1 and TINCR),
p o ein modi ica ion genes (MANBA, UBE2D3, and RANGAP1) and ene gy p oduc ion genes (XYLB,
MTRF1 and ENOX1) ha we e associa ed wi h bo h condi ions. Fu he analyses e ealed ha hese
sha ed genes we e en iched in calcium signaling, long- e m po en ia ion and neu oac i e ligand-
ecep o in e ac ion pa hways ha played a c i ical ole in cogni i e unc ions and neu onal plas ici y.
1Ne ada Ins i u e o Pe sonalized Medicine, Uni e si y o Ne ada a Las Vegas, 4505 S. Ma yland Pa kway, Las Vegas,
NV 89154, USA. 2Vi ginia Ins i u e o Psychia ic and Beha io al Gene ics, Vi ginia Commonweal h Uni e si y, 800
E. Leigh S ee , Richmond, VA 23298, USA. 3Depa men o Psychia y Vi ginia, Commonweal h Uni e si y, 800
E. Leigh S ee , Richmond, VA 23298, USA. 4Depa men s o Biomedical In o ma ics and Psychia y, Vande bil
Uni e si y School o Medicine, Nash ille, TN 37203, USA. 5Depa men o Psychia y, Uni e si y o Pennsyl ania
Pe elman School o Medicine and VISN4 MIRECC, Philadelphia VA Medical Cen e , Philadelphia, PA, USA. 6Di ision
o Human Gene ics, Depa men o Psychia y, Yale Uni e si y School o Medicine, and VA CT Heal hca e Cen e ,
New Ha en, CT 06516, USA. 7Depa men o Medicine (Biomedical Gene ics), Bos on Uni e si y School o Medicine,
Bos on, MA, USA. 8Depa men o Biological Psychology, VU Uni e si y, Ams e dam, Ne he lands. 9Depa men
o Psychia y and EMGO Ins i u e o Heal h and Ca e Resea ch, VU Uni e si y Medical Cen e , Ams e dam,
Ne he lands. 10Depa men o Pha macology and Toxicology, Uni e si y o To on o, To on o, Canada. 11MRC
In eg a i e Epidemiology Uni , Uni e si y o B is ol, B is ol, UK. 12Depa men o Biological Psychology, V ije
Uni e si ei , Ams e dam, The Ne he lands. 13Beha iou al Science Ins i u e, Radboud Uni e si y, Nijmegen, The
Ne he lands. 14Uni e si y o Helsinki, Depa men o Public Heal h, P.O.Box 41 (Manne heimin ie 172), 00014
Helsinki, Finland. 15Na ional Ins i u e o Heal h and Wel a e, Depa men o Men al Heal h and Subs ance Abuse
Se ices, P.O. Box 30 (Manne heimin ie 166), 00300 Helsinki, Finland. 16Uni e si y o Helsinki, Ins i u e o Molecula
Medicine, P.O. Box 20 (Tukholmanka u 8), 00014 Helsinki, Finland. 17UK Cen e o Tobacco and Alcohol S udies,
School o Expe imen al Psychology, Uni e si y o B is ol, B is ol, UK. 18Depa men o Psychology, Uni e si y o
Ne ada, Las Vegas, 4505 S. Ma yland Pa kway, Las Vegas, NV 89154, USA. *These au ho s con ibu ed equally o
his wo k. Co espondence and eques s o ma e ials should be add essed o X.C. (email: Xiangning.chen@unl .edu)
Recei ed: 21 Janua y 2016
Accep ed: 20 Ap il 2016
Published: 10 May 2016
OPEN
www.na u e.com/scien i ic epo s/
2
Scien i ic RepoR s | 6:25671 | DOI: 10.1038/s ep25671
La ge scale genome wide associa ion s udies (GWASs) ha e iden i ied isk genes o many complex human dis-
eases and ai s (h p://www.genome.go /gwas udies/), including psychia ic diso de s such as schizoph enia and
nico ine dependence (ND)1–3. These GWASs also show ha many human diseases and ai s a e polygenic in
na u e and he con ibu ion o indi idual genes is limi ed4–6. Many o hese s udies ha e been deposi ed in he
da abase o Geno ypes and Pheno ypes (dbGaP, h p://www.ncbi.nlm.nih.go /gap) and a e a ailable o second-
a y analyses. These da ase s p o ide an oppo uni y o examine he gene ic ela ionship be ween co ela ed ai s,
and o disco e and iden i y isk genes sha ed ac oss hese ai s.
Pleio opy is a phenomenon in which a single locus a ec s mul iple ai s7,8. I accoun s o a leas a pa o
he gene ic mechanism o many co ela ed human beha io s and diseases. Pleio opy can ake wo o ms: ei he
a single p ocess, leading o a cascade o downs eam e ec s (some imes desc ibed as “media ed pleio opy”), o a
single locus in luencing mul iple ai s (some imes desc ibed as “biological pleio opy”)9. Schizoph enia is highly
como bid wi h ciga e e smoking10. Howe e , he unde lying biology o his como bidi y is no well unde s ood11.
Se e al hypo heses ha e been p oposed. The sel -medica ion hypo hesis pos ula es ha schizoph enia pa ien s
smoke o educe symp oms and an ipsycho ics-induced side e ec s and o imp o e hei a en ion and wo king
memo y12. Al e na i ely, schizoph enia and ND could ha e sha ed some gene ic liabili y (i.e., biological pleio -
opy)13, which is suppo ed by ecen s udies o indi idual genes14–21. A hi d possibili y is ha smoking may be
causal o schizoph enia (i.e., media ed pleio opy)22. To explo e he gene ic ela ionship be ween schizoph enia
and ND, we ob ained he GWAS summa y s a is ics om he Psychia ic Genomics Conso ium (PGC) schizo-
ph enia analyses and ND ela ed ai s om ou unpublished s udies, and conduc ed polygenic analyses. Unde
he hypo hesis o biological pleio opy, we expec ha gene ic isk sco es o schizoph enia and ND ela ed ai s
p edic each o he ; whe eas sel -medica ion would an icipa e unidi ec ional (schizoph enia o ND ai s) p edic-
ion. In his a icle, we epo he indings om hese analyses.
Resul s
Nico ine dependence and schizoph enia sha e gene ic liabili y. In hese analyses, we calcula ed
gene ic isk sco es o schizoph enia (supplemen a y Figu e 1A) and es ed whe he he isk sco es p edic ed
FTND and CPD. The esul s we e summa ized in Table1. Schizoph enia isk sco es p edic ed FTND sco e and
CPD a he h esholds o P ≤ 5 × 10−3, 5 × 10−2 and 5 × 10−1. The co ela ion coe icien s a hese h esholds we e
all posi i e, sugges ing ha a schizoph enia diagnosis was posi i ely associa ed wi h ciga e e smoking, consis en
wi h he well-known como bidi y be ween schizoph enia and ND. Howe e , schizoph enia isk sco es explained
only a e y small ac ion o he FTND and CPD ai s.
FTND and COT isk sco es (supplemen a y Figu e 1B,C) we e calcula ed o he subjec s o he phase I PGC
schizoph enia GWAS samples23 using he summa y s a is ics om he FTND (n = 17,781) and COT (n = 4,548)
GWAS me a-analyses. We hen e alua ed whe he he gene ic isk sco es o COT and FTND could p edic he
schizoph enia diagnosis using logis ic eg ession. The esul s we e p esen ed in Table2. The COT isk sco es
calcula ed a he P- alues o 5 × 10−5, 5 × 10−4 and 5 × 10−3 p edic ed schizoph enia diagnosis, bu FTND isk
sco es ailed o do so. Fo he P- alues h esholds a which he COT isk sco es p edic ed schizoph enia diagnosis,
he be a coe icien s we e also posi i e, again, con i ming he posi i e pheno ypic co ela ion be ween ND and
schizoph enia.
Iden i ica ion o sha ed a ian s be ween ND and schizoph enia. Ou ecip ocal polygenic anal-
yses sugges ed ha he e we e some sha ed gene ic liabili y be ween schizoph enia and ND as de ined by he
FTND and COT ai s. We hen p oceeded o iden i y he a ian s associa ed wi h bo h schizoph enia and ND
ai s. We compu ed join P- alues o each ma ke using he summa y s a is ics om he schizoph enia and
COT/FTND/TFC me a-analyses, and assigned a q- alue o each o he join P- alues using an FDR me hod24,25.
Table3 lis ed he loci iden i ied by he join analyses wi h q- alues ≤ 0.05. F om he join analyses be ween schiz-
oph enia and COT, 11 loci eached genome-wide signi icance o associa ion wi h bo h COT and schizoph enia,
o which 2 loci had no known genes nea by and 6 we e spliced ESTs o long non-coding RNAs. In he analyses
be ween schizoph enia and FTND, 10 loci we e iden i ied, and 3 o hem we e ESTs o non-coding RNAs. The
Th eshold (P) Be a S.E. T_ alue P (>|T|) R2
FTND
5 × 10−52.41E-04 0.000269 0.90 0.3708 0
5 × 10−43.30E-04 0.000235 1.41 0.1599 1.00E-04
5 × 10−33.91E-04 0.000194 2.01 0.0440 3.00E-04
5 × 10−23.53E-04 0.000153 2.31 0.0211 4.00E-04
5 × 10−13.22E-04 0.000118 2.73 0.0063 7.00E-04
CPD
5 × 10−51.03E-04 8.77E-05 1.17 0.2424 0
5 × 10−41.37E-04 7.64E-05 1.79 0.0736 1.00E-04
5 × 10−31.71E-04 6.32E-05 2.71 0.0067 5.00E-04
5 × 10−21.56E-04 4.99E-05 3.13 0.0018 6.00E-04
5 × 10−11.29E-04 3.84E-05 3.37 0.0008 8.00E-04
Table 1. Schizoph enia isk sco e p edic ion o FTND and CPD.
www.na u e.com/scien i ic epo s/
3
Scien i ic RepoR s | 6:25671 | DOI: 10.1038/s ep25671
join analyses be ween schizoph enia and TFC yielded 15 signi ican loci. The CHRNA5-CHRNA3-CHRNB4
locus was he only one iden i ied by all h ee smoking ai s. In addi ion o some genes known o be associa ed
wi h schizoph enia (HLA-B and MAD1L1), we also iden i ied no el non-coding RNAs and RNA binding p o ein
genes (DA376252, BX089737, LOC101927273, LINC01029, LOC101928622, HY157071, DA902558, RBFOX1
and TINCR), pos - ansla ion modi ica ion genes (MANBA, UBE2D3 and RANGAP1) and ene gy p oduc ion
genes (XYLB, MTRF1 and ENOX1).
Pa hway en ichmen and ne wo k in e ac ion analyses. We u he explo ed he pa hways sha ed by
schizoph enia and ND by selec ing all ma ke s wi h q- alues less han 0.16 om he join analyses be ween schiz-
oph enia and smoking ai s. A e mapping he ma ke s o genes, he genes showing po en ial associa ion wi h
schizoph enia and COT/FTND/TFC we e pooled o sea ch o pa hways en iched in bo h condi ions. In hese
analyses, we selec ed only he genes iden i ied by a leas 2 o he 3 smoking ai s, yielding a o al o 146 genes.
A e il e ing ou he human leukocy e an igen genes (HLA-B, HLA-C, HLA-DOA, HLA-DQA1, HLA-DQB1,
HLA-DRB1, and HLA-G) due o hei s ong linkage disequilib ium26, we used he emaining 139 genes in pa h-
way analyses.
Ou analyses iden i ied 16 unique pa hways ha we e sha ed be ween schizoph enia and ND (Table4). The
mos no iceable pa hways we e Calcium Signaling, Long-Te m Po en ia ion, Neu oac i e Ligand-Recep o
In e ac ion, Phospha idylinosi ol Signaling, Cell Adhesion Molecules, and Regula ion o Ac in Cy oskele on
pa hways. Some o hese pa hways (Calcium Signaling, Long-Te m Po en ia ion, Cell Adhesion Molecules, and
Regula ion o Ac in Cy oskele on) had been epo ed o be in ol ed in schizoph enia27–32, o he s (Cell Adhesion
Molecules and Neu oac i e Ligand-Recep o In e ac ion) had been implica ed in ND33,34. We ound ha hese
pa hways we e en iched in he genes associa ed wi h bo h ND and schizoph enia. Addi ionally, pa hways in ol ed
in ca diomyopa hy, GnRH signaling, gas ic acid sec e ion and Alzheime ’s disease we e also ound o be sha ed
be ween schizoph enia and ND. In he pa hway ne wo k in e ac ion analyses, we ound a ne wo k o c oss alk
be ween pa hways (Fig.1), wi h he Long-Te m Po en ia ion loca ed a he cen e o hese in e ac ions.
Discussion
I is well known in psychia ic clinics ha a la ge p opo ion o schizoph enia pa ien s smoke ciga e es and
smoke hea ily13. The dominan hypo hesis o explain he como bidi y is sel -medica ion12, i.e., ha schizoph e-
nia pa ien s smoke o amelio a e impai men s in cogni i e unc ion and supp ess psycho ic symp oms. Ano he
hypo hesis con ends ha schizoph enia and ND sha e some gene ic liabili y, and he high p e alence a e o
ciga e e smoking in schizoph enia pa ien s is a mani es a ion ha is pa ially due o he common liabili y13. A
hi d possibili y is ha smoking may be a isk ac o o he de elopmen o schizoph enia, gi en ha smoking
ini ia ion ypically p eda es he onse o schizoph enia22. These h ee hypo heses a e no mu ually exclusi e, and
all h ee may con ibu e o he obse ed co-occu ence o schizoph enia and smoking.
P e ious s udies examining his issue ha e la gely ocused on indi idual unc ions/symp oms o genes using
ela i ely small sample sizes. He e we ook a sys ema ic app oach, and examined he en i e genome using la ge
GWAS da ase s and mul iple ai s. We obse ed di e en pa e ns be ween he ecip ocal polygenic analyses
(compa ing Tables1 and 2). When we used he gene ic isk sco es o schizoph enia o p edic ND ai s, he
associa ion was e iden a P- alues ≥ 5 × 10−3, wi h he associa ion s eng h inc eased as he P- alue h eshold
became la ge (Table1). Gi en ha he PGC schizoph enia GWAS did no con ol o smoking s a us and quan-
i y, and he e was a la ge di e ence o smoking p e alence be ween schizoph enia pa ien s and con ols (on
a e age, 65% o mo e schizoph enia pa ien s smoke, and abou 20% people smoke in he gene al popula ion), we
would expec ha he PGC schizoph enia GWAS iden i y op candida es o ND ela ed ai s. Bu wha we ound
was no he case. These op anked candida es (i.e. hose wi h P- alues ≤ 5 × 10−5) om he PGC schizoph enia
me a-analysis1 we e no p edic ND ela ed ai s. A likely explana ion o hese esul s is ha genes mos s ongly
associa ed wi h schizoph enia do no di ec ly con ibu e o he smoking beha io s in schizoph enia pa ien s. In
o he wo ds, he eason why schizoph enia pa ien s smoke is ha hey wan o imp o e hei cogni i e unc ions
Th eshold (P) Be a S.E. Wald Z P (>|Z|) R2
Co inine
5 × 10−50.0459 0.0169 2.72 0.0066 0.0006
5 × 10−40.0583 0.0169 3.45 0.0006 0.0010
5 × 10−30.0435 0.0169 2.58 0.0100 0.0005
5 × 10−20.0035 0.0170 0.20 0.8384 3.4E-06
5 × 10−1− 0.0226 0.0172 − 1.32 0.1886 0.0001
FTND
5 × 10−50.0220 0.0242 0.91 0.3641 0.0001
5 × 10−40.0227 0.0507 0.45 0.6537 2.5E-05
5 × 10−30.0331 0.0617 0.54 0.5913 3.5E-05
5 × 10−20.0033 0.0323 0.10 0.9174 1.3E-06
5 × 10−10.0281 0.0292 0.96 0.3362 0.0001
Table 2. Gene ic isk sco e o nico ine dependence p edic ion o schizoph enia diagnosis*. *R2 is he
Nagelke ke’s R2 ob ained by he R package msb.
www.na u e.com/scien i ic epo s/
4
Scien i ic RepoR s | 6:25671 | DOI: 10.1038/s ep25671
and o supp ess psycho ic symp oms, no because ha hey a e addic ed o nico ine as egula smoke s in he
gene al popula ion do. These esul s a e consis en wi h he sel -medica ion hypo hesis.
In con as , when we used COT isk sco es o p edic schizoph enia diagnosis, we ound ha smalle P- alues
p oduced s onge signals (Table2), indica ing ha genes mos s ongly associa ed wi h ND we e associa ed wi h
schizoph enia. The esul s imply ha ei he ND and schizoph enia sha e some gene ic liabili y, o ND is a isk
ac o o schizoph enia. These i he p edic ions o he sha ed liabili y hypo hesis and ha smoking is a causal isk
o schizoph enia. O no e, hese wo explana ions a e no mu ually exclusi e. Bu wi hou da a on smoking o he
pa ien s we a e unable o es he la e possibili y (e.g., by s a i ying ou sample on smoking s a us).
Assuming biological pleio opy o be he unde lying mechanism, we de ised a es o disco e he a ian s
sha ed be ween ND and schizoph enia. Using his app oach, we iden i ied mul iple genes associa ed wi h bo h
condi ions (Table3). O hese genes, he CHRNA5-CHRNA3-CHRNB4 clus e had been ound o be associa ed
wi h CPD2,3 and o he ND ela ed ai s, and i was epo ed o be associa ed wi h schizoph enia in he la es
schizoph enia GWAS me a-analysis om PGC1. Se e al o he genes had been epo ed o be associa ed wi h
schizoph enia (HLA-B and MAD1L1)28 and epilepsy (KCNT1, PRICKLE2 and RBFOX1)35–37, sugges ing ha hey
migh play a ole in smoking beha io s as well. Ou analyses also iden i ied some no el genes sha ed be ween
schizoph enia and ND, including a g oup o long non-coding RNAs and RNA binding p o ein genes (DA376252,
BX089737, LOC101927273, LINC01029, LOC101928622, HY157071, DA902558, RBFOX1 and TINCR), a g oup
o pos - ansla ion modi ica ion genes (MANBA, UBE2D3, and RANGAP1) and a g oup o ene gy p oduc ion
SNP Ch Loca ion (bp) Z (ND) Z (SCZ) P- alue Q- alue Gene symbol # ma ke s
COT
s798015 1 117,320,907 − 3.71 − 3.69 5.08E-08 0.0020 DA376252 3
s9850756 3 18,905,739 − 3.71 3.62 8.72E-08 0.0030 DA733783 1
s709071 3 191,426,311 − 3.46 3.51 2.85E-07 0.0081 – 1
s12640124 4 118,775,172 3.61 − 3.50 2.12E-07 0.0063 BX089737 3
s2442720 6 31,320,277 − 3.49 4.62 2.26E-07 0.0067 HLA-B 1
s11779524 8 8,618,613 3.85 3.81 1.89E-08 0.0008 CF594265 4
s56235824 9 11,039,320 3.44 3.55 3.38E-07 0.0090 – 1
s11788261 9 138,611,139 3.80 3.51 1.95E-07 0.0060 KCNT1 2
s8042374 15 78,908,032 7.69 7.04 3.48E-24 1.68E-17 CHRNA5/CHRNA3/CHRNB4 270
s6650723 18 53,524,269 3.76 3.51 2.07E-07 0.0062 DA696352/LOC101927273 5
s7228837 18 75,817,606 4.23 3.65 6.64E-08 0.0024 LINC01029 19
FTND
s56335113 1 30,427,639 3.80 5.85 2.02E-08 0.0021 – 10
s36025078 2 155,883,716 − 3.90 − 3.59 1.13E-07 0.0061 – 1
s188499496 3 38,450,183 − 3.93 − 3.62 8.82E-08 0.0050 XYLB 2
s11917643 3 64,171,754 3.62 − 4.17 8.41E-08 0.0048 PRICKLE2 6
s76923559 4 34,053,926 − 3.93 − 3.79 2.35E-08 0.0023 LOC101928622 3
s147093127 5 152,086,293 3.67 4.01 5.70E-08 0.0037 LINC01470 1
s9322751 6 104,015,759 − 3.51 − 3.54 2.03E-07 0.0089 HY157071 6
s4994764 7 1,928,662 − 3.90 − 4.32 9.17E-09 0.0012 MAD1L1 18
s3910267 11 130,810,282 − 3.84 5.71 1.50E-08 0.0018 SNX19 21
s147144681 15 78,900,908 − 7.62 − 5.55 7.85E-16 5.66E-09 CHRNA5/CHRNA3/CHRNB4 106
TFC
s4658015 1 196,053,435 3.51 3.36 5.91E-07 0.0094 – 1
s1069267 3 38,435,023 − 3.63 − 4.43 8.02E-08 0.0015 XYLB 3
s11722779 4 103,827,488 4.22 − 4.30 6.00E-10 0.0001 MANBA/UBE2D3/SLC9B2 315
s2717737 8 18,459,343 − 3.36 3.73 6.05E-07 0.0096 PSD3 1
s13264022 8 21,293,046 3.50 4.01 2.16E-07 0.0038 DA902558 15
s7959287 12 103,601,638 3.84 4.49 1.54E-08 0.0003 – 5
s9594516 13 41,849,360 3.64 3.77 7.33E-08 0.0014 MTRF1 1
s112531467 13 43,865,047 − 3.66 3.52 1.86E-07 0.0033 ENOX1 1
s181676509 14 104,242,531 − 3.67 − 3.98 5.73E-08 0.0011 C14ORF2 15
s147144681 15 78,900,908 − 5.50 − 5.55 1.49E-15 1.08E-08 CHRNA5/CHRNA3/CHRNB4 72
s17665477 16 6,700,889 − 3.69 3.80 5.16E-08 0.0010 RBFOX1 11
s12462853 19 5,538,936 3.45 − 3.39 4.82E-07 0.0078 TINCR 2
s62202174 20 20,461,125 − 3.38 − 4.24 5.26E-07 0.0085 RALGAPA2 1
s5758274 22 41,664,539 3.64 − 4.45 7.43E-08 0.0014 RANGAP1 1
s8135804 22 42,334,660 3.40 3.57 4.54E-07 0.0074 CENPM 12
Table 3. Join es ing o associa ion wi h schizoph enia and smoking ai s.
www.na u e.com/scien i ic epo s/
5
Scien i ic RepoR s | 6:25671 | DOI: 10.1038/s ep25671
genes (XYLB, MTRF1 and ENOX1). Long non-coding RNAs we e sugges ed o play a ole in schizoph enia38,39,
he iden i ica ion o mul iple long non-coding RNAs was in iguing.
Pheno ype como bidi y is common in complex diseases and ai s7,8. Pleio opy, o sha ed gene ic liabili y,
may be an unde lying mechanism o hese como bidi ies. Unde his condi ion, di e en app oaches ha e been
de eloped o iden i y genes sha ed by he como bid condi ions40,41, and hese app oaches seem mo e powe ul
han s anda d GWAS8,42. Ano he ad an age o hese me hods is ha hey can use he la ge numbe o GWAS
da ase s p oduced by a single pheno ype/ ai analyses. The app oach we used o iden i y hese sha ed loci is
conse a i e. In ou analyses, we excluded all ma ke s eaching genome-wide signi icance om bo h schizoph e-
nia and smoking ai s and equi ed a balanced con ibu ion om bo h ai s. Unde his condi ion, i a ma ke
eached genome wide signi icance o schizoph enia bu had a modes associa ion wi h ND ai s (say P- alues
be ween 10−4 o 5 × 10−6), i was excluded om ou join es ing. Simila ly, some ma ke s would be excluded i
hey eached genome wide signi icance in ND ai s. Because he GWASs used ha e di e en sample sizes, and
Pa hway Genes ound in pa hway
# gene in
pa hway
# gene
obse ed
# gene
expec ed
Obse ed/
expec ed a io
Raw
P- alue
Adjus ed
P- alue
Calcium signaling pa hway
ATP2B2, CACNA1C,
CACNA1I, CHRM3,
ITPR1, ITPR2
177 6 0.57 10.59 2.41E-05 0.0004
Long- e m po en ia ion CACNA1C, ITPR1, ITPR2,
PPP1CB 70 4 0.22 17.86 7.81E-05 0.0007
Neu oac i e ligand- ecep o in e ac ion
CHRM3, CHRNA3,
CHRNA5, CHRNB4,
NR3C1, THRB
272 6 0.87 6.89 0.0003 0.0011
Sali a y sec e ion ATP2B2, CHRM3, ITPR1,
ITPR2 89 4 0.28 14.05 0.0002 0.0011
Panc ea ic sec e ion ATP2B2, CHRM3, ITPR1,
ITPR2 101 4 0.32 12.38 0.0003 0.0011
Vascula smoo h muscle con ac ion CACNA1C, ITPR1, ITPR2,
PPP1CB 116 4 0.37 10.78 0.0005 0.0013
Oocy e meiosis ITPR1, ITPR2, PPP1CB,
SPDYA 112 4 0.36 11.16 0.0005 0.0013
Phospha idylinosi ol signaling sys em INPP5K, ITPR1, ITPR2 78 3 0.25 12.02 0.0020 0.0036
Gas ic acid sec e ion CHRM3, ITPR1, ITPR2 74 3 0.24 12.67 0.0018 0.0036
A hy hmogenic igh en icula
ca diomyopa hy (ARVC) CACNA1C, ITGAV, SGCD 74 3 0.24 12.67 0.0018 0.0036
Hype ophic ca diomyopa hy (HCM) CACNA1C, ITGAV, SGCD 83 3 0.27 11.30 0.0024 0.0039
Dila ed ca diomyopa hy CACNA1C, ITGAV, SGCD 90 3 0.29 10.42 0.0031 0.0046
GnRH signaling pa hway CACNA1C, ITPR1, ITPR2 101 3 0.32 9.28 0.0042 0.0058
Cell adhesion molecules (CAMs) ITGAV, NCAM2, PTPRM 133 3 0.43 7.05 0.0091 0.0117
Alzheime ’s disease CACNA1C, ITPR1, ITPR2 167 3 0.53 5.61 0.0167 0.0188
Regula ion o ac in cy oskele on CHRM3, ITGAV, PPP1CB 213 3 0.68 4.40 0.0313 0.0331
Table 4. Pa hways en iched in schizoph enia and smoking ai s.
Figu e 1. Pa hway c oss alk ne wo k. The size o he node is p opo ional o he P- alues o pa hway
en ichmen es . The hickness o he edge is p opo ional o he P- alues o pa hway c oss alk.

www.na u e.com/scien i ic epo s/
6
Scien i ic RepoR s | 6:25671 | DOI: 10.1038/s ep25671
he e o e a ied in hei s a is ical powe , i is ine i able ha we would miss some ma ke s om he mo e powe -
ul GWAS when we equi ed balanced summa y s a is ics in he join es ing.
Ou pa hway analyses iden i ied mul iple pa hways sha ed by schizoph enia and ND. The mos signi ican
pa hways we e Calcium Signaling, Long-Te m Po en ia ion and Neu oac i e Ligand-Recep o In e ac ion. These
pa hways a e in ol ed in neu o ansmi e ansduc ion and communica ion be ween neu ons, and hey a e
essen ial o cogni i e unc ions. These pa hways ha e been shown o be in ol ed in schizoph enia28,43,44 and
ND45,46. The Cell Adhesion Molecules and Regula ion o Ac in Cy oskele on pa hways ha e also been epo ed
in schizoph enia31,47–49 and ND45,50,51. Thus, ou esul s a e consis en wi h hese s udies. I is wo h no ing ha
he ca diomyopa hy pa hways we e iden i ied in ou analyses and ha , in a p e ious s udy, we ound ha CMYA5
was associa ed wi h schizoph enia52. Ano he gene, NDUFV2, causa i e o hype ophic ca diomyopa hy53,54,
he gene ic o m o ca diomyopa hy, was also ound o be associa ed wi h schizoph enia55–57. Pa hway c oss alk
analyses showed ha many o hese pa hways in e ac wi h each o he and oge he hey o m an in e linked
ne wo k wi h he Long-Te m Po en ia ion pa hway a he cen e o hese in e ac ions. In animal s udies, nico-
ine al e s long- e m po en ia ion58–60 and lea ning and memo y61. In humans, smoking may alle ia e cogni i e
impai men 62, and bo h nico ine wi hd awal and schizoph enia a e associa ed wi h cogni i e impai men s63,64.
Thus, compensa ing cogni i e impai men s may be a common mo i a ional ac o be ween egula smoke s and
schizoph enia pa ien s.
In summa y, ou esul s suppo ed he sel -medica ion hypo hesis. We also ound e idence ha schizoph enia
and ND sha e some gene ic liabili y and hese esul s did no con adic he hypo hesis ha smoking was a causal
isk ac o o schizoph enia. Assuming sha ed liabili y and a balanced con ibu ion, we iden i ied no el candi-
da e genes associa ed wi h bo h schizoph enia and ND. Analyses o he sha ed genes e ealed mul iple pa hways
and an in e ac ing ne wo k cen e ed on long- e m po en ia ion. These esul s p o ided some new insigh s o ou
unde s anding o smoking beha io s in bo h schizoph enia pa ien s and he gene al popula ion.
Me hods
Pheno ypes and GWAS da ase s. Fo schizoph enia, we ob ained he summa y s a is ics om he
PGC GWAS o schizoph enia1. This s udy used 52 independen samples, o hem 46 we e case con ol samples
o Eu opean ances y, 3 we e Asian case con ol samples and 3 we e Eu opean amily samples. Since he sam-
ples we e collec ed om di e en coun ies, bo h he c i e ia o Diagnos ic and S a is ical Manual o Men al
Diso de s (DSM) and In e na ional Classi ica ion o Diseases (ICD) we e used in he diagnosis o he pa ien s.
Please see o iginal pape 1 o de ails. We selec ed o use he summa y s a is ics o he 46 Eu opean case con ol
samples (32,405 cases and 46,839 con ols). Fo ND- ela ed ai s, we used he summa y s a is ics o ou co inine
s udy65 and 2 unpublished da ase s (manusc ip s in p epa a ion). One da a used he sum sco es o he Fage s öm
Tes o Nico ine Dependence (FTND)66 as a ai , which is a commonly used pheno ype o ND based on sel - e-
po ed smoking beha io s. The second da a used a single i em o he FTND ques ionnai e, “How soon a e you
wake up do you smoke you i s ciga e e”, o ime o smoke he i s ciga e e (TFC) as a ai . This ques ion can
be seen as a measu e o nico ine wi hd awal since he hal -li e o nico ine in he human body is abou 2 hou s67.
Smoke s o en expe ience nico ine wi hd awal in he mo ning a e no smoking o e nigh . The hi d da a65 used
he plasma co inine concen a ion (COT) as a ai . Co inine is he majo me aboli e o nico ine, and i s hal -li e
is much longe han ha o nico ine. The e o e, i s concen a ion in plasma can be conside ed an index o nico ine
in ake in ecen days68,69. Because he quan i y o nico ine in ake is one o he mos impo an measu es o ND,
COT may be conside ed a measu e o ND as well. In hese s udies, FTND, TFC and COT we e ea ed as quan-
i a i e ai s. The sample size o FTND was 16,237, excluding he Ne he lands Twin Regis y sample because
some o i s subjec s we e also used in COT GWAS. The sample sizes o TFC and COT we e 15,705 and 4,575
espec i ely. The FTND and TFC measu es we e de i ed om he same subjec s, he e o e, only FTND was used
in polygenic analyses. TFC we e used only o he iden i ica ion o sha ed genes be ween schizoph enia and ND
ela ed pheno ypes. The samples used in hese 3 ND ela ed GWASs we e lis ed in Supplemen a y Table S1. All
subjec s used in his s udy we e o Eu opean ances y.
Polygenic analyses. Schizoph enia isk sco es we e calcula ed o 9 independen smoking ela ed s udies
(Table S1, n = 10,794) wi h FTND and CPD measu es using he summa y s a is ics om he PGC schizoph enia
me a-analysis. The con ol subjec s om he Molecula Gene ics o Schizoph enia (MGS) we e included in he
GWASs o bo h FTND and PGC schizoph enia, he e o e hey we e excluded om his analysis. Risk sco es o
COT and FTND we e calcula ed o 13,326 indi iduals om he NIMH gene ics conso ium eposi o y (h ps://
www.nimhgene ics.o g/). We es ima ed he isk sco es o each ai using he algo i hms implemen ed in he
PLINK so wa e70. Speci ically, he isk sco e o an indi idual was he sum o he numbe o isk alleles mul-
iplied by he loga i hm o odds a io (OR, o schizoph enia) o be a coe icien ( o FTND and COT), which
was hen no malized subsequen ly by he p oduc o maximal numbe o isk alleles and log(OR)s/be a coe i-
cien s. Fo each ai , we calcula ed isk sco es a 5 P- alue h esholds: 5 × 10−5, 5 × 10−4, 5 × 10−3, 5 × 10−2 and
5 × 10−1. The numbe s o ma ke s used o calcula e schizoph enia isk sco es a hese h esholds we e 6,014,
94,804, 268,070, 1,021,476 and 5,370,899. The numbe s o ma ke s used o FTND and COT we e 731, 6,312,
55,378, 500,542 and 4,752,196; and 1,621, 6,357, 48,575, 473,100, and 4,737,313 espec i ely. We hen es ed
whe he schizoph enia isk sco es p edic ed FTND sco es and ice e sa using logis ic (schizoph enia) and linea
eg ession (FTND sco es). Since he numbe o ciga e es smoked pe day (CPD) was a ailable om he FTND
da ase s, we also es ed whe he he gene ic isk sco es o schizoph enia p edic ed he CPD pheno ype. Because
we did no ha e indi idual geno ypes o all da ase s used in he COT me a-analyses, we used only he COT isk
sco e o p edic schizoph enia diagnosis. Sex, age and s udy we e included as co a ia es in eg ession analyses.
www.na u e.com/scien i ic epo s/
7
Scien i ic RepoR s | 6:25671 | DOI: 10.1038/s ep25671
Iden i ica ion o sha ed isk genes. While he e a e pape s looking a pleio opy om a condi ional FDR
poin o iew71, we a i e o quali a i ely simila conclusions using a somewha simple app oach o amily-wise
e o a e. Ou es a emp s o disco e sha ed isk genes be ween schizoph enia and ND using summa y s a is-
ics om hei espec i e GWASs. To ensu e ha such a es is no o e ly in luenced by a s ong signal in jus one
ai , we implemen ed a “weakes link” app oach (i.e., choosing he la ge P- alue o he pai o ai es s a he
SNP unde in es iga ion)72. In mo e de ail, le Xj and Pj be he χ
2 dis ibu ed s a is ics and hei associa ed (back-
g ound en ichmen adjus ed) P- alues, j = 1, … , m, o associa ion es s be ween he m ai s and a SNP. As he
o e lap s a is ic o all ai s we use
=R Pmax
jj
(o , al e na i ely,
=||TXmin
j
j). Unde he assump ion ha he
ai es s a e independen , he P- alue (also deno ed as o e lap P- alue) o a gi en o e lap s a is ic, , a a SNP is
≤=
∏≤
=
PR PP () ()
j
m
j
1
. I we u he assume ha (unde he null hypo hesis - H0) none o he ai s is asso-
cia ed wi h he gene ic a ian , he o e lap P- alue simpli ies o P(R ≤ ) = m (1). O he wise, P(Pj ≤ ) can be
compu ed based on he dis ibu ion o he j- h ai P- alues. Fo ins ance, o wo pheno ype con igu a ion and
a pu a i e h eshold o 5 × 10−8, he pa ame ic e sion o ou me hod equi es ha , o a signi ican pleio opic
signal, he p- alues o bo h pheno ypes o be < 2.2 × 10−4 (
=
−
x510
8). This subs an ially less han 5 × 10−8
p- alue h eshold is simila in spi i o he one om Andeassen e al.71 While he o e lap p- alue (1) does elimi-
na e mos o he in luence o an ex eme signal o one pheno ype, i does no elimina e i comple ely. Howe e ,
o a pu a i e h eshold o 5 × 10−8 in (1), unde he wo s case scena io o an ex eme signal in one pheno ype,
he alse posi i e a e pe SNP is s ill a he small, i.e. 2.2 × 10−4. E en mo e, as seen in And eassen e al., he alse
posi i e a e is likely o be subs an ially lowe . Mo eo e , a wo s -case-scena io 2.2 × 10−4 alse posi i e a e is
adequa e o he pa hway analyses73. We used FDR24 o e alua e he app oxima e signi icance o he gene ic o e -
lap (desc ibed by ela ion (1)) be ween schizoph enia and smoking pheno ypes. To selec p omising ma ke s o
pa hway and ne wo k analyses we applied a h eshold o q- alue ≤ 0.16, co esponding o a ac o o 2 in Akaike
In o ma ion C i e ion penal y in a likelihood a io χ
2 es wi h 1 deg ee o eedom.
Pa hway and ne wo k analyses. We conduc ed pa hway en ichmen analysis o genes wi h a leas one
ma ke wi h q- alues lowe han 0.16 om he join es ing o schizoph enia and COT/FTND/TFC ai s. I a
ma ke was wi hin a gene egion, i was assigned o he gene; o he wise, i was mapped o i s mos p oxima e
gene using he 50-kb lanking egions (bo h 5′ and 3′ sides). Genes iden i ied using SNPs associa ed wi h COT,
FTND, o TFC we e me ged o he pa hway en ichmen analysis, o which we used he hype geome ic es
implemen ed in he ool WebGes al (2013 upda e)74 and he canonical pa hways om he Kyo o Encyclopedia
o Genes and Genomes (KEGG) da abase. We equi ed each pa hway o ha e a leas h ee genes om ou gene
lis and no mo e han 300 genes om he e e ence genome. The P- alues om hype geome ic es s we e u he
adjus ed by he Benjamini-Hochbe g me hod23. Only pa hways wi h adjus ed P- alues < 0.05 we e conside ed
s a is ically signi ican ly en iched.
We u he examined pa hways in e ac ion using he Cha ac e is ic Sub-Pa hway Ne wo k (CSPN) algo-
i hm31,75 he human p o ein-p o ein in e ac ion (PPI) ne wo k76. We es ic ed he analysis speci ically o he
a o emen ioned me ged gene se and hei en iched pa hways. In he inal s ep, we selec ed he signi ican pa h-
way in e ac ion pai s based on pe mu a ion P- alues less han 0.05.
Re e ences
1. Schizoph enia Wo king G oup o he Psychia ic Genomics Conso ium. Biological insigh s om 108 schizoph enia-associa ed
gene ic loci. Na u e 511, 421–427 (2014).
2. Tho gei sson, T. E. e al. Sequence a ian s a CHRNB3-CHRNA6 and CYP2A6 a ec smoking beha io . Na . Gene . 42, 448–453
(2010).
3. Tobacco and Gene ics Conso ium. Genome-wide me a-analyses iden i y mul iple loci associa ed wi h smoking beha io . Na .
Gene . 42, 441–447 (2010).
4. Da ies, G. e al. Genome-wide associa ion s udies es ablish ha human in elligence is highly he i able and polygenic. Mol. Psychia y
16, 996–1005 (2011).
5. Ka hi esan, S. e al. Common a ian s a 30 loci con ibu e o polygenic dyslipidemia. Na . Gene . 41, 56–65 (2009).
6. In e na ional Schizoph enia Conso ium e al. Common polygenic a ia ion con ibu es o isk o schizoph enia and bipola
diso de . Na u e 460, 748–752 (2009).
7. Si akuma an, S. e al. Abundan pleio opy in human complex diseases and ai s. Am. J. Hum. Gene . 89, 607–618 (2011).
8. Solo ie , N., Co sapas, C., Lee, P. H., Pu cell, S. M. & Smolle , J. W. Pleio opy in complex ai s: challenges and s a egies. Na . Re .
Gene . 14, 483–495 (2013).
9. Da ey Smi h, G. & Hemani, G. Mendelian andomiza ion: gene ic ancho s o causal in e ence in epidemiological s udies. Hum.
Mol. Gene . 23, R89–98 (2014).
10. Ziedonis, D. e al. Tobacco use and cessa ion in psychia ic diso de s: Na ional Ins i u e o Men al Heal h epo . Nico ine Tob. Res.
O . J. Soc. Res. Nico ine Tob. 10, 1691–1715 (2008).
11. de Leon, J. & Diaz, F. J. Gene ics o schizoph enia and smoking: an app oach o s udying hei como bidi y based on epidemiological
indings. Hum. Gene . 131, 877–901 (2012).
12. Kuma i, V. & Pos ma, P. Nico ine use in schizoph enia: he sel medica ion hypo heses. Neu osci. Biobeha . Re . 29, 1021–1034
(2005).
13. de Leon, J. & Diaz, F. J. A me a-analysis o wo ldwide s udies demons a es an associa ion be ween schizoph enia and obacco
smoking beha io s. Schizoph . Res. 76, 135–157 (2005).
14. De Luca, V. e al. E idence o associa ion be ween smoking and alpha7 nico inic ecep o subuni gene in schizoph enia pa ien s.
Neu opsychopha macol. O . Publ. Am. Coll. Neu opsychopha macol. 29, 1522–1526 (2004).
15. Hong, L. E. e al. A CHRNA5 allele ela ed o nico ine addic ion and schizoph enia. Genes B ain Beha . 10, 530–535 (2011).
16. No ak, G. e al. Associa ion o polymo phisms in he BDNF, DRD1 and DRD3 genes wi h obacco smoking in schizoph enia. Ann.
Hum. Gene . 74, 291–298 (2010).
17. No ak, G., Boukhad a, J., Shaikh, S. A., Kennedy, J. L. & Le Foll, B. Associa ion o a polymo phism in he NRXN3 gene wi h he
deg ee o smoking in schizoph enia: a p elimina y s udy. Wo ld J. Biol. Psychia y O . J. Wo ld Fed. Soc. Biol. Psychia y 10, 929–935
(2009).
www.na u e.com/scien i ic epo s/
8
Scien i ic RepoR s | 6:25671 | DOI: 10.1038/s ep25671
18. S ephens, S. H. e al. Associa ion o he 5′ -ups eam egula o y egion o he alpha7 nico inic ace ylcholine ecep o subuni gene
(CHRNA7) wi h schizoph enia. Schizoph . Res. 109, 102–112 (2009).
19. Zhang, X. Y. e al. Associa ion o unc ional dopamine-be a-hyd oxylase (DBH) 19 bp inse ion/dele ion polymo phism wi h
smoking se e i y in male schizoph enic smoke s. Schizoph . Res. 141, 48–53 (2012).
20. Jackson, K. J., Fanous, A. H., Chen, J., Kendle , K. S. & Chen, X. Va ian s in he 15q25 gene clus e a e associa ed wi h isk o
schizoph enia and bipola diso de . Psychia . Gene . 23, 20–28 (2013).
21. Loukola, A. e al. Genome-wide associa ion s udy on de ailed p o iles o smoking beha io and nico ine dependence in a win
sample. Mol. Psychia y 19, 615–624 (2014).
22. Weise , M. e al. Highe a es o ciga e e smoking in male adolescen s be o e he onse o schizoph enia: a his o ical-p ospec i e
coho s udy. Am. J. Psychia y 161, 1219–1223 (2004).
23. Schizoph enia Psychia ic Genome-Wide Associa ion S udy (GWAS) Conso ium. Genome-wide associa ion s udy iden i ies i e
new schizoph enia loci. Na . Gene . 43, 969–976 (2011).
24. Benjamini, Y. & Hochbe g, Y. Con olling he False Disco e y Ra e: A P ac ical and Powe ul App oach o Mul iple Tes ing. J. R.
S a . Soc. Se . B Me hodol. 57, 289–300 (1995).
25. Benjamini, Y. & Yeku ieli, D. Quan i a i e ai Loci analysis using he alse disco e y a e. Gene ics 171, 783–790 (2005).
26. Jia, P. e al. A bias- educing pa hway en ichmen analysis o genome-wide associa ion da a con i med associa ion o he MHC egion
wi h schizoph enia. J. Med. Gene . 49, 96–103 (2012).
27. Jia, P., Wang, L., Mel ze , H. Y. & Zhao, Z. Common a ian s con e ing isk o schizoph enia: a pa hway analysis o GWAS da a.
Schizoph . Res. 122, 38–42 (2010).
28. Föcking, M. e al. P o eomic and genomic e idence implica es he pos synap ic densi y in schizoph enia. Mol. Psychia y 20,
424–432 (2015).
29. Ripke, S. e al. Genome-wide associa ion analysis iden i ies 13 new isk loci o schizoph enia. Na . Gene . 45, 1150–1159 (2013).
30. Fan, Y. e al. Focal adhesion dynamics a e al e ed in schizoph enia. Biol. Psychia y 74, 418–426 (2013).
31. Zhao, Z. e al. T ansc ip ome sequencing and genome-wide associa ion analyses e eal lysosomal unc ion and ac in cy oskele on
emodeling in schizoph enia and bipola diso de . Mol. Psychia y 20, 563–572 (2015).
32. Sala a i, B. e al. Imaging-based neu ochemis y in schizoph enia: a sys ema ic e iew and implica ions o dys unc ional long- e m
po en ia ion. Schizoph . Bull. 41, 44–56 (2015).
33. Hishimo o, A. e al. Neu exin 3 polymo phisms a e associa ed wi h alcohol dependence and al e ed exp ession o speci ic iso o ms.
Hum. Mol. Gene . 16, 2880–2891 (2007).
34. Tho gei sson, T. E. e al. A a ian associa ed wi h nico ine dependence, lung cance and pe iphe al a e ial disease. Na u e 452,
638–642 (2008).
35. Lal, D. e al. RBFOX1 and RBFOX3 mu a ions in olandic epilepsy. PloS One 8, e73323 (2013).
36. Ba cia, G. e al. De no o gain-o - unc ion KCNT1 channel mu a ions cause malignan mig a ing pa ial seizu es o in ancy. Na .
Gene . 44, 1255–1259 (2012).
37. Tao, H. e al. Mu a ions in p ickle o hologs cause seizu es in lies, mice, and humans. Am. J. Hum. Gene . 88, 138–149 (2011).
38. Ba y, G. In eg a ing he oles o long and small non-coding RNA in b ain unc ion and disease. Mol. Psychia y 19, 410–416 (2014).
39. Ba y, G. e al. The long non-coding RNA Goma u is acu ely egula ed in esponse o neu onal ac i a ion and in ol ed in
schizoph enia-associa ed al e na i e splicing. Mol. Psychia y 19, 486–494 (2014).
40. Zhe nako a, A., an Diemen, C. C. & Wijmenga, C. De ec ing sha ed pa hogenesis om he sha ed gene ics o immune- ela ed
diseases. Na . Re . Gene . 10, 43–55 (2009).
41. And eassen, O. A. e al. Imp o ed de ec ion o common a ian s associa ed wi h schizoph enia by le e aging pleio opy wi h
ca dio ascula -disease isk ac o s. Am. J. Hum. Gene . 92, 197–209 (2013).
42. And eassen, O. A., Thompson, W. K. & Dale, A. M. Boos ing he powe o schizoph enia gene ics by le e aging new s a is ical ools.
Schizoph . Bull. 40, 13–17 (2014).
43. Hall, J., T en , S., Thomas, K. L., O’Dono an, M. C. & Owen, M. J. Gene ic isk o schizoph enia: con e gence on synap ic pa hways
in ol ed in plas ici y. Biol. Psychia y 77, 52–58 (2015).
44. Pu cell, S. M. e al. A polygenic bu den o a e dis up i e mu a ions in schizoph enia. Na u e 506, 185–190 (2014).
45. Wang, J. & Li, M. D. Common and Unique Biological Pa hways Associa ed wi h Smoking Ini ia ion/P og ession, Nico ine
Dependence, and Smoking Cessa ion. Neu opsychopha macology 35, 702–719 (2010).
46. Saccone, S. F. e al. Choline gic nico inic ecep o genes implica ed in a nico ine dependence associa ion s udy a ge ing 348
candida e genes wi h 3713 SNPs. Hum. Mol. Gene . 16, 36–49 (2007).
47. Jenkins, A. K. e al. Neu exin 1 (NRXN1) splice iso o m exp ession du ing human neoco ical de elopmen and aging. Mol.
Psychia y, doi: 10.1038/mp.2015.107 (2015).
48. Lionel, A. C. e al. Ra e exonic dele ions implica e he synap ic o ganize Gephy in (GPHN) in isk o au ism, schizoph enia and
seizu es. Hum. Mol. Gene . 22, 2055–2066 (2013).
49. Toda ello, G. e al. Incomple e pene ance o NRXN1 dele ions in amilies wi h schizoph enia. Schizoph . Res. 155, 1–7 (2014).
50. Nussbaum, J. e al. Signi ican associa ion o he neu exin-1 gene (NRXN1) wi h nico ine dependence in Eu opean- and A ican-
Ame ican smoke s. Hum. Mol. Gene . 17, 1569–1577 (2008).
51. Bie u , L. J. e al. No el genes iden i ied in a high-densi y genome wide associa ion s udy o nico ine dependence. Hum. Mol. Gene .
16, 24–35 (2007).
52. Chen, X. e al. GWA s udy da a mining and independen eplica ion iden i y ca diomyopa hy-associa ed 5 (CMYA5) as a isk gene
o schizoph enia. Mol. Psychia y 16, 1117–1129 (2011).
53. Béni , P. e al. Mu an NDUFV2 subuni o mi ochond ial complex I causes ea ly onse hype ophic ca diomyopa hy and
encephalopa hy. Hum. Mu a . 21, 582–586 (2003).
54. Liu, H.-Y., Liao, P.-C., Chuang, K.-T. & Kao, M.-C. Mi ochond ial a ge ing o human NADH dehyd ogenase (ubiquinone)
la op o ein 2 (NDUFV2) and i s associa ion wi h ea ly-onse hype ophic ca diomyopa hy and encephalopa hy. J. Biomed. Sci. 18,
29 (2011).
55. Ayalew, M. e al. Con e gen unc ional genomics o schizoph enia: om comp ehensi e unde s anding o gene ic isk p edic ion.
Mol. Psychia y 17, 887–905 (2012).
56. Aka su, S. e al. Mi ochond ial complex I and III gene mRNA le els in schizoph enia, and hei ela ionship wi h clinical ea u es. J.
Mol. Psychia y 2, 6 (2014).
57. Washizuka, S. e al. Associa ion o mi ochond ial complex I subuni gene NDUFV2 a 18p11 wi h schizoph enia in he Japanese
popula ion. Am. J. Med. Gene . Pa B Neu opsychia . Gene . O . Publ. In . Soc. Psychia . Gene . 141B, 301–304 (2006).
58. Jia, Y., Yamazaki, Y., Nakauchi, S., I o, K.-I. & Sumikawa, K. Nico ine acili a es long- e m po en ia ion induc ion in o iens-
lacunosum molecula e cells ia Ca2+ en y h ough non-alpha7 nico inic ace ylcholine ecep o s. Eu . J. Neu osci. 31, 463–476
(2010).
59. Han, G., An, L., Yang, B., Si, L. & Zhang, T. Nico ine-induced impai men s o spa ial cogni ion and long- e m po en ia ion in
adolescen male a s. Hum. Exp. Toxicol. 33, 203–213 (2014).
60. Reisige , A.-R. e al. Nico ine sel -adminis a ion induces CB1-dependen LTP in he bed nucleus o he s ia e minalis. J. Neu osci.
O . J. Soc. Neu osci. 34, 4285–4292 (2014).
www.na u e.com/scien i ic epo s/
9
Scien i ic RepoR s | 6:25671 | DOI: 10.1038/s ep25671
61. Ku lu, M. G. & Gould, T. J. Nico inic modula ion o hippocampal cell signaling and associa ed e ec s on lea ning and memo y.
Physiol. Beha . 155, 162–171 (2016).
62. Hall, F. S. e al. Nega i e a ec i e s a es and cogni i e impai men s in nico ine dependence. Neu osci. Biobeha . Re . 58, 168–185
(2015).
63. Asha e, R. L., Falcone, M. & Le man, C. Cogni i e unc ion du ing nico ine wi hd awal: Implica ions o nico ine dependence
ea men . Neu opha macology 76 P B, 581–591 (2014).
64. Timo ee a, O. A. & Le in, E. D. Glu ama e and nico inic ecep o in e ac ions in wo king memo y: impo ance o he cogni i e
impai men o schizoph enia. Neu oscience 195, 21–36 (2011).
65. Wa e, J. J. e al. Genome-Wide Me a-Analysis o Co inine Le els in Ciga e e Smoke s Iden i ies Locus a 4q13.2. Sci. Rep. 6, 20092
(2016).
66. Hea he on, T. F., Kozlowski, L. T., F ecke , R. C. & Fage s öm, K. O. The Fage s öm Tes o Nico ine Dependence: a e ision o
he Fage s öm Tole ance Ques ionnai e. B . J. Addic . 86, 1119–1127 (1991).
67. Luck, W. & Nau, H. Nico ine and co inine concen a ions in se um and milk o nu sing smoke s. B . J. Clin. Pha macol. 18, 9–15
(1984).
68. Malaiyandi, V., Goodz, S. D., Selle s, E. M. & Tyndale, R. F. CYP2A6 geno ype, pheno ype, and he use o nico ine me aboli es as
bioma ke s du ing ad libi um smoking. Cance Epidemiol. Bioma k. P e . Publ. Am. Assoc. Cance Res. Cosponso ed Am. Soc. P e .
Oncol. 15, 1812–1819 (2006).
69. Benowi z, N. L., Dains, K. M., Dempsey, D., Yu, L. & Jacob, P. Es ima ion o nico ine dose a e low-le el exposu e using plasma and
u ine nico ine me aboli es. Cance Epidemiol. Bioma k. P e . Publ. Am. Assoc. Cance Res. Cosponso ed Am. Soc. P e . Oncol. 19,
1160–1166 (2010).
70. Pu cell, S. e al. PLINK: a ool se o whole-genome associa ion and popula ion-based linkage analyses. Am. J. Hum. Gene . 81,
559–575 (2007).
71. And eassen, O. A. e al. Imp o ed de ec ion o common a ian s associa ed wi h schizoph enia and bipola diso de using
pleio opy-in o med condi ional alse disco e y a e. PLoS Gene . 9, e1003455 (2013).
72. Bigdeli, T. B. e al. On schizoph enia as a ‘disease o humani y’. Schizoph . Res. 143, 223–224 (2013).
73. Holmans, P. e al. Gene on ology analysis o GWA s udy da a se s p o ides insigh s in o he biology o bipola diso de . Am. J. Hum.
Gene . 85, 13–24 (2009).
74. Zhang, B., Ki o , S. & Snoddy, J. WebGes al : an in eg a ed sys em o explo ing gene se s in a ious biological con ex s. Nucleic
Acids Res. 33, W741–748 (2005).
75. Huang, Y. & Li, S. De ec ion o cha ac e is ic sub pa hway ne wo k o angiogenesis based on he comp ehensi e pa hway ne wo k.
BMC Bioin o ma ics 11 Suppl 1, S32 (2010).
76. Wu, J. e al. In eg a ed ne wo k analysis pla o m o p o ein-p o ein in e ac ions. Na . Me hods 6, 75–77 (2009).
Acknowledgemen s
This wo k was suppo ed in pa by NIH g an s ML011177, MH101054 and DA032246. JK has been suppo ed by
he Academy o Finland (g an s # 265240 and 263278). We a e g a e ul o he PGC schizoph enia analysis g oup
o p o iding he summa y s a is ics o i s GWAS me a-analysis. Al hough un ela ed o his esea ch, H. K anzle
has been a consul an o ad iso y boa d membe o Alke mes, Lilly, Lundbeck, O suka, P ize , and Roche. He is
also a membe o he Ame ican Socie y o Clinical Psychopha macology’s Alcohol Clinical T ials Ini ia i e, which
is suppo ed by AbbVie, Alke mes, E hypha m, Lilly, Lundbeck, and P ize .
Au ho Con ibu ions
J.C. and S.-A.B. pe o med polygenic and joined analyses, and w o e he pape ; H.Y., Z.Z. and P.J. pe o med
pa hway and ne wo k analyses; K.S.K., H.R.K., J.G., L.F., C.M., R.P., Y.M., D.I.B., B.W.J.H.P., R.F.T., J.J.W., J.V., J.K.
and M.M. con ibu ed o he samples used his manusc ip and commen ed on he ex ; co inine me a-analysis
g oup and FTND me a-analysis g oup con ibu ed samples o his pape ; and XC concei ed, designed and w o e
he pape . All au ho s ha e ead and ag eed on he con en o his manusc ip .
Addi ional In o ma ion
Supplemen a y in o ma ion accompanies his pape a h p://www.na u e.com/s ep
Compe ing inancial in e es s: The au ho s decla e no compe ing inancial in e es s.
How o ci e his a icle: Chen, J. e al. Gene ic ela ionship be ween schizoph enia and nico ine dependence.
Sci. Rep. 6, 25671; doi: 10.1038/s ep25671 (2016).
This wo k is licensed unde a C ea i e Commons A ibu ion 4.0 In e na ional License. The images
o o he hi d pa y ma e ial in his a icle a e included in he a icle’s C ea i e Commons license,
unless indica ed o he wise in he c edi line; i he ma e ial is no included unde he C ea i e Commons license,
use s will need o ob ain pe mission om he license holde o ep oduce he ma e ial. To iew a copy o his
license, isi h p://c ea i ecommons.o g/licenses/by/4.0/