MODY mu a ions in ansc ip ion ac o s HNF1A and HNF1B
a ec he p oduc ion o in e e on signaling p o eins: e idence a
he p o eome le el
Ksenia G Kuzne so a1,2,3,*, Jakub Vašíček1,2, Da ni Skiadopoulou1,2, Lucas Unge 1, Rachel
Anand Ne hala1, Michael Wie e 4, Luiza Ghila1, S e an Johansson1,5, Pål Rasmus Njøls ad1,6,
Simona Che a1, Ben e Johansson1, Alisa Manning3,7,8, and Ma c Vaudel1,2,9
1Mohn Cen e o Diabe es P ecision Medicine Depa men o Clinical Science, Uni e si y o Be gen, No way
2Compu a ional Biology Uni , Depa men o In o ma ics, Uni e si y o Be gen, Be gen, No way
3B oad Ins i u e o MIT and Ha a d, Camb idge, MA, USA
4P o eomics Resea ch In as uc u e, Cen e o Co e Facili ies, Uni e si y o Copenhagen, Denma k
5Depa men o Medical Gene ics, Haukeland Uni e si y Hospi al, Be gen, No way
6Depa men o Pedia ics and Adolescen s, Haukeland Uni e si y Hospi al, Be gen, No way
7Depa men o Medicine, Massachuse s Gene al Hospi al, Bos on, MA, USA
8Depa men o Medicine, Ha a d Medical School, Bos on, MA, USA
9Depa men o Gene ics and Bioin o ma ics, No wegian Ins i u e o Public Heal h, Be gen, No way
Supplemen a y igu es
465 6987013
All iden i ied p o eins
S age4 S age4
S age0 S age0
213 77102
DDA
DDA
DIA
DIA
DDA
DDA
DIA
DIA
Di e en ially abundan p o eins
1465 1796281
All iden i ied p o eins
144 599
Di e en ially abundan p o eins
A. B.
C. D.
Figu e S.1: Venn diag am o iden i ied and di e en ially abundan p o eins in hiPSC da ase s
A. Compa ison o all iden i ied p o eins in s age 4 panc ea ic p ogeni o cells using DDA and DIA mass
spec ome y me hods. B. Di e en ially abundan p o eins in s age 4 cells iden i ied by DDA and DIA. C.
Compa ison o all iden i ied p o eins in s age 0 s em cells using DDA and DIA. D. Di e en ially abundan
p o eins in s age 0 cells iden i ied by DDA and DIA.
6 4 2 0 2 4
Log2 Fold Change
0.0
0.5
1.0
1.5
2.0
2.5
3.0
3.5
-Log10 adj.P- alue
COX7A2L
NDUFB4
RIGI LDHA
OAS1
ISG15
IFIT1 COX5B
NCAM1
COX7A2
MX1
CACNA2D1
B2M
IRF9
IFITM3
H1-1
IFIT5
PDE12
NDUFS8
NDUFS4
NDUFA3
GSR
HLA-B
HLA-H MT-ND1
MT-ND4
MT-ND5
MT-ND6 HLA-A
COX6A1 TUBA1B
BST2
IFIH1
NDUFA12
NDUFAF1
Di e en ially exp essed p o eins
Pa hways
in e e on signaling
ene gy exchange
8 6 4 2 0 2 4
Log2 Fold Change
0
1
2
3
4
-Log10 adj.P- alue
SLC25A12
RIGI
OAS1
ISG15
HSPA1L
CACNA2D1IRF9
IFITM3
H1-1
BST2
IFIT5
PDE12
NDUFB9
IFIT3
UQCR11
NDUFB3
NDUFA7 GSR
MT-CO3
HLA-B
MT-ND5
MT-ND6
IFIT1
SLC25A6
TOMM20
IFIH1
OAS3
Di e en ially exp essed p o eins
Pa hways
in e e on signaling
ene gy exchange
A. S age 4 DDA
B. S age 4 DIA
WT mu
WT mu
Figu e S.2: Volcano plo s o di e en ially abundan p o eins in s age 4 panc ea ic p ogeni o cells
Compa ison o cells wi h he HNF1A ameshi mu a ion o con ol cells. Colo s highligh p o eins
ela ed o in e e on signaling and ene gy exchange pa hways iden i ied by Qiagen IPA.
A. DDA mass spec ome y da ase . B. DIA mass spec ome y da ase .
6 4 2 0 2 4
Log2 Fold Change
0.0
0.5
1.0
1.5
2.0
-Log10 adj.P- alue
UQCR11
TIMM17B
NDUFB8
MT-CYB
MT-CO1
MT-ND5
MT-ND6
COX6A1
NDUFB7
PSEN2
ATP5MF
NDUFV3
H1-1
ITPR2
PDE12
CPT1C
TOMM6
CMC2
TOMM7
NDUFB9
COX11
Di e en ially exp essed p o eins
Pa hways
in e e on signaling
ene gy exchange
6 4 2 0 2 4
Log2 Fold Change
0
1
2
3
4
-Log10 adj.P- alue
NDUFS8
UQCR11 MRPS12
OGG1
CYB5B
MT-CO3
HLA-H
MT2A
MT-ND1
MT-ND5
H1-0
COX6B1
PSEN2
MRPS25
H1-1
PDE12
NDUFA12
Di e en ially exp essed p o eins
Pa hways
in e e on signaling
ene gy exchange
A. S age 0 DDA
B. S age 0 DIA
WT mu
WT mu
Figu e S.3: Volcano plo s o di e en ially abundan p o eins in s age 0 s em cells Compa ison o cells
wi h he HNF1A ameshi mu a ion o con ol cells. Colo s highligh p o eins ela ed o in e e on
signaling and ene gy exchange pa hways iden i ied by Qiagen IPA.
A. DDA mass spec ome y da ase . B. DIA mass spec ome y da ase .
2 4 6 8 10 12 14
-log(p- alue)
Oxida i e Phospho yla ion
G anzyme A Signaling
Mi ochond ial Dys unc ion
In e e on alpha/be a signaling
Hema oma Resolu ion Signaling Pa hway
Pa kinson's Signaling Pa hway
Pos - ansla ional p o ein phospho yla ion
In e e on Signaling
Si uin Signaling Pa hway
OAS an i i al esponse
Regula ion o Insulin-like G ow h Fac o (IGF)
anspo and up ake by IGFBPs
Cy op o ec ion by HMOX1
signi icance
Numbe o P o eins
1 p o eins
2 p o eins
3 p o eins 3
2
1
0
1
2
3
4
z-sco e
z-sco e
4
2
0
2
4
Top 12 pa hways wi h z-sco e no less han 2
signi icance
In e e on gamma signaling
Syn hesis, sec e ion, and deacyla ion o Gh elin
In e e on Signaling
Cy op o ec ion by HMOX1
In e e on alpha/be a signaling
Neu ophil Ex acellula T ap Signaling Pa hway
Si uin Signaling Pa hway
Pa kinson's Signaling Pa hway
Hema oma Resolu ion Signaling Pa hway
Mi ochond ial Dys unc ion
Oxida i e Phospho yla ion
G anzyme A Signaling
-log(p- alue)
2015105
Numbe o P o eins
1 p o eins
2 p o eins
3 p o eins
2 4 6 8 10
-log(p- alue)
Oxida i e Phospho yla ion
Respi a o y elec on anspo
Mi ochond ial Dys unc ion
Complex I biogenesis
G anzyme A Signaling
Neu ophil Ex acellula T ap Signaling Pa hway
Mi ochond ial RNA deg ada ion
Mi ochond ial p o ein impo
RNA p ocessing in he mi ochond ion
Complex IV assembly
Pa kinson's Signaling Pa hway
Mi ochond ial p o ein deg ada ion
signi icance
Numbe o P o eins
1 p o eins
2 p o eins
3 p o eins 3
2
1
0
1
2
3
z-sco e
2 4 6 8
-log(p- alue)
Oxida i e Phospho yla ion
Respi a o y elec on anspo
G anzyme A Signaling
Mi ochond ial Dys unc ion
Complex I biogenesis
Hema oma Resolu ion Signaling Pa hway
Pa kinson's Signaling Pa hway
Neu ophil Ex acellula T ap Signaling Pa hway
Molecula Mechanisms o Cance
signi icance
Numbe o P o eins
1 p o eins
2 p o eins
3 p o eins
2
1
0
1
2
3
z-sco e
A. S age 4 DDA
B. S age 4 DIA
C. S age 0 DDA
D. S age 0 DIA
Figu e S.4: Mos signi ican ly en iched pa hways p edic ed by Qiagen IPA Based on di e en ially abundan
p o eins wi h a leas 2- old change and BH-adjus ed p- alues < 0.05. Z-sco es indica e he di ec ion o
egula ion (≥2). Plo s show he op 12 pa hways selec ed by z-sco es.
S4_DDA S4_DIA S0_DDA S0_DIA
Mi ochond ial Dys unc ion
Oxida i e Phospho yla ion
G anzyme A Signaling
Neu ophil Ex acellula T ap Signaling Pa hway
Hema oma Resolu ion Signaling Pa hway
Si uin Signaling Pa hway
Pa kinson's Signaling Pa hway
Neu ophil deg anula ion
Oxy ocin Signaling Pa hway
HER-2 Signaling in B eas Cance
Se o onin Recep o Signaling
Eicosanoid Signaling
Pos - ansla ional p o ein phospho yla ion
G Be a Gamma Signaling
Eph in Recep o Signaling
Se oli Cell-Se oli Cell Junc ion Signaling
DHCR24 Signaling Pa hway
Regula ion o Insulin-like G ow h Fac o (IGF) anspo and up ake by IGFBPs
Mi ochond ial p o ein impo
ISG15 an i i al mechanism
In e e on Signaling
In e e on gamma signaling
Complex I biogenesis
Role o Hype cy okinemia/hype chemokinemia in he Pa hogenesis o In luenza
Cy op o ec ion by HMOX1
Respi a o y elec on anspo
Elec on anspo , ATP syn hesis, and hea p oduc ion by uncoupling p o eins
In e e on alpha/be a signaling
Co ona i us Pa hogenesis Pa hway
Ex a-nuclea es ogen signaling
Pla ele homeos asis
Complex IV assembly
Mi ochond ial RNA deg ada ion
G alpha (12/13) signalling e en s
DNA Damage/Telome e S ess Induced Senescence
OAS an i i al esponse
RNA p ocessing in he mi ochond ion
Nec op osis Signaling Pa hway
DDX58/IFIH1-media ed induc ion o in e e on-alpha/be a
G alpha (s) signalling e en s
Class B/2 (Sec e in amily ecep o s)
NAD Signaling Pa hway
Mi ochond ial p o ein deg ada ion
Syn hesis, sec e ion, and deacyla ion o Gh elin
Meio ic synapsis
4
2
0
2
4
Figu e S.5: Hea map o he mos
egula ed pa hways p edic ed by
Qiagen IPA This hea map illus a es
he mos egula ed pa hways
p edic ed by Qiagen IPA so wa e,
compa ing pa hways en iched
ac oss all da ase s. The colo
indica es z-sco es, showing he
di ec ion and magni ude o
egula ion. The igu e demons a es
he ep oducibili y o he mos
egula ed pa hways among he
da ase s. Ene gy exchange-
ela ed pa hways show consis en
egula ion in bo h s age 0 and s age
4, while in e e on signaling-
ela ed pa hways a e only
down egula ed in samples a s age
4.
M x
IS
M x
M x
M x
M x
M x
M x
IS
IS
IS
IS
IS
IS
IS
IS
M x
M x
M x
M x
M x
M x
M x
A. S age 4 DDA
B. S age 4 DIA
C. S age 0 DDA
D. S age 0 DIA
Figu e S.6: Hallma k gene se en ichmen o down egula ed p o eins Analysis pe o med by F agPipe-
Analys ool ac oss all hiPSC da ase s.
1234567
-log10(Adjus ed.P. alue)
Oxida i e Phospho yla ion
Panc eas Be a Cells
In e e on Gamma Response
In e e on Alpha Response
Epi helial Mesenchymal T ansi ion
Ppe oxisome
UV Response Dn
Xenobio ic Me abolism
IL-2/STAT5 Signaling
Apop osis
signi icance
Numbe o P o eins
1 p o eins
2 p o eins
3 p o eins 4
6
8
10
12
14
16
18
Odds Ra io
1 2 3 4 5 6 7 8
-log10(Adjus ed.P. alue)
In e e on Alpha Response
Oxida i e Phospho yla ion
In e e on Gamma Response
Panc eas Be a Cells
Coagula ion
Es ogen Response La e
Apical Junc ion
Epi helial Mesenchymal T ansi ion
KRAS Signaling Up
UV Response Dn
signi icance
Numbe o P o eins
1 p o eins
2 p o eins
3 p o eins 4
6
8
10
12
14
16
18
Odds Ra io
0.25 0.50 0.75 1.00 1.25 1.50 1.75 2.00 2.25
-log10(Adjus ed.P. alue)
Oxida i e Phospho yla ion
PI3K/AKT/mTOR Signaling
Ppe oxisome
Adipogenesis
Es ogen Response Ea ly
Es ogen Response La e
No ch Signaling
Spe ma ogenesis
Wn -be a Ca enin Signaling
Reac i e Oxygen Species Pa hway
signi icance
Numbe o P o eins
1 p o eins
2 p o eins
3 p o eins 3.0
3.5
4.0
4.5
5.0
5.5
6.0
6.5
Odds Ra io
0.4 0.6 0.8 1.0 1.2 1.4 1.6
-log10(Adjus ed.P. alue)
Oxida i e Phospho yla ion
Apop osis
Adipogenesis
mTORC1 Signaling
UV Response Up
Hypoxia
Myc Ta ge s V1
Choles e ol Homeos asis
And ogen Response
Ppe oxisome
signi icance
Numbe o P o eins
1 p o eins
2 p o eins
3 p o eins
5
6
7
8
9
Odds Ra io
C18o 32C18o 32
COX5BCOX5B
COX6A1COX6A1
COX7A2COX7A2
COX7CCOX7C
ECSITECSIT
FILIP1LFILIP1L
GGNBP2GGNBP2
MT-ATP6MT-ATP6
MT-ATP8MT-ATP8
MT-CO3MT-CO3
MT-ND1MT-ND1
MT-ND2MT-ND2
MT-ND4MT-ND4
MT-ND5MT-ND5
MT-ND6MT-ND6
NDUFA10NDUFA10
NDUFA12NDUFA12
NDUFA13NDUFA13
NDUFA3NDUFA3
NDUFA4NDUFA4
NDUFA7NDUFA7
NDUFAF1NDUFAF1
NDUFB1NDUFB1
NDUFB11NDUFB11
NDUFB3NDUFB3
NDUFB4NDUFB4
NDUFB7NDUFB7
NDUFB8NDUFB8
NDUFB9NDUFB9
NDUFS4NDUFS4
NDUFS8NDUFS8
TMEM126BTMEM126B
UQCR11UQCR11
BST2BST2
CMPK2CMPK2 DDX58DDX58
DTX3LDTX3L
EPSTI1EPSTI1
HELZ2HELZ2
HERC5HERC5
IFI16IFI16
IFIH1IFIH1
IFIT1IFIT1
IFIT3IFIT3
IFIT5IFIT5
IFITM3IFITM3
IRF9IRF9
ISG15ISG15
MX1MX1
OAS1OAS1
OAS3OAS3
PARP14PARP14
PARP9PARP9
PGGHGPGGHG
RALBRALB
A. S age 4 STRING clus e ing
B. Oxida i e phospho yla ion
C. An i i al de ense
Figu e S.7: P o ein in e ac ion analysis in s age 4 panc ea ic p ogeni o cells Pe o med by STRING on
di e en ially abundan p o eins. MCL clus e ing wi h in la ion pa ame e 3.
A. Ne wo k o all p o eins wi h highligh ed clus e s. B. Oxida i e Phospho yla ion/Respi a o y Elec on
T anspo clus e . C. Nega i e Regula ion o Vi al Genome Replica ion/In e e on Alpha/Be a Signaling/
An i i al De ense clus e .
ATP5IF1ATP5IF1
ATP5MFATP5MF
ATP6V0CATP6V0C
COX11COX11
COX6A1COX6A1
COX6B1COX6B1
DECR2DECR2
FDX2FDX2
GHITMGHITM
HIGD2AHIGD2A
MPC2MPC2
MT-CO1MT-CO1
MT-CO3MT-CO3
MT-CYBMT-CYB
MT-ND1MT-ND1
MT-ND5MT-ND5
MT-ND6MT-ND6
NDUFA12NDUFA12
NDUFB7NDUFB7
NDUFB8NDUFB8
NDUFB9NDUFB9
NDUFS8NDUFS8
NDUFV3NDUFV3
TIMM17BTIMM17B
UQCR11UQCR11
A. S age 0 STRING clus e ing
B. Oxida i e phospho yla ion
Figu e S.8: P o ein in e ac ion analysis in s age 0 s em cells Pe o med by STRING on di e en ially
abundan p o eins. MCL clus e ing wi h in la ion pa ame e 3.
A. Ne wo k o all p o eins wi h highligh ed clus e s. B. Oxida i e Phospho yla ion/Mi ochond ial ATP
Syn hesis Coupled Elec on T anspo clus e .
