p o ein phospha ase 2A s uc u al/sca old subuni A, alpha
iso o m (PPP2R1A) : Time beha iou al s udy o 3 d o de
combina ions in WNT3A s imula ed HEK 293 cells
sh ip akash sinha
Independen Resea che ; O cid ID : o cid.o g/0000-0001-7027-5788
Add ess : 104-Madhu isha Heigh s Phase 1, Risali, Bhilai-490006, India
Co esponding au ho email : sinha.sh ip [email protected]
Abs ac
PPP2R1A o ms a componen o he PP2A holoenzyme complex. PPP2R1A is he
p edominan PP2A sca old A-subuni ha is equi ed o unc ional PP2A complex
o ma ion and PPP2R1A deple ion esul s in comp ehensi e PP2A complex inhibi-
ion. Guj al and MacBea h [1] p o ides a quan i a i e, and dynamic s udy o WNT3A-
media ed s imula ion o HEK 293 cells, whe e hey eco d ime based exp ession p o-
iles o se e al esponse genes which co ela ed signi ican ly wi h p oli e a ion and mi-
g a ion. By moni o ing he dynamics o gene exp ession using sel -o ganizing maps,
hey iden i ied clus e s o genes ha exhibi simila exp ession dynamics and unco -
e ed p e iously un ecognized posi i e and nega i e eedback loops. Howe e , hei
s udy depic s/uses singula measu emen s o indi idual gene exp ession a di e en
ime snapsho s/poin s o in e he sys em wide analysis o he pa hway. A any pa -
icula ime poin , i is o en he case ha genes a e wo king syne gis ically in combi-
na ions, e en hough hei exp ession measu emen s a e singula in na u e. He e, I •
enume a e and ank all 2415 PPP2R1A ela ed 3 d o de combina ions in a o es o
71C3combina ions using ou di e en sensi i i y me hods; •show he conse ed ank-
ings o PPP2R1A-X-X combina ions, which poin o exis ence o biological syne gy
o some o hese combina ions ac oss he di e en sensi i i y me hods; and •s udy he
beha iou o some o hese combina ions ela ed o WNT3A esponse genes ha a e
anked by he machine lea ning sea ch engine (Sinha [2]) in ime. Pa e ns o combina-
ions eme ge, some o which ha e been es ed in we lab, while o he s equi e u he
we lab analysis.
Keywo ds: Sensi i i y analysis, Suppo ec o anking, Hilbe Schmid
Independence C i e ion indices (HSIC) and Sobol indicies, WNT3A
ITime beha iou al s udy o 3-od PPP2R1A comb. in WNT3A s imula ed cells
1Aspec s o unpublished wo k we e p esen ed in a pos e session a Cell Symposia: Technology. Biology.
Da a Science, 9-11 Oc obe 2016, Be keley, Cali o nia, USA.
P ep in submi ed o P ep in Ma ch 12, 2025
1. Signi icance
Sinha [2] ecen ly demons a ed he use o machine lea ning based sea ch engine o
ank/ e eal gene combina ions a 2nd o de o he ime se ies da a by Guj al and
MacBea h [1] and showed how i is possible o loca e combina ions o p io i y ha
migh be wo king syne gis ically, using sensi i i y me hods and powe ul suppo ec-
o anking algo i hm. Howe e , he p oblem explodes combina o ially wi h e en a
small se o 71 eco ded genes in he s udy by Guj al and MacBea h [1], when one
s eps o explo e 3 d o de combina ions. Wi h he o al numbe o 71C3(= 57155)
combina ions, i becomes nea ly impossible o any biologis o s udy he sys em wide
dynamics o any pa hway. Also, he amoun o ime usually needed o sea ch o and
es a combina ion is a mo e han he sea ch down by he machine lea ning based
sea ch engine. He e, I ex end he esea ch wo k by Sinha [2] o conduc a beha io al
s udy o 3 d o de PPP2R1A ela ed combina ions using indi idual gene exp essions
measu ed in ime, in WNT3A s imula ed HEK 293 cells.
2. In oduc ion
The de ails o he machine lea ning based sea ch engine has been ecen ly published in
Sinha [2] and deployed o explo e he 2nd o de combina ions o genes in he da a se
p o ided by Guj al and MacBea h [1]. Ne e heless, he e, I poin o he undamen als
o he published wo k o comple eness.
2.1. A combina o ial p oblem
Sensi i i y analysis plays a majo ole in compu ing he s eng h o he in luence o
in ol ed ac o s in any phenomena unde in es iga ion. When applied o exp ession
p o iles o a ious in a/ex acellula ac o s ha o m an in eg al pa o a signaling
pa hway, he a iance and densi y based analysis yields a ange o sensi i i y indices
o indi idual as well as a ious combina ions o ac o s. These combina ions deno e
he highe o de in e ac ions among he in ol ed ac o s. Compu a ion o highe o -
de in e ac ions is o en ime consuming bu i gi es a chance o explo e he a ious
combina ions ha migh be o in e es in he wo king mechanism o he pa hway. Fo
example, in a ange o ou h o de combina ions among he a ious ac o s o he Wn
pa hway, i would be easy o assess he in luence o he des uc ion complex o med by
APC, AXIN, CSKI and GSK3 in e ac ion. Bu he e ec o hese combina ions a y
o e ime as measu emen s o old changes and de ia ions in old changes a y. So
i is impe a i e o know how an in e ac ion o a combina ion o he in ol ed ac o s
beha e in ime and Sinha [2] de elops a p ocedu e o ack he beha iou by exploi ing
he in luences o hese in ol ed ac o s.
2.2. A possible solu ion
In his wo k, a e es ima ing he indi idual e ec s o ac o s o a highe o de combi-
na ion, he indi idual indices a e conside ed as disc imina i e ea u es. A combina ion,
2
hen, is a ea u e se in highe o de (≥2 ,i.e mul i a ia e). Wi h an excessi ely la ge
numbe o ac o s in ol ed in he pa hway, i is di icul o sea ch o impo an com-
bina ions in a wide sea ch space o e di e en o de s. Exploi ing he analogy wi h
he issues o p io i izing webpages using anking algo i hms, o a pa icula o de , a
ull se o combina ions o in e ac ions can hen be p io i ized based on hese ea u es
using a powe ul anking algo i hm ia suppo ec o s Joachims [3]. Reco ding he
changing ankings o he combina ions o e ime e eals how highe o de in e ac ions
beha e wi hin he pa hway and when an in e en ion migh be necessa y o in luence
he in e ac ion wi hin he pa hway.
2.3. p o ein phospha ase 2A s uc u al/sca old subuni A, alpha iso-
o m (PPP2R1A)
P o ein phospho yla ion is a e e sible p o ein pos ansla ional modi ica ion (PTM).
Phospho yla ion in ol es he ans e o phospha e g oups om ATP o he enzyme,
he ene gy o which comes om hyd olysing ATP in o ADP o AMP. P o ein kinases
(PKs) a e he e ec o s o phospho yla ion and ca alyse he ans e o a γ-phospha e
om ATP o speci ic amino acids on p o eins. P o eins a e phospho yla ed p edom-
inan ly on Se , Th and Ty esidues. In con as , p o ein phospha ases (PPs) a e he
p ima y e ec o s o dephospho yla ion and can be g ouped in o h ee main classes
based on sequence, s uc u e and ca aly ic unc ion. Dephospho yla ion eleases phos-
pha es in o solu ion as ee ions, because a aching hem back o ATP would equi e
ene gy inpu .
PP2A holoenzyme complex comp ises a sca olding (A), egula o y (B), and ca -
aly ic (C) subuni , wi h p o ein phospha ase 2A, ca aly ic subuni , alpha iso o m (PPP2CA)
being he p incipal ca aly ic subuni . The e a e wo iso o ms o he ca aly ic (PPP2CA
aka Cαand PPP2CB aka Cβ), wo iso o ms o he sca old A subuni (PPP2R1A aka
Aαand PPP2R1B aka Aβ) and a leas 17 di e en B subuni p o eins ha a e mem-
be s o p edominan ly o h ee amilies iden i ied as B amily (aka B55; gene symbol
PPP2R2), B’ amily (aka B56; gene symbol PPP2R5) and B” amily (aka PR72/130;
gene symbol PPP2R3); and Ru olo [4] abula e a ew o hem and p o ide e e ences
o hem. Shi [5] s udied he mechanism h ough s uc u e o he se ine/ h eonine phos-
pha ases. The enzyme p o ein se ine/ h eonine phospha ase ac s upon phospho yla ed
se ine/ h eonine esidues as ollows ( om Wikipedia con ibu o s [6]) :
[p o ein]−se ine/ h eonine−phospha e+H2O= [p o ein]−se ine/ h eonine+phospha e
(1)
In hei e iew, Seshacha yulu e al. [7] ocus on he s uc u al complexi y o se -
ine/ h eonine phospha ase PP2A and summa ize i s exp ession pa e n in cance while
discussing abou he PP2A in e ac ing and egula o y p o eins and subs a es. Finally,
hey also e iew he mouse models de eloped o unde s and he biological ole o PP2A
subuni s in an in i o model sys em. Fu he , Reynhou and Janssens [8] summa ize
cu en knowledge on physiologic unc ions o PP2A in ge m cell ma u a ion, umo
supp ession, me abolic egula ion, emb yonic de elopmen , and homeos asis o adul
b ain, li e , hea , immune sys em, lung, kidney, in es ine, skin, eye and bone, all o
which we e e ie ed om in i o s udies using PP2A ansgenic, knockou o knockin
3
mice.
Hemmings e al. [9] pu i ied P o ein phospha ase 2A (polyca ion-s imula ed p o ein
phospha ase L), om po cine kidney and skele al muscle. Via e e se-phase HPLC,
hey sepa a ed he 36-kDa ca aly ic and he 65-kDa pu a i e egula o y (he ea e e med
PR65) subuni s o p o ein phospha ase 2A2. Molecula cloning showed ha wo dis-
inc mRNAs ( e med α(PP2A-Aalpha)and β(PP2A-Abe a)) encoded he PR65 sub-
uni . The cDNA encoding he α-iso ype spanned 2.2 kilobases (kb) and con ained an
open eading ame o 1767 bases p edic ing a p o ein o 65 kDa, while he cDNAs en-
coding he β-iso ype con ained an open eading ame o size simila o ha o α- o m
bu lacked an ini ia o ATG. Fu he , Zhou e al. [10] gene a ed Aβ-speci ic an ibod-
ies and de e mined he cell cycle exp ession, subcellula dis ibu ion, and me abolic
s abili y o Aβin compa ison wi h Aβ.
I p esen 3 d o de combina ions o PPP2R1A wi h o he genes, ha he machine
lea ning based sea ch engine poin s o, as possible syne gis ic combina ions ha migh
be wo king in ime.
3. Me hods
Please e e o sec ions o Sinha [2] o me hods, design o s udy and analysis o da a
o 2nd o de combina ions. The same me hod and design o s udy is used o gene a e
esul s o 3 d o de combina ions p esen ed in his s udy.
4. Time se ies da a
Guj al and MacBea h [1] p esen a se o 71 WNT- ela ed gene exp ession alues o 6
di e en imes poin s o e a ange o 24-hou pe iod using qPCR. The changes ep e-
sen he old-change in he exp ession le els o genes in 200 ng/mL WNT3A-s imula ed
HEK 293 cells in ime ela i e o hei le els in uns imula ed, se um-s a ed cells a 0-
hou . Guj al and MacBea h [1] s a e ha qPCR da a a e he means o h ee biological
eplica es. Only genes whose mean ansc ip le els changed by mo e han wo- old a
one o mo e ime poin s du ing he 24-hou ime cou se we e conside ed signi ican .
Posi i e (nega i e) numbe s ep esen up (down) - egula ion. We ha e al eady co e ed
he issues ela ed o hese da a se s in de ail in Sinha [11]. Reade s a e eques ed o
go h ough hem in he poin ed e e ence. The ools o s udy which a e used he e ha e
been published in ano he ounda ional wo k in Sinha [11].
5. Design o expe imen
5.1. Pipeline o ime se ies da a
Fo he case o ime se ies da a, in e ac ions among he con ibu ing ac o s a e s udied
by compa ing iple s o old-changes a single ime poin s. The p odecu e begins wi h
he gene a ion o dis ibu ion a ound measu emen s a single ime poin s wi h added
noise is done o es ima e he indices. A dis ibu ion is gene a ed o he old changes
4
a single ime poin s. Then o e e y gene, he e is a ec o o alues ep esen ing old
changes as well as de ia ions in old changes o di e en ime poin s and du a ions
be ween ime poin s, espec i ely. Nex a lis ing o all Cn
kcombina ions o knumbe
o genes om a o al o ngenes is gene a ed. kis ≥2 and ≤(n−1). Each o he com-
bina ion o o de k ep esen s a unique se o in e ac ion be ween he in ol ed gene ic
ac o s. A e his, he da ase s a e combined in a speci ed o ma which go as inpu
as pe he equi emen o a pa icula sensi i i y analysis me hod. Thus o each p h
combina ion in Cn
kcombina ions, he da ase is p epa ed in he equi ed o ma om
he dis ibu ions o wo sepa a e cases which ha e been discussed abo e. (See .R code
in mainSc ip -1-1.R). A e he da a has been ans o med, ec o ized p og amming
is employed o densi y based sensi i i y analysis and looping is employed o a i-
ance based sensi i i y analysis o compu e he equi ed sensi i i y indices o each o
he pcombina ions. This p ocedu e is done o di e en kinds o sensi i i y analysis
me hods.
A e he abo e sensi i i y indices ha e been s o ed o each o he p h combina-
ion, he nex s ep in he design o expe imen is conduc ed. Since he e is only one
eco ding o sensi i i y index pe combina ion, each combina ion o ms a aining ex-
ample which is allo ed a aining index and he sensi i i y indices o he indi idual
gene ic ac o s o m he aining example. Thus he e a e Cn
k aining examples o k h
o de in e ac ion. Using his aining se SVMRank
lea n Joachims [3] is used o gene a e a
model on de aul alue C alue o 20. In he cu en expe imen on oy model C alue
has no been unned. The aining se helps in he gene a ion o he model as he di -
e en gene combina ions a e numbe ed in o de which a e used as ank indices. The
model is hen used o gene a e sco e on he obse a ions in he es ing se using he
SV MRank
classi y Joachims [3]. No e ha due o a ailabili y o only one example pe com-
bina ion, a e he model has been buil , he same aining da a is used as es da a o
gene a es he sco es. This p ocedu e is execu ed o each and e e y sensi i i y analysis
me hod. This is ollowed by so ing o hese sco es along wi h he ank indices (i.e he
aining indices) al eady assigned o he gene combina ions. The end esul is a so ed
o de o he gene combina ions based on he anking sco e lea ned by he SV MRank
algo i hm. Finally, his en i e p ocedu e is compu ed o sensi i i y indices gene a ed
o each and e e y old change a ime poin and de ia ions in old change a di e en
du a ions. Obse ing he changing ank o a pa icula combina ion a di e en imes
and di e en ime pe iods will e eal how a combina ion is beha ing.
No e ha he ollowing is he o de in which he iles should be execu ed in R, in
o de , o ob aining he desi ed esul s (No e ha he code will no be explained he e) - •
use sou ce(”mainSc ip -1-1.R”) wi h a gumen s o Dynamic da a •sou ce(”SVMRank-
Resul s-D.R”), o ank he in e ac ions (again his needs o be done sepa a ely o
di e en kinds o SA me hods), •use sou ce(”Combine-Time- iles.R”), i compu -
ing indices sepa a ely ia p e ious ile, •sou ce(”So -n-Plo -D.R”) o so he in e -
ac ions. No e ha he so ing is chages he in e ac ion anking in ime. Thus •use
sou ce(”In e ac ion-P io i y-In ime.R”) o ind he p io i ized anking o each and e -
e y in e ac ion o e he di e en ime poin s and inally •use sou ce(”P in -Ranking-
AND-In e ac ion-Rank.R”) o p in indi idual anking o he equi ed inpu ac o wi h
o he in e ac ion ac o s.
5
6. Resul s & Discussion
6.1. Time se ies da a by Guj al and MacBea h [1]
NOTE - Ranking was assigned on sco es ha we e so ed in DECREASING alues.
So, 1 was assigned o highes sco e and ice e sa.
Resul s o he 3 d o de in e ac ions a e p esen ed he e. The esul s i s discuss
he beha iou o in e ac ions ac oss he snapsho s o ime using he compu ed sensi-
i i ies on old change measu emen s pe ime snapsho . The analysis was done us-
ing 4 di e en sensi i i y indices. Ou o he 71C3combina ions, I conside /p esen
only hose combina ions ha show a anking wi hin i s 10,000 ou o 57,155. This
choice is libe al and biologis s/oncologis s can ha e a mo e s ic e choice as pe need.
Two obse a ions a e made, • he anking o a pa icula combina ion is conse ed (i.e
wi hin he 10,000 ange) in a pa icula ime poin o in he ea ly phase o la e phase
o WNT3A s imula ion, ac oss he majo i y o he ou sensi i i y me hods, which is a
s ic c i e ia o assessmen o • he anking o a pa icula combina ion is conse ed
ac oss ime poin s/phase (i.e hey a e wi hin he 10,000 ange) and he majo i y o he
ou sensi i i y me hods, which is elaxed c i e ia o assessmen . Applying his il e
helps e eal impo an combina ions o in e es ha migh be wo king syne gis ically
a a highe o de le el in he cell.
Rega ding echnical poin s o implemen a ion, he ankings we e gene a ed wi h-
ou scaling/no malizing he ime se ies da a p o ided by Guj al and MacBea h [1].
Fo es ima ing he sensi i i y indices, a small gaussian dis ibu ion using he unc ion
no m ha gene a es a ec o o no mally dis ibu ed andom a iables gi en a ec o
leng h n (he e 9, he 10 h one is he mean/ eco ded gene egula ion i sel ), a popula ion
mean µand popula ion s anda d de ia ion σ. The syn ax o using no m is as ollows:
no m(n, mean, sd). Fu he , I use he ji e un ion o add a li le bi o noise o he
da a. This helps o see i he gene a ed ankings a e obus o no .
6.2. Enume a ion and anking o 2415 PPP2R1A-X-X combina ions
om Guj al and MacBea h [1]
In he supplemen a y sec ion, I p esen ou iles, each con aining he ankings o 3 d
o de combina ions, ha wa y in ime (shown o 5 ime poin s). Each ile ep esen s
he ankings compu ed using a pa icula sensi i i y me hod. The changing ankings
in ime o a pa icula combina ion ep esen s he impo ance o con ibu ion/ ole ha
combina ion plays in he cell s imula ed wi h WNT3A. The sensi i i y me hods used
a e Hilbe Schmid Independence C i e ion indices (HSIC) indices (wi h b and linea
ke nel in Da Veiga [12]) and Sobol indicies (wi h 2002 implemen a ion in Sal elli [13]
and ma inez implemen a ion in Ma inez [14] and Baudin e al. [15]).
6.3. Conse ed machine lea ning ankings o es ed PPP2R1A-X-
X combina ions
A o al o 2415, 3 d o de combina ions in ol ing PPP2R1A we e ob ained om a ull
se o 71C3= 57155 combina ions. Fu he , om his selec ed se , using he abo e c i-
6
e ia o conse ed ankings, I epo / abula e he meaning ul combina ions ha migh
be wo king syne gis ically. Tables 2, 3 and 4 show he ankings o he same combi-
na ions as in able 1, bu using b ke nel o HSIC, 2002 implemen a ion o SOBOL
and ma inez implemen a ion o SOBOL, espec i ely. As one allies he ankings o
ac oss hese ables o a pa icula combina ion, one inds ha he ole o he combina-
ion o in e es is conse ed. This conse a ion poin s o he exis ence o he biological
syne gy, whe he he combina ion has been es ed o unexplo ed/un es ed.
6.3.1. Examining he beha iou o PPP2CA-PPP2R1A-X combina ions
Goud eaul e al. [16] indica e ha he PP2A ca aly ic (PP2A-C) subuni binds di ec ly
o he PP2A-A sca olding subuni ( wo 85% iden ical p o eins, PP2A-Aαand PP2A-
Aβ, a e p esen in human cells), o o m he PP2A dime ic co e. This co e se es as a
pla o m o he associa ion o a egula o y o B subuni o gene a e a ime ic complex
impo an o subs a e ec ui men and subcellula a ge ing.
The co e enzyme o PP2A comp ises a 65 kDa sca olding subuni and a 36 kDa
ca aly ic subuni . Xing e al. [17] epo he c ys al s uc u es o he PP2A co e enzyme
bound o wo o i s inhibi o s. They obse e ha he ca aly ic subuni ecognizes one
end o he elonga ed sca olding subuni by in e ac ing wi h he conse ed idges o
HEAT epea s 11-15. Fo ma ion o he co e enzyme o ced he sca olding subuni o
unde go p onounced s uc u al ea angemen . The sca olding subuni exhibi ed con-
side able con o ma ional lexibili y, which is p oposed o play an essen ial ole in PP2A
unc ion. These s uc u es, oge he wi h biochemical analyses, e ealed signi ican in-
sigh s in o PP2A unc ion and se e as a amewo k o deciphe ing he di e se oles o
PP2A in cellula physiology. Fu he , inac i a ion o bo h he αand βiso o ms o he
PP2A sca olding subuni has been linked o cance . They ci e a ious e e ences whe e
mu a ions in he sca olding subuni esul in comp omised binding o he egula o y o
ca aly ic subuni o PP2A o a o al absence o subs an ial educ ion o he sca olding
subuni , which a e closely associa ed wi h a a ie y o p ima y human umo s.
PPP2R1A is he p edominan PP2A sca old A-subuni ha is equi ed o unc-
ional PP2A complex o ma ion. Kauko e al. [18] obse ed ha unlike deple ion o
he ca aly ic PP2A subuni PPP2CA, siRNA o PPP2R1A did no cause cell le hal-
i y and, on he o he hand, did no a ec he PPP2CA exp ession. Howe e , and
as expec ed, PPP2R1A deple ion esul ed in des abiliza ion o PPP2R5A (B56) and
PPP2R2A (B55) B-subuni s. Thei esul s con i med ha PPP2R1A deple ion esul s
in comp ehensi e PP2A complex inhibi ion.
One inds he ollowing combina ions o PPP2CA along wi h PPP2R1A, o be
p ominen a 3 d o de le el - LEF1-PPP2CA-PPP2R1A, FZD7-PPP2CA-PPP2R1A,
PPP2CA-PPP2R1A-FBXW4, NKD1-PPP2CA-PPP2R1A, PPP2CA-PPP2R1A-SENP2,
PPP2CA-PPP2R1A-TLE2, PPP2CA-PPP2R1A-WNT5A, PPP2CA-PPP2R1A-WNT3A,
KREMEN1-PPP2CA-PPP2R1A, FZD5-PPP2CA-PPP2R1A, DVL1-PPP2CA-PPP2R1A,
GSK3A-PPP2CA-PPP2R1A, AES-PPP2CA-PPP2R1A, AXIN1-PPP2CA-PPP2R1A,
EP300-PPP2CA-PPP2R1A, CCND2-PPP2CA-PPP2R1A, PPP2CA-PPP2R1A-WNT2B,
FOXN1-PPP2CA-PPP2R1A, FZD1-PPP2CA-PPP2R1A, PPP2CA-PPP2R1A-TCF7, DAAM1-
PPP2CA-PPP2R1A, CXXC4-PPP2CA-PPP2R1A, FBXW11-PPP2CA-PPP2R1A, APC-
PPP2CA-PPP2R1A, DVL2-PPP2CA-PPP2R1A, FZD6-PPP2CA-PPP2R1A, FBXW2-
7
RANKING @ iUSING HSIC - LINEAR
3 d o de comb. 1 3 6 12 24 3 d o de comb. 1 3 6 12 24
CSNK1D-FGF4-PPP2R1A 72 17401 22364 53716 30729 FSHB-NKD1-PPP2R1A 134 11978 48147 4744 11658
FOXN1-KREMEN1-PPP2R1A 187 38390 45372 22596 7296 FSHB-FZD2-PPP2R1A 216 20883 30530 35125 19903
CTNNBIP1-JUN-PPP2R1A 222 17930 41664 52992 44848 CCND1-FGF4-PPP2R1A 231 42431 52577 39266 5985
CXXC4-FOSL1-PPP2R1A 255 24314 35136 31526 39110 FOSL1-PPP2R1A-SENP2 256 39545 1842 16944 18375
DKK1-JUN-PPP2R1A 267 12255 56230 48454 54215 FRZB-GSK3A-PPP2R1A 353 14275 17584 12248 25992
CSNK2A1-CTBP1-PPP2R1A 386 22561 33967 27086 25647 DAAM1-FGF4-PPP2R1A 419 31801 52927 54325 31945
CXXC4-PORCN-PPP2R1A 424 27798 37533 50501 37618 DKK1-PPP2R1A-SENP2 442 14095 52078 45675 54675
AES-FOXN1-PPP2R1A 486 23646 9985 11397 37399 DVL2-JUN-PPP2R1A 555 45651 45029 17035 30388
AES-AXIN1-PPP2R1A 562 47451 24435 49898 51110 LEF1-NKD1-PPP2R1A 793 3084 55944 23057 25903
FZD8-PORCN-PPP2R1A 807 27524 31540 26322 40650 FOSL1-PPP2R1A-RHOU 846 41555 5035 55239 46031
FBXW11-LRP6-PPP2R1A 920 16519 19037 17797 45281 CSNK1G1-FOXN1-PPP2R1A 960 4562 8931 10045 26824
CTNNB1-FOXN1-PPP2R1A 966 1729 7371 11775 25639 CSNK1D-PPP2R1A-WNT5A 992 931 1207 30631 56811
PITX2-PORCN-PPP2R1A 1003 8071 39783 44256 5481 FBXW11-FGF4-PPP2R1A 1030 29187 47593 48874 21413
CXXC4-FGF4-PPP2R1A 1044 30931 36251 44472 52608 CSNK1D-PPP2R1A-TCF7L1 1128 12625 3602 38061 56712
LEF1-PORCN-PPP2R1A 1139 34004 43790 26178 5620 CCND1-CTBP1-PPP2R1A 1192 36857 14658 39423 20532
DKK1-FGF4-PPP2R1A 1228 16772 51023 37645 49558 FZD1-PORCN-PPP2R1A 1234 19388 36871 41947 10191
DVL1-FOXN1-PPP2R1A 1316 40931 10069 3721 36477 PPP2R1A-WNT1-WNT4 1345 13482 18287 10132 56367
DVL2-FGF4-PPP2R1A 1363 45199 42753 22929 46333 CSNK1D-PPP2R1A-TCF7 1430 4169 153 38743 7414
CSNK2A1-MYC-PPP2R1A 1454 17389 25178 16938 14057 FBXW11-FOXN1-PPP2R1A 1485 2012 6552 10843 25217
CTBP1-FGF4-PPP2R1A 1692 30523 34482 40227 19588 FBXW2-FGF4-PPP2R1A 1759 32973 44562 51245 8907
CSNK2A1-FOXN1-PPP2R1A 1773 10252 16688 5889 9126 CXXC4-JUN-PPP2R1A 1782 11540 37923 13434 43762
PPP2R1A-WNT3-WNT3A 1817 55448 5096 45267 43648 CSNK2A1-FGF4-PPP2R1A 1819 25704 42101 34434 17125
FRZB-PORCN-PPP2R1A 1881 14863 41848 44601 12655 AXIN1-FOXN1-PPP2R1A 1913 4756 8847 11042 32343
FOSL1-PPP2R1A-SFRP4 1952 52448 1955 16120 30096 CSNK1G1-JUN-PPP2R1A 1986 10228 52696 13904 47706
LEF1-MYC-PPP2R1A 1990 40461 15570 31458 22391 FBXW11-JUN-PPP2R1A 2029 7720 56156 47859 37754
FZD2-PORCN-PPP2R1A 2085 13234 40114 30182 21029 CCND3-PORCN-PPP2R1A 2099 25783 29032 23766 18843
CSNK1A1-FGF4-PPP2R1A 2100 34624 20608 35480 22746 DKK1-GSK3A-PPP2R1A 2104 13726 28756 56201 53104
DIXDC1-NKD1-PPP2R1A 2140 5484 54992 25998 568 FZD6-PORCN-PPP2R1A 2181 22169 35065 11807 6867
FZD1-JUN-PPP2R1A 2184 21063 36959 28810 6175 BCL9-FGF4-PPP2R1A 2209 19748 39118 49100 20100
FZD5-PPP2R1A-WNT5A 2239 9275 9172 22179 32268 FSHB-GSK3A-PPP2R1A 2267 11196 31968 18565 24240
PPP2R1A-WNT3-WNT4 2411 43365 6520 45456 48427 FRAT1-JUN-PPP2R1A 2465 21726 41887 23096 41465
FBXW11-FZD2-PPP2R1A 2469 12611 33445 15277 21128 DAAM1-GSK3A-PPP2R1A 2495 39121 35124 30013 51000
CSNK1G1-FGF4-PPP2R1A 2535 19539 51865 57137 46652 PPP2R1A-TLE1-TLE2 2603 23452 51446 28086 54181
FZD8-JUN-PPP2R1A 2633 37008 34949 19872 55616 APC-FZD6-PPP2R1A 2668 19187 290 54948 5882
FOSL1-JUN-PPP2R1A 2696 46872 41797 35276 27908 CSNK1G1-PORCN-PPP2R1A 2697 18740 49826 20704 24737
CCND2-LRP6-PPP2R1A 2763 48463 13066 23230 6578 DKK1-FOXN1-PPP2R1A 2783 23484 22053 10586 44403
CSNK2A1-GSK3A-PPP2R1A 2846 28306 32715 6544 36708 CSNK1D-PORCN-PPP2R1A 2896 17111 34991 43683 19157
PPP2R1A-TLE1-WNT4 2902 4217 52852 23987 31073 CTNNBIP1-FGF4-PPP2R1A 2959 22853 37005 28725 35681
PPP2R1A-WNT1-WNT3A 2989 13277 15619 27990 53390 BCL9-PORCN-PPP2R1A 3009 23888 28332 49136 12024
FGF4-PPP2R1A-SFRP4 3037 8718 1707 14759 34549 EP300-FOXN1-PPP2R1A 3054 31254 9485 1045 4738
FZD1-NLK-PPP2R1A 3063 6647 16715 10003 26509 DAAM1-FOXN1-PPP2R1A 3097 26397 35409 10550 45683
PPP2R1A-SFRP1-TCF7 3233 44109 34973 47932 35401 DVL1-FGF4-PPP2R1A 3242 41242 45411 17324 23922
FZD7-PORCN-PPP2R1A 3293 54918 29516 41742 23131 FZD5-FGF4-PPP2R1A 3315 19006 41149 46199 17261
FOSL1-PORCN-PPP2R1A 3418 54803 40086 41005 20335 FBXW11-GSK3A-PPP2R1A 3471 17513 23616 47087 26387
AXIN1-FZD2-PPP2R1A 3530 36160 24224 14226 14076 DVL1-GSK3A-PPP2R1A 3570 44275 16001 23234 34855
EP300-PORCN-PPP2R1A 3588 55435 38638 36180 44771 FBXW11-PORCN-PPP2R1A 3600 13551 28934 48860 10946
PPP2R1A-SFRP1-FBXW4 3602 34385 50714 10310 44807 FZD5-NKD1-PPP2R1A 3621 21515 54524 36048 1557
CTNNB1-PORCN-PPP2R1A 3628 8334 43683 23768 39432 FRAT1-PORCN-PPP2R1A 3641 17091 37502 41949 11356
DAAM1-PORCN-PPP2R1A 3682 30772 17215 29018 29847 CCND1-JUN-PPP2R1A 3683 12869 49497 55359 13160
LRP5-NLK-PPP2R1A 3749 6866 25722 95 55900 CSNK1G1-NLK-PPP2R1A 3754 21618 10600 22928 48421
CCND3-PPP2R1A-SENP2 3947 20724 4140 11034 41552 DKK1-PORCN-PPP2R1A 4028 22121 57008 12032 54395
EP300-FGF4-PPP2R1A 4059 54172 38740 54434 30530 GSK3B-LRP6-PPP2R1A 4082 43470 10296 43375 25140
EP300-JUN-PPP2R1A 4089 45635 48485 28347 10942 FZD5-PORCN-PPP2R1A 4090 33288 41287 38390 34991
FRAT1-NLK-PPP2R1A 4096 7150 14882 4380 42041 CTBP1-PPP2R1A-TCF7 4108 3719 931 22058 13655
CSNK2A1-NKD1-PPP2R1A 4118 2001 56920 13318 8736 CTNNBIP1-NLK-PPP2R1A 4168 17696 21970 43414 47292
DKK1-PPP2R1A-TLE2 4213 1676 48827 40467 57091 CTNNBIP1-FRAT1-PPP2R1A 4272 14548 33170 16600 48598
CTBP1-GSK3A-PPP2R1A 4275 19056 10307 24065 37785 GSK3B-JUN-PPP2R1A 4299 50524 49319 35755 3146
PPP2R1A-TLE1-WIF1 4307 33741 44977 32847 32390 DIXDC1-FOXN1-PPP2R1A 4318 4042 7718 10315 5136
PPP2R1A-SFRP1-WNT3A 4336 49933 48304 18593 24856 FZD7-JUN-PPP2R1A 4369 47090 33547 30519 53889
BCL9-JUN-PPP2R1A 4379 12860 38522 50713 4351 CSNK1A1-PORCN-PPP2R1A 4422 33823 41491 28773 10648
CXXC4-PPP2R1A-RHOU 4427 19193 3464 42655 56387 FOSL1-PPP2R1A-TCF7 4468 34122 1739 41424 25089
FZD8-GSK3A-PPP2R1A 4484 40441 18881 46804 54756 PPP2R1A-RHOU-SLC9A3R1 4485 42742 45200 38226 53842
DKK1-PPP2R1A-WNT5A 4534 3478 36759 50853 55700 FZD1-NKD1-PPP2R1A 4562 26290 43026 35994 1774
Table 1: Rankings o PPP2R1A-X-X. A lis o app oxima ely i s 125 combina ions wi h ankings below
10,000 ou o 57,155. SA - HSIC; Ke nel - linea
PPP2CA-PPP2R1A, CSNK2A1-PPP2CA-PPP2R1A, CTNNB1-PPP2CA-PPP2R1A, FOSL1-
PPP2CA-PPP2R1A, LRP5-PPP2CA-PPP2R1A, FZD8-PPP2CA-PPP2R1A, MYC-PPP2CA-
PPP2R1A, CSNK1D-PPP2CA-PPP2R1A, PPP2CA-PPP2R1A-PYGO1, PORCN-PPP2CA-
PPP2R1A, FRAT1-PPP2CA-PPP2R1A, JUN-PPP2CA-PPP2R1A, CTBP1-PPP2CA-
8
RANKING @ iUSING HSIC - RBF
3 d o de comb. 1 3 6 12 24 3 d o de comb. 1 3 6 12 24
CSNK1D-FGF4-PPP2R1A 3004 29048 12442 15684 23801 FSHB-NKD1-PPP2R1A 25236 3206 25555 29398 54336
FOXN1-KREMEN1-PPP2R1A 21547 15130 581 7154 55001 FSHB-FZD2-PPP2R1A 10535 30086 26859 11239 24594
CTNNBIP1-JUN-PPP2R1A 42662 30325 24952 5762 37211 CCND1-FGF4-PPP2R1A 9841 27457 12592 18053 2791
CXXC4-FOSL1-PPP2R1A 52227 34156 6226 46113 43359 FOSL1-PPP2R1A-SENP2 36531 47500 56688 1297 8711
DKK1-JUN-PPP2R1A 19726 15606 1085 29841 36603 FRZB-GSK3A-PPP2R1A 1658 24598 48047 40183 47791
CSNK2A1-CTBP1-PPP2R1A 51425 30212 13474 42814 33263 DAAM1-FGF4-PPP2R1A 1363 39705 27194 16188 12922
CXXC4-PORCN-PPP2R1A 20998 30567 5511 22186 56640 DKK1-PPP2R1A-SENP2 4320 17195 24869 14464 3866
AES-FOXN1-PPP2R1A 723 21691 22365 18788 29319 DVL2-JUN-PPP2R1A 7790 48428 6855 9490 40633
AES-AXIN1-PPP2R1A 37649 36390 27090 29535 33374 LEF1-NKD1-PPP2R1A 24944 9286 39491 44583 37109
FZD8-PORCN-PPP2R1A 3136 21194 9602 10973 55135 FOSL1-PPP2R1A-RHOU 19254 49825 54278 50968 41085
FBXW11-LRP6-PPP2R1A 2990 7171 41891 45594 39934 CSNK1G1-FOXN1-PPP2R1A 3415 1125 22606 474 39586
CTNNB1-FOXN1-PPP2R1A 6266 597 36708 568 27942 CSNK1D-PPP2R1A-WNT5A 27528 4279 14277 4265 42405
PITX2-PORCN-PPP2R1A 11355 50277 26063 28070 55628 FBXW11-FGF4-PPP2R1A 2311 3713 32222 41780 18993
CXXC4-FGF4-PPP2R1A 1192 9614 5570 26405 23051 CSNK1D-PPP2R1A-TCF7L1 34388 5648 48876 25681 52823
LEF1-PORCN-PPP2R1A 9650 37275 29706 14200 48587 CCND1-CTBP1-PPP2R1A 42960 11026 30626 24182 7494
DKK1-FGF4-PPP2R1A 1885 5747 727 4631 30783 FZD1-PORCN-PPP2R1A 24806 24942 1636 2232 55350
DVL1-FOXN1-PPP2R1A 7337 28739 5315 11310 23091 PPP2R1A-WNT1-WNT4 13056 3776 48355 444 25289
DVL2-FGF4-PPP2R1A 3678 46957 3278 19048 26196 CSNK1D-PPP2R1A-TCF7 34317 14103 3740 45791 33515
CSNK2A1-MYC-PPP2R1A 8973 18254 44398 29894 43896 FBXW11-FOXN1-PPP2R1A 848 15861 49514 22629 20720
CTBP1-FGF4-PPP2R1A 2812 38280 137 44051 39921 FBXW2-FGF4-PPP2R1A 849 18830 22979 9327 14927
CSNK2A1-FOXN1-PPP2R1A 647 14324 25472 4074 30161 CXXC4-JUN-PPP2R1A 8147 19410 4343 32567 48732
PPP2R1A-WNT3-WNT3A 9441 54192 34392 53766 7535 CSNK2A1-FGF4-PPP2R1A 166 29600 18823 44833 19787
FRZB-PORCN-PPP2R1A 13914 23845 13959 7815 56301 AXIN1-FOXN1-PPP2R1A 12949 15322 34068 9033 35734
FOSL1-PPP2R1A-SFRP4 50064 57024 56666 31648 53883 CSNK1G1-JUN-PPP2R1A 2410 8342 5954 20586 31871
LEF1-MYC-PPP2R1A 5271 38043 45068 15629 15850 FBXW11-JUN-PPP2R1A 15642 5206 44646 46199 19057
FZD2-PORCN-PPP2R1A 335 12575 8770 1810 55522 CCND3-PORCN-PPP2R1A 23176 16220 12632 6835 44417
CSNK1A1-FGF4-PPP2R1A 4863 12539 3164 12998 34074 DKK1-GSK3A-PPP2R1A 37 15243 34284 9621 35620
DIXDC1-NKD1-PPP2R1A 41282 2633 37452 52221 22216 FZD6-PORCN-PPP2R1A 23 17577 25321 670 56053
FZD1-JUN-PPP2R1A 32015 23065 8067 12950 35467 BCL9-FGF4-PPP2R1A 10398 5395 4459 43209 26087
FZD5-PPP2R1A-WNT5A 17060 9682 37942 54060 54700 FSHB-GSK3A-PPP2R1A 2994 22740 47062 16574 48029
PPP2R1A-WNT3-WNT4 6466 47384 44643 26384 8285 FRAT1-JUN-PPP2R1A 14775 16627 12246 41797 26468
FBXW11-FZD2-PPP2R1A 8700 4798 40674 36207 15746 DAAM1-GSK3A-PPP2R1A 6522 35629 52023 19728 17125
CSNK1G1-FGF4-PPP2R1A 8938 29139 2598 16353 38899 PPP2R1A-TLE1-TLE2 44598 3120 16931 19408 1179
FZD8-JUN-PPP2R1A 7769 37927 11864 24690 38173 APC-FZD6-PPP2R1A 26156 38611 29925 13305 29320
FOSL1-JUN-PPP2R1A 20816 55928 16147 47523 47242 CSNK1G1-PORCN-PPP2R1A 16024 19421 9392 5370 55173
CCND2-LRP6-PPP2R1A 7525 49696 47315 30017 29589 DKK1-FOXN1-PPP2R1A 1768 15517 15329 5073 18412
CSNK2A1-GSK3A-PPP2R1A 6662 21693 51937 52594 38018 CSNK1D-PORCN-PPP2R1A 16940 28022 22571 2476 54099
PPP2R1A-TLE1-WNT4 34919 1417 25861 8678 8293 CTNNBIP1-FGF4-PPP2R1A 2426 9206 12675 669 32498
PPP2R1A-WNT1-WNT3A 2644 9345 37570 29489 17577 BCL9-PORCN-PPP2R1A 28259 20478 5854 26873 52990
FGF4-PPP2R1A-SFRP4 8036 9755 54750 29227 49177 EP300-FOXN1-PPP2R1A 1354 35385 45759 2306 27930
FZD1-NLK-PPP2R1A 20834 8886 52092 12766 24248 DAAM1-FOXN1-PPP2R1A 1334 13230 49009 5916 8662
PPP2R1A-SFRP1-TCF7 8562 33991 8051 54700 29578 DVL1-FGF4-PPP2R1A 5991 18327 77 43200 54479
FZD7-PORCN-PPP2R1A 39388 55931 21995 3462 52550 FZD5-FGF4-PPP2R1A 1273 30877 9798 36227 30025
FOSL1-PORCN-PPP2R1A 1690 56373 15424 4340 55845 FBXW11-GSK3A-PPP2R1A 2166 8382 55946 44477 32821
AXIN1-FZD2-PPP2R1A 26985 37883 10434 10353 20291 DVL1-GSK3A-PPP2R1A 15051 28660 39098 46332 48932
EP300-PORCN-PPP2R1A 9705 56176 25373 738 50930 FBXW11-PORCN-PPP2R1A 5633 5510 29166 19086 52513
PPP2R1A-SFRP1-FBXW4 43447 35660 2162 20015 15609 FZD5-NKD1-PPP2R1A 23335 9105 47323 31744 56453
CTNNB1-PORCN-PPP2R1A 12296 20951 22147 236 56429 FRAT1-PORCN-PPP2R1A 14510 12147 3493 8420 55974
DAAM1-PORCN-PPP2R1A 43717 12829 27614 274 42068 CCND1-JUN-PPP2R1A 28970 7761 24201 8661 5096
LRP5-NLK-PPP2R1A 22739 10079 12169 17484 38120 CSNK1G1-NLK-PPP2R1A 35195 9424 21823 20710 43474
CCND3-PPP2R1A-SENP2 10144 14970 33230 89 13210 DKK1-PORCN-PPP2R1A 15567 20860 1442 5709 55732
EP300-FGF4-PPP2R1A 434 56284 13608 15792 27194 GSK3B-LRP6-PPP2R1A 6362 47681 43483 14542 49585
EP300-JUN-PPP2R1A 5997 52619 15125 40032 31600 FZD5-PORCN-PPP2R1A 23669 41306 11440 2543 56519
FRAT1-NLK-PPP2R1A 47257 5675 39028 27369 25057 CTBP1-PPP2R1A-TCF7 13922 7113 7010 44002 53010
CSNK2A1-NKD1-PPP2R1A 19188 9240 34119 49629 44582 CTNNBIP1-NLK-PPP2R1A 27842 23336 43647 19091 40032
DKK1-PPP2R1A-TLE2 18876 4979 33058 36302 34591 CTNNBIP1-FRAT1-PPP2R1A 19452 31715 19287 3657 50902
CTBP1-GSK3A-PPP2R1A 193 46150 47414 42441 47384 GSK3B-JUN-PPP2R1A 4762 52417 19413 19919 45463
PPP2R1A-TLE1-WIF1 18734 28938 477 39566 970 DIXDC1-FOXN1-PPP2R1A 3585 17552 18249 8440 13079
PPP2R1A-SFRP1-WNT3A 10638 51919 14638 49471 17076 FZD7-JUN-PPP2R1A 15754 47453 8319 37051 11201
BCL9-JUN-PPP2R1A 38825 31345 7280 45954 33797 CSNK1A1-PORCN-PPP2R1A 32307 17216 8460 87 56661
CXXC4-PPP2R1A-RHOU 24725 6975 48923 38600 48066 FOSL1-PPP2R1A-TCF7 32156 40396 19240 52936 29464
FZD8-GSK3A-PPP2R1A 442 39080 49490 18545 37574 PPP2R1A-RHOU-SLC9A3R1 50539 48128 21287 4442 19281
DKK1-PPP2R1A-WNT5A 17268 5548 34963 48461 43857 FZD1-NKD1-PPP2R1A 38340 8464 17462 30009 50089
Table 2: Rankings o PPP2R1A-X-X. A lis o app oxima ely i s 125 combina ions wi h ankings below
10,000 ou o 57,155. SA - HSIC; Ke nel - b
PPP2R1A, CTNNBIP1-PPP2CA-PPP2R1A, FGF4-PPP2CA-PPP2R1A, CSNK1A1-
PPP2CA-PPP2R1A, CCND1-PPP2CA-PPP2R1A, PPP2CA-PPP2R1A-T, and NLK-
PPP2CA-PPP2R1A. All hese combina ions indica e he exis ence o a possible syn-
e gy when hey ake a highe ank in he lis o combina ions (Table no shown, bu
da a a ailable in supplemen a y iles).
9
manne .
Fu he , he nuclea phosphop o ein c-JUN is a majo componen o he AP1 an-
sc ip ion ac o , whose ac i i y is augmen ed by many oncogenes. An impo an mech-
anism o s imula e AP1 unc ion is N- e minal phospho yla ion o c-JUN a he se ine
esidues 63 and 73 by he c-JUN N- e minal kinases (JNKs). To de e mine he unc ion
o c-JUN N- e minal phospho yla ion (JNP) du ing oncogenic ans o ma ion in i o
and in i o, Beh ens e al. [32] used mice and cells ha bo ing a mu an allele o c-JUN,
which has he JNK phosphoaccep o se ines changed o alanines (JUN-AA). JUN-AA
immo alized ib oblas s exp essing -RAS and -FOS showed educed umo igenici y
in nude mice, bu he e iciency o -SRC ans o ma ion was una ec ed by he lack o
JNP. To assess he signi icance o JNP in umou de elopmen in i o, wo ansgenic
mouse umou models we e employed. Skin umou de elopmen caused by cons i-
u i e ac i a ion o he RAS pa hway by K5-SOS-F exp ession and c-FOS-induced
os eosa coma o ma ion we e impai ed in mice lacking JNP. Thus he e is a connec-
ion be ween c-JUN and FOSL1, ha migh be exis ing. Finally, igu e 4 in Cla k and
Ohlmeye [33] shows c-JUN which combines wi h c-FOS and p o ein dephospho yla-
ion is ini ia ed by PP2A.
Looking a he ables abo e, one inds he ollowing combina ions o FOSL1
along wi h PPP2R1A, o be p ominen a 3 d o de le el - CXXC4-FOSL1-PPP2R1A,
FOSL1-PPP2R1A-SFRP4, FOSL1-JUN-PPP2R1A, FOSL1-PORCN-PPP2R1A, FOSL1-
PPP2R1A-SENP2, FOSL1-PPP2R1A-RHOU and FOSL1-PPP2R1A-TCF7. All hese
combina ions indica e he exis ence o a possible syne gy when hey ake a highe ank
in he lis o combina ions.
6.4.10. Examining he beha iou o FOX-PPP2CA-X combina ions
CONNECTION OF FOX-PPP2CA - PP2A is a umou supp esso whose s ong inhi-
bi ion unde lies he phospho yla ion-dependen , an i-apop o ic mechanisms in ch onic
lymphocy ic leukemia (CLL). Inac i a ion o PP2A is due o he coope a i e ac ion o
he phospho yla ion o Y307 o i s ca aly ic subuni by he abe an cy osolic pool o
he SRC amily kinase LYN and he in e ac ion wi h i s p o ein inhibi o SET, which
is o e exp essed in CLL. Pagano e al. [34] de eloped a lib a y o compounds, he
mos po en being he one named CC11, which es o es PP2A ac i i y by dis up ing
he PP2A/SET complex, he eby igge ing he mi ochond ial pa hway o apop osis.
They obse e ha his p ocess in ol es he ec ui men o he p oapop o ic BH3-only
p o eins BAD and BIM o mi ochond ia, he o me upon di ec dephospho yla ion and
he la e being newly exp essed upon dephospho yla ion and ac i a ion o i s ansc ip-
ion ac o FOXO3A. Thei indings highligh ed ha PP2A an agonized he p osu i al
pa hways con olled by AKT, which phospho yla es and he eby supp esses a a ie y
o p o-apop o ic ac o s and umou supp esso s including BAD and FOXO3A.
Looking a he ables abo e, one inds he ollowing combina ions o membe s
o FOX amily along wi h PPP2R1A, o be p ominen a 3 d o de le el - FOXN1-
KREMEN1-PPP2R1A, AES-FOXN1-PPP2R1A, CTNNB1-FOXN1-PPP2R1A, DVL1-
FOXN1-PPP2R1A, CSNK2A1-FOXN1-PPP2R1A, CSNK1G1-FOXN1-PPP2R1A, FBXW11-
FOXN1-PPP2R1A, AXIN1-FOXN1-PPP2R1A, DKK1-FOXN1-PPP2R1A, EP300-FOXN1-
PPP2R1A, DAAM1-FOXN1-PPP2R1A and DIXDC1-FOXN1-PPP2R1A. All hese
16
combina ions indica e he exis ence o a possible syne gy when hey ake a highe ank
in he lis o combina ions.
6.4.11. Examining he beha iou o EP300-PPP2R1A-X combina ions
CONNECTION OF EP300-PPP2CA - T ansc ip ional coac i a o p300 (o EP300) is
equi ed o emb yonic de elopmen and cell p oli e a ion. Valp oic acid, a his one
deace ylase inhibi o , is widely used in he he apy o epilepsy and bipola diso de .
Chen e al. [35] epo ha alp oic acid s imula es p o easome-dependen p300 deg a-
da ion h ough augmen a ion o gene exp ession o he B56γ egula o y subuni s o
p o ein phospha ase 2A. The B56γ3 egula o y and ca aly ic subuni s o p o ein phos-
pha ase 2A in e ac wi h p300. O e exp ession o he B56γ3 subuni led o p o easome-
media ed p300 deg ada ion and ep essed p300-dependen ansc ip ional ac i a ion,
which equi ed he B56γ3 in e ac ion domain o p300. Con e sely, silencing o he
B56γsubuni exp ession by RNA in e e ence inc eased he s abili y and ansc ip-
ional ac i i y o p300. Via quan i a i e phospho-p o eomic analysis, B ewe e al. [23]
iden i ied EP300 o be subs a e o PPP2CA.
Looking a he ables abo e, one inds he ollowing combina ions o EP300 along
wi h PPP2R1A, o be p ominen a 3 d o de le el - EP300-PORCN-PPP2R1A, EP300-
FGF4-PPP2R1A, EP300-JUN-PPP2R1A and EP300-FOXN1-PPP2R1A. All hese com-
bina ions indica e he exis ence o a possible syne gy when hey ake a highe ank in
he lis o combina ions.
7. Conclusion
This manusc ip s udies he ime beha iou o 3 d o de combina ions o PPP2R1A in
WNT3A s imula ed HEK 293 cells. Based on he ex ablished 2nd o de combina ions
o he PPP2R1A, 3 d o de combina ions eme ge using he machine lea ning based
sea ch engine. These 3 d o de combina ions migh be o in e es o u he we lab
in es iga ions.
Compe ing in e es s
No compe ing in e es is decla ed.
Au ho con ibu ions s a emen
SS concei ed and designed he expe imen s; w o e he code; pe o med he expe i-
men s; analyzed he da a; w o e he manusc ip .
17
A ailabili y o code
Code o ime se ies da a a ailable a CERN based Zenodo on h ps://zenodo.o g/
eco ds/14637456.
Acknowledgmen s
Special hanks o M s. Ri a Sinha and la e M . P abha Sinha o suppo ing he au ho
inancially, wi hou which his wo k could no ha e been made possible.
Supplemen a y
The ollowing iles (ending wi h . x and can be opened in R o in simple ex p o-
cessing p og am) wi h hese names a e made a ailable wi h his manusc ip . Fo
PPP2R1A, (1) -3-od -TP- anking-linea . x , (2) -3-od -TP- anking- b . x , (3) -
3-od -TP- anking-2002. x , and (4) -3-od -TP- anking-ma inez. x , con ain ank-
ings o 3 d o de combina ions ac oss each ime poin o , HSIC (linea ke nel), HSIC
( b ke nel), SOBOL (2002 implemen a ion) and SOBOL (ma inez implemen a ion),
espec i ely.
Re e ences
[1] T. S. Guj al, G. MacBea h, A sys em-wide in es iga ion o he dynamics o wn signaling e eals no el phases o
ansc ip ional egula ion, PloS one 5 (2010) e10024.
[2] S. Sinha, Machine lea ning anking o plausible (un) explo ed syne gis ic gene combina ions using sensi i i y indices
o ime se ies measu emen s o wn signaling pa hway, In eg a i e Biology 16 (2024) zyae020.
[3] T. Joachims, T aining linea s ms in linea ime, in: P oceedings o he 12 h ACM SIGKDD in e na ional con e ence
on Knowledge disco e y and da a mining, ACM, 2006, pp. 217–226.
[4] P. P. Ru olo, The b oken o swi ch in cance signaling: Pp2a as a egula o o umo igenesis, d ug esis ance, and
immune su eillance, BBA clinical 6 (2016) 87–99.
[5] Y. Shi, Se ine/ h eonine phospha ases: mechanism h ough s uc u e, Cell 139 (2009) 468–484.
[6] Wikipedia con ibu o s, P o ein se ine/ h eonine phospha ase — Wikipedia, he ee encyclopedia, h ps://en.
wikipedia.o g/w/index.php? i le=P o ein_se ine/ h eonine_phospha ase&oldid=1226576715,
2024. [Online; accessed 6-Ma ch-2025].
[7] P. Seshacha yulu, P. Pandey, K. Da a, S. K. Ba a, Phospha ase: Pp2a s uc u al impo ance, egula ion and i s
abe an exp ession in cance , Cance le e s 335 (2013) 9–18.
[8] S. Reynhou , V. Janssens, Physiologic unc ions o pp2a: Lessons om gene ically modi ied mice, Biochimica E
Biophysica Ac a (BBA)-Molecula Cell Resea ch 1866 (2019) 31–50.
[9] B. A. Hemmings, C. Adams-Pea son, F. Mau e , P. Mulle , J. Go is, W. Me le ede, J. Ho s eenge, S. R. S one, alpha-
and be a- o ms o he 65-kda subuni o p o ein phospha ase 2a ha e a simila 39 amino acid epea ing s uc u e,
Biochemis y 29 (1990) 3166–3173.
[10] J. Zhou, H. T. Pham, R. Ruedige , G. Wal e , Cha ac e iza ion o he aalpha and abe a subuni iso o ms o p o ein
phospha ase 2a: di e ences in exp ession, subuni in e ac ion, and e olu ion, Biochemical Jou nal 369 (2003)
387–398.
18
[11] S. Sinha, Hilbe -schmid and sobol sensi i i y indices o s a ic and ime se ies wn signaling measu emen s in
colo ec al cance -pa a, BMC sys ems biology 11 (2017) 120.
[12] S. Da Veiga, Global sensi i i y analysis wi h dependence measu es, Jou nal o S a is ical Compu a ion and Simula-
ion 85 (2015) 1283–1305.
[13] A. Sal elli, Making bes use o model e alua ions o compu e sensi i i y indices, Compu e physics communica ions
145 (2002) 280–297.
[14] J. Ma inez, Analyse de sensibili e globale pa decomposi ion de la a iance, P esen a ion in Jou n´
ee des GdR
Ondes & Masco 13 (2011) 207.
[15] M. Baudin, K. Boumhaou , T. Delage, B. Iooss, J.-M. Ma inez, Nume ical s abili y o sobol’indices es ima ion
o mula, in: P oceedings o he 8 h In e na ional Con e ence on Sensi i i y Analysis o Model Ou pu (SAMO
2016), olume 30, 2016, pp. 50–51.
[16] M. Goud eaul , L. M. D’Amb osio, M. J. Kean, M. J. Mullin, B. G. La sen, A. Sanchez, S. Chaudh y, G. I. Chen,
F. Siche i, A. I. Nes izhskii, e al., A pp2a phospha ase high densi y in e ac ion ne wo k iden i ies a no el s ia in-
in e ac ing phospha ase and kinase complex linked o he ce eb al ca e nous mal o ma ion 3 (ccm3) p o ein, Molec-
ula & Cellula P o eomics 8 (2009) 157–171.
[17] Y. Xing, Y. Xu, Y. Chen, P. D. Je ey, Y. Chao, Z. Lin, Z. Li, S. S ack, J. B. S ock, Y. Shi, S uc u e o p o ein
phospha ase 2a co e enzyme bound o umo -inducing oxins, Cell 127 (2006) 341–353.
[18] O. Kauko, S. Y. Imanishi, E. Kulesskiy, L. Ye uku i, T. D. Laajala, M. Sha ma, K. Pa ic, A. Aakula, C. Rupp,
M. Jumppanen, e al., Phosphop o eome and d ug- esponse e ec s media ed by he h ee p o ein phospha ase 2a
inhibi o p o eins cip2a, se , and pme-1, Jou nal o Biological Chemis y 295 (2020) 4194–4211.
[19] K. Wille , S. Shibamo o, R. Nusse, Wn -induced dephospho yla ion o axin eleases β-ca enin om he axin
complex, Genes & de elopmen 13 (1999) 1768–1773.
[20] S. Ikeda, M. Kishida, Y. Ma suu a, H. Usui, A. Kikuchi, Gsk-3β-dependen phospho yla ion o adenoma ous poly-
posis coli gene p oduc can be modula ed by β-ca enin and p o ein phospha ase 2a complexed wi h axin, Oncogene
19 (2000) 537–545.
[21] J. M. Seeling, J. R. Mille , R. Gil, R. T. Moon, R. Whi e, D. M. Vi shup, Regula ion o β-ca enin signaling by he
b56 subuni o p o ein phospha ase 2a, Science 283 (1999) 2089–2091.
[22] X. Deng, T. I o, B. Ca , M. Mumby, W. S. May, Re e sible phospho yla ion o bcl2 ollowing in e leukin 3 o
b yos a in 1 is media ed by di ec in e ac ion wi h p o ein phospha ase 2a, Jou nal o Biological Chemis y 273
(1998) 34157–34163.
[23] A. B ewe , G. Sa he, B. E. P lug, R. G. Cla ke, T. J. Maca ney, G. P. Sapko a, Mapping he subs a e landscape o
p o ein phospha ase 2a ca aly ic subuni ppp2ca, Iscience 27 (2024).
[24] D. A. Bennin, A. S. A. Don, T. B ake, J. L. McKenzie, H. Rosenbaum, L. O iz, A. A. DePaoli-Roach, M. C.
Ho ne, Cyclin g2 associa es wi h p o ein phospha ase 2a ca aly ic and egula o y b’ subuni s in ac i e complexes
and induces nuclea abe a ions and a g1/s phase cell cycle a es , Jou nal o Biological Chemis y 277 (2002)
27449–27467.
[25] C. Shen, W. Lu, S. B. Me ugu, A. Bha i, S. M. A i y, L. Schni key, D. T. Wynn, F. Yang, T. M. Rohwe e , A. Nayak,
e al., Wn signaling inhibi s casein kinase 1αac i i y by modula ing i s in e ac ion wi h p o ein phospha ase 2a,
Cell Repo s 44 (2025).
[26] N. Yu, M. Kakunda, V. Pham, J. R. Lill, P. Du, M. Wongchenko, Y. Yan, R. Fi es ein, X. Huang, Hsp105 ec ui s
p o ein phospha ase 2a o dephospho yla e β-ca enin, Molecula and cellula biology 35 (2015) 1390–1400.
[27] K.-i. Tago, T. Nakamu a, M. Nishi a, J. Hyodo, S.-i. Nagai, Y. Mu a a, S. Adachi, S. Ohwada, Y. Mo ishi a,
H. Shibuya, e al., Inhibi ion o wn signaling by ica , a no el β-ca enin-in e ac ing p o ein, Genes & de elop-
men 14 (2000) 1741–1749.
[28] D. Chu, J. Tan, S. Xie, N. Jin, X. Yin, C.-X. Gong, K. Iqbal, F. Liu, Gsk-3βis dephospho yla ed by pp2a in a leu309
me hyla ion-independen manne , Jou nal o Alzheime ’s Disease 49 (2016) 365–375.
19
[29] O. Gilan, J. Diesch, M. Amalia, K. Jas zebski, A. C. Chueh, N. M. Ve ills, R. B. Pea son, J. M. Ma iadason,
E. Tulchinsky, R. D. Hannan, e al., P 55α-con aining p o ein phospha ase 2a complexes p omo e cance cell
mig a ion and in asion h ough egula ion o ap-1 ansc ip ional ac i i y, Oncogene 34 (2015) 1333–1339.
[30] Q. Shi, B. Xiong, J. Zhong, H. Wang, D. Ma, C. Miao, M has1 supp esses l 4 signaling pa hway ia induc ion o
pp2a c subuni cy oplasm ansloca ion and inhibi ion o c-jun dephospho yla ion a h 239, Molecula Immunology
88 (2017) 79–88.
[31] P. Pognonec, K. E. Boulukos, C. Ape lo, M. Fujimo o, H. A iga, A. Nomo o, H. Ka o, C oss- amily in e ac ion
be ween he bhlhzip us and bzip a1 p o eins esul s in down- egula ion o ap1 ac i i y, Oncogene 14 (1997)
2091–2098.
[32] A. Beh ens, W. Jochum, M. Sibilia, E. F. Wagne , Oncogenic ans o ma ion by as and os is media ed by c-jun
n- e minal phospho yla ion, Oncogene 19 (2000) 2657–2663.
[33] A. R. Cla k, M. Ohlmeye , P o ein phospha ase 2a as a he apeu ic a ge in in lamma ion and neu odegene a ion,
Pha macology & he apeu ics 201 (2019) 181–201.
[34] M. A. Pagano, E. Tibaldi, P. Molino, F. F ezza o, V. T ima co, M. Facco, G. Zago o, G. Ribaudo, L. Leanza,
R. Pe uzzo, e al., Mi ochond ial apop osis is induced by alkoxy phenyl-1-p opanone de i a i es h ough pp2a-
media ed dephospho yla ion o bad and oxo3a in cll, Leukemia 33 (2019) 1148–1160.
[35] J. Chen, J. R. S -Ge main, Q. Li, B56 egula o y subuni o p o ein phospha ase 2a media es alp oic acid-induced
p300 deg ada ion, Molecula and cellula biology 25 (2005) 525–532.
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