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Current Trends in Biotechnology and PharmacyVol. 10 (3) 194-221 July 2016, ISSN 0973-8916 (Print), 2230-7303 (Online)
194
Identification of Secreted Proteins during Protease-Activated Receptor 2 Activation in Gastrointestinal
Smooth Muscle Cells
Sorratod Bosuwan1, Sittiruk Roytrakul2, Karnam S. Murthy3 and Wimolpak Sriwai4*
1Department of Medical Technology, School of Allied Health Sciences, Thammasat University,PathumThani, 12121, Thailand
2Proteomics Research Laboratory, National Center for Genetic Engineering and Biotechnology,PathumThani, 12120, Thailand
3Department of Physiology, VCU Program in Enteric Neuromuscular Sciences, Virginia CommonwealthUniversity, Richmond, Virginia, United States of America
4Department of Medical Technology, School of Allied Health Sciences, Thammasat University,PathumThani, 12121, Thailand
*For Correspondence - [email protected]
Activation in Gastrointestinal Smooth Muscle Cells
AbstractProtease-activated receptor 2 is a
member of G protein-coupled receptor andexpressed in a wide variety of cells. PAR2 isinvolved in several physiological andpathophysiological processes, including growthand development, inflammation, migration, andapoptosis depending on cell types. However, therole of PAR2 in the context of secretory functionof inflammatory proteins in smooth muscle cellsremains unknown. The aim of the present studywas to determine the secretory proteins involvedin inflammatory process upon PAR2 activationin smooth muscle cells. Gastric smooth musclecells were left untreated or treated with PAR2activating peptide (PAR2-AP) SLIGKV (1 µM) forup to 48 hours in serum-free medium. Untreatedmedia were used as negative controls.Secretome were collected at 48 hours andsubjected to proteomic analysis by LC-MS/MS.A total of 310 peptides were detected and foundto correspond to 275 proteins. This approachidentified 160 significant changes in proteinlevels. These proteins were expressed atsignificantly different levels in treated sample ascompared with untreated sample. These proteinscould be classified by their functions ininflammation, proliferation and apoptosis, and
response to stress. It resulted in the first LC-MS/MS based secretome profiles of gastrointestinalsmooth muscle cells. Such secretory protein maybe of pathological significance in the role of PAR2in regulating the inflammation, proliferation, andapoptotic process and may offer protection ofcells against physiological stress.
Keyword: Protease-activated receptor 2, PAR2,Proteomics, LC-MS, Inflammation
IntroductionThe proteinase-activated receptors
(PARs) belong to the family of G protein-coupledreceptors. PARs consist of four members, PAR1,PAR2, PAR3 and PAR4, which can be cleavedby certain serine proteases. These serineproteases derive from leukocyte, coagulationfactors, pathogen, and many different sources.The unique mechanism of activation involvesirreversible enzymatic cleavage of the N-terminusdomains at a specific site and unmasking atethered ligand that triggers intracellular signaling(1-4). Signaling by activated PARs is terminatedby receptor phosphorylation and association withβ-arrestins. PARs also can be activated withoutenzymatic cleavage by synthetic activatingpeptides (PAR-APs), as short as six amino acids.
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Sorratod Bosuwan et al
PAR-APs correspond to the tethered liganddomain that can directly bind to and activatePARs (5, 6).
PAR2 signaling has been implicated in thedevelopment of inflammatory bowel diseases.PAR2 are found on the surface of several celltypes (7) including epithelial cell (1), fibroblasts,endothelial cells (8), keratinocytes (9, 10),sensory neurons (11), inflammatory cells (12),and smooth muscle cell (13). The primaryfunction of smooth muscle cells is to alter thestiffness or diameter of hollow organs bycontracting and relaxing. It has been reportedthat gastric smooth muscle cells constitutivelyexpress high levels of PAR2 and are able tomediate PAR2-AP-induced contraction (13).Growing evidence has shown that smoothmuscle cells secrete highly active signalingproteins, which have a regulatory role in themuscles and other organs via endocrine,autocrine, or paracrine actions (14). It hassignificant capacity to synthesize and secretevarious signaling proteins including cytokines,chemokines, and peptide growth factors (15-17).These active signaling proteins are suggestedto mediate the course of several common andhighly debilitating chronic diseases, such asatherosclerosis (18,19), asthma (20,21), andinflammatory bowel diseases (22). Despiteextensive research on the secretory function ofvascular and airway smooth muscle, there isconsiderably less study regarding gastrointestinalsmooth muscle.
Characterization of the sets of proteinssecreted from smooth muscle cells andsubsequent analysis of their functions are acritical first step in better understanding theregulation of muscle during normal andpathological processes. Here, we sought toidentify the secreted proteome induced by PAR2-AP, SLIGKV.This study uses the rabbit gastricsmooth muscle cell as a model system and aproteomics approach to analyze the secretomeof smooth muscle during PAR2 activation. Weidentified 172 significant changes in protein levelscompared to control and associated with wide
range of biological processes. Among theseproteins, inflammatory proteins such as IL-25,IL-17RE, and TLR2 were found to be secreted.This work expands our knowledge of thesecretory function and potential roles of PAR2on smooth muscle cell. Mediators released fromsmooth muscle may serve as autocrine andparacrine factors that are involved in progressionof an inflammatory process.
Materials and MethodsCell culture : Rabbit gastric smooth muscle cells(a kind gift from Murthy KS., the VCU Programin Enteric Neuromuscular Sciences, VirginiaCommonwealth University, Richmond, Virginia,United States of America) were cultured in DMEMcontaining 200 units/milliliter (U/ml) penicillin, 200milligrams/milliliter(mg/ml)streptomycin, 100 mg/ml gentamycin, 2.5 mg/ml amphotericin B and10% fetal bovine serum (DMEM-10)(13). Thecultured plate was incubated at 37°C in aCO
2incubator. DMEM-10 medium was replaced
every three days for 2–3 weeks until the cellsattained confluence. All experiments were doneon cells in the first passage.
PAR2 activation of smooth muscle cells : ForPAR2 activation experiment, cells were dividedinto two groups: control and PAR2-AP (SLIGKV)(Bachem, Torrance, CA) stimulated smoothmuscle cells. Smooth muscle cells were washedtwice with sterile PBS and then exposed to serumfree medium for 18 - 24 h. PAR2-AP was directlydiluted in cell culture medium of treatment groupto achieve a final concentration of 1 μm. After48-h treatment the serum free conditionedmedium was collected. The resulting supernatantcontains secreted proteins. The supernatant weresubjected to lyophilization and stored at -80°Cuntil experiment was performed. An experimentwas repeated three independent times.
Determination of protein concentration byLowry method : The freeze dry media wereresuspended in 0.5% sodium dodecyl sulfate andprotein concentration was determined by Lowrymethod (23). Absorbance of the solution wasmeasured at 750 nm using a spectrophotometer.
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Activation in Gastrointestinal Smooth Muscle Cells
The protein concentration was be calculatedusing a standard curve of BSA solution.
Prefractionation protein by sodium dodecylsulfate polyacrylamide gel electrophoresis(SDS-PAGE) : Proteins were separated on SDS-PAGE mini gel with the HoeferMiniVEelectrophoresis system (Amersham Biosciences,UK) (8 x 9 x 0.1 cm). The polyacrylamide gelwas prepared according to the method aspreviously described (24). For PAGE, thestacking gel had 5% acrylamide while theseparating gel contained 12.5% in Tris-HCl pH8.3. Fifty micrograms of each protein samplewas then mixed with equal volume of 5Xconcentrated sample buffer (0.125M Tris-HCl pH6.8, 20% glycerol, 5% SDS, 0.2 M dithiothreitol(DTT), 0.02% bromophenol blue) and heat at95oC for 10 min before placingon the gel. Lowmolecular weight protein standard marker(Amersham Biosciences, UK) was used toestimate size of polypeptides.Electrophoresiswas performed in SDS electrophoresis buffer(25mMTris-HCl pH 8.3, 192mM glycine, 0.1%SDS) until the tracking dye reached the bottomof the gel. Performed gels were stained bysilver (25).
In-gel digestion : The gel pieces were subjectedto in-gel digestion using an in-house methoddeveloped by Proteomics Laboratory, GenomeInstitute, National Center for Genetic Engineeringand Biotechnology (BIOTEC), National Scienceand Technology Development Agency (NSTDA),Thailand. In short, protein bands were cut into15 segments according to size and transferredto 96-well plate. The gel pieces were dehydratedwith 100% acetonitrile (ACN), reduced with 10milimolars (mM) DTT in 10mM ammoniumbicarbonate at room temperature for 1 h andalkylated with 100mMiodoacetamide (IAA) in10mM ammonium bicarbonate at roomtemperature for 1 h in the dark. The gel pieceswere dehydrated twice with 100% ACN for 5 minand 10 microliters (µl) of trypsin solution (10 ng/µl trypsin in 50% ACN / 10mM ammoniumbicarbonate) was added for in-gel digestion ofproteins followed by incubation for 20 min at room
temperature. To keep the gels immersedthroughout digestion, 20 µl of 30% ACN wasadded and incubation continued for a few hoursto over night at 37ºC.The digested peptides wereextracted from the gel using 30 µl of 50% ACN in0.1% formic acid and incubation continued whileshaking for 10 min at room temperature.Extracted peptides were collected andtransferred into the new tube. The extractedpeptides were dried by using a speed-vacconcentrator and stored the vial at -80 ºC formass spectrometric analysis.
Identification of protein by liquidchromatography coupled to massspectrometry (LC/MS-MS) configuration :Quantitative LC/MS-MS was performed on 1 μgof protein digest per sample, using ananoACQUITY UPLC system (Waters Corp.,Milford, MA, USA) coupled to a WatersSYNAPT™ HDMS™ system (Waters Corp.,Manchester, UK) via a nanoelectrosprayionization source. Briefly, the sample wasseparated using ananalytical reversed phasecolumn (75 μm × 250 mm, Waters Corp., Milford,MA, USA) packed with 1.7 μm ethylene bridgedhybrid (BEH) C
18 stationary phase. The A solvent
is HPLC grade water with 0.1% formic acid. TheB solvent is acetonitrile with 0.1% formic acid.The sample was initially transferred with a solventto the trap column with a flow rate of 15microliters/minute (μl/min) for 1 min. After whichthe analytical separation was performed using a60-min gradient of 2 to 40% acetonitrile with 0.1%formic acid at a flow rate of 350 nl/min followedby a 15 min rinse of 80% acetonitrile. The columntemperature was maintained at 35 ºC. Theanalysis of tryptic peptides was performed usinga SYNAPT™ HDMS™ mass spectrometer whichwas operated in the V-mode of analysis with aresolution of at least 10,000 full-width half-maximum, using positive nanoelectrospray ionmode. The time-of-flight analyzer of the massspectrometer was externally calibrated with a(Glu1) fibrinopeptide B mixture from m/z 50 to1600. The collision gas used was argon,maintained at a constant pressure of 2.0×10-3
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mbar in the collision cell. The lock mass, (Glu1)fibrinopeptide B, was delivered from the auxiliarypump of the nanoACQUITY system with aconcentration of 100 fmol/μl at 0.5 μl/min to thereference sprayer of the nanolock spray source.The data were post-acquisition lock-masscorrected using the monoisotopic mass of thedoubly charged precursor of (Glu1) fibrinopeptideB, delivered through the reference sprayer, whichwas sampled every 20 s. Accurate massprecursor and fragment ion LC-MS data werecollected with data direct acquisition mode. TheMS/MS survey was over range from 50 to 1990.The intact mass spectra were deconvoluted tothe zero charge state (Ensemble 1, Iterations 50,auto peak width determination) using MaxEnt 3,a deconvolution software available withinMassLynx 4.0.
Proteins quantitation and identification :DeCyder MS differential analysis software(DeCyderMS, GE Healthcare) was used foridentification and quantitation of peptides basedon MS signal intensities of individual LC-MS.Quantitation of peptides was performed usingthe PepDetect module. Peptides were matchedacross different signal intensity maps betweenthe control and treated samples using thePepMatch module. The relative abundances ofpeptides were expressed as log
2 intensities. All
log2 intensities of the sample were normalized
with the ion intensity distribution of a referencestandard, bovine serum albumin (BSA).
The analyzed MS/MS data fromDeCyderMS were submitted to database searchusing the Mascot software version 2.2 (MatrixScience, London, UK). The data was searchedagainst the NCBI database for proteinidentification. Search parameters were taxonomy(Oryctolagus cuniculus); enzyme (trypsin);variable modifications (carbamidomethyl,oxidation of methionine residues); mass values(monoisotopic); protein mass (unrestricted);peptide mass tolerance (1 Da); fragment masstolerance (±0.4 Da); peptide charge state (1+,2+ and 3+); max missed cleavages (1) andinstrument = ESI-QUAD-TOF. Proteins
considered as identified proteins had at least onepeptides with an individual mascot scorecorresponding to p<0.05.
To assign proteins to gene symbols, proteinlists are mapped to corresponding entries inUniProt Knowledgebase (UniProtKB) of all knownproteins based on protein names and sequences.Searches were performed against the Homosapiens protein data sets.
Bioinformatic analysis : Normalizedquantitative data sets were used for subsequentanalyses. A 2-fold cutoff value was set to identifyproteins whose expression was significantlyincreased or decreased. To assign biologicalfunctions and processes to the entire data set ofover-expressed or highly suppressed proteins,Gene ontologies of identified and quantifiedproteins were determined with PANTHERsoftware (http://www.pantherdb.org) andUniprotKB databases (http://www.uniprot.org).Proteins with 2-fold or greater changes inexpression upon treatment were used for gene-pathway annotations using Reactome tools(Reactome V57) (http://www.reactome.org/) andto create protein-protein interaction networks viaSTRING database (Ingenuity Systems, version10.0 (http://string-db.org/). Networks representa highly interconnected set of proteins derivedfrom the input data set. To predict which pathwaysare being affected by the changes in proteinexpression, a Fisher’s exact test was applied tothe mapping of significantly over-expressedproteins in the data set to each pathway todetermine the significance of any over-representation of the proteins to that pathway.
Results
Protein identification and characterization :To identify secretory proteins upon PAR2activation in gastric smooth muscle cell, wesystematically assessed the supernatantcontains secreted proteins or secretome ofsmooth muscle cell activated with specificpeptide, SLIGKV, for 48 hours compared tountreated cells. After LC-MS/MS analysis of theisolated peptides, all MS/MS spectra were
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Activation in Gastrointestinal Smooth Muscle Cells
searched against rabbit protein database. MSanalysis results are summarized in Table 1. A totalof 300 peptides were detected from supernatantacross all samples. The analysis of thesesupernatant samples resulted in the identificationof 271 and 256 peptides under untreated andPAR2-induced conditions, respectively. Weassigned protein names and sequences tohuman gene symbols using UniProtKB based ona target reference of human proteins. Total 300GI numbers obtained from the MS data wereconverted to UniProtKB accession numbers andfound to correspond to275genes.From theseproteins, 212 proteins were common to bothcontrol and treatment sample.
Smooth muscle secretome composition ischanged by PAR2-AP treatment : Functionalclassification of secreted proteins revealed achange in secretome composition after PAR-2AP treatment. Protein expression profiles werecompared between untreated and PAR2-inducedsample. Of the 275 differentially expressedproteins we found that 160 proteins hadexpression levels that differed by more than 2.0fold in treatment sample when compared tountreated sample, comprising 61 up-regulatedand 99 down-regulated proteins (Figure 2A). Weselected the 160 differentially expressed proteinsas candidate secreted proteins associated withPAR2 activation. Details of these proteins arepresented in Table 1. Those proteins weresubjected to K-means clustering having the K-means performs optimally for 6 clusters asdetermined by Figures of Merit (FOM) method(Figure 2B). Cluster analysis classified samplesinto a small number of groups based on thesimilarities of expression. Clearly each of the 6clusters shows proteins specifically expressedin one of the conditions.
Proteins in cluster 2 were highlyexpressed at control condition (Figure 2C),whereas proteins in cluster 3 were highlyexpressed at PAR2 treatment condition (Figure2D). Proteins in cluster 1 and 6 were highlyexpressed in both treated and untreated
conditions but the expressions of proteins incluster 4 and 5 were relatively repressed in bothconditions. In cluster 2, results showed severalproteins involved in metabolic processes, cellularprocesses, and biological regulation.Interestingly, proteins related to immune systemprocess, apoptotic process, and response tostimulus were found. Immune-related protein wasincluded complement component C1q receptor(CD93). Apoptotic-related protein was includedapoptosis-stimulating of p53 protein 2(TP53BP2).In addition, the expressions of dualspecificity mitogen-activated protein kinasekinase 5 (MAP2K5), leucine-rich repeat-containing protein 16A (LRRC16A), low-densitylipoprotein receptor-related protein 6 (LRP6),collagen alpha-1(VII) chain (COL7A1), andpleckstrin homology domain-containing family Gmember 4B (PLEKHG4B) were also observedin this cluster. In cluster 3, immune-relatedproteins (interleukin-25) was identified.
Protein annotation and ontology enrichmentanalysis : To investigate the properties ofidentified proteins, we then performed functionalenrichment of secreted proteins usingPANTHER. The biological characterization ofsecreted proteins could be classified accordingto molecular function, biological process, andcellular component (Figure 1). Gene setenrichment analysis revealed that all thedifferentially expressed proteins were enrichedin 31Gene Ontology (GO) terms (p<0.05),including 10 molecular functions, 13 biologicalprocesses, and 8 cellular components. The geneontology analysis of our secretome suggestedthese genes were associated with GO molecularfunction such as binding (33%), catalytic activity(29%), and receptor activity (10%). The GObiological process results revealed severalproteins involved in metabolic processes (24%),cellular processes (22%), and biologicalregulation (13%). In addition, the GO cellularcomponent results revealed several proteinslocated in cell part (42%), organelle (23%), andextracellular region (11%), and. Proteins thatwere not described or unspecified in the
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Fig. 1. Analysis of functional distribution of smooth muscle phosphoproteins. Gene ontology characterizationof identified phosphoproteins whose expression found to be increased or decreased by 2-fold or greatercompared to control, according to (A) GO molecular functions, (B) GO biological processes, and (C) GOcellular component.
B
C
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A
B
C
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Fig. 2. Heat map of hierarchical clustering analysis of proteins differentially regulated by PAR2.Clustering was done using MeV tools. Analysis was performed based on log2 intensities of 160proteins differentially expressed, between the 1 µM PAR2 treatment and control groups. Rows rep-resent genes and columns represent samples. Color bar indicates log2-intensity value and corre-sponding colors (red, black, and green for up-regulated, not changing and down regulated, respec-tively). The color scale is shown by the bar at the top. Protein genes grouped into 10 clusters on thebasis of the similarity of expression (clustering type: K-means clustering, Distance metric: Euclideandistance). The number of the expressed genes and the percentage in each cluster are indicated. (A)Total, (B) protein clusters, (C) cluster 2, and (D) cluster 3.
Sorratod Bosuwan et al
D
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UniProtKB and GO database were screened outand not further assessed for this report.
Functional classification of secretedproteins revealed a change in secretomecomposition after treatment. Protein expressionprofiles were compared between untreated andPAR2-induced sample. Of the 275 differentiallyexpressed proteins we found that 160 proteinshad expression levels that differed by more than2.0 fold in treatment sample when compared tountreated sample, comprising 61 upregulatedand 99 downregulated proteins (Table 1). Weselected the 160 differentially expressed proteinsas candidate secreted proteins associated withPAR2 activation. Details of these proteins arepresented in Table 1.
In order to identify significantly enrichedpathways and biological processes within thegene sets, pathway and gene ontology wereanalyzed using 160 differentially expressedproteins via DAVID tools. Functional annotationin DAVID showed that10 clusters (cluster 1, 2, 3,4, 5, 6, 8, 9, 13, and 15) were found to besignificantly enriched (p-value < 0.05) for 31 GOterms (Table 2).The majority of enriched clustersof pathways and GObiological processes arerelated to regulation of signal transduction(cluster 1 and 2), developmental process andsegmentation (cluster 3 and 4), cytokinesis andcell cycle (cluster 5 and 6), response to bioticstimulus (cluster 8 and 15), programmed celldeath (cluster 9), nitrogen compound and nucleicacid metabolic process (cluster 13).
To further interpret the likely roles ofdifferentially expressed proteins involved in PAR2activation, these proteins were categorized byReactome cellular pathway. Of the 160differentially expressed proteins we found that99 proteins were mapped into 20 pathways asbeing significantly (p < 0.05) overrepresentedafter PAR2 stimulation. Twenty four biologicalpathways from the Reactome database relevantfor the PAR2 signaling were investigated, andthe most significantly enriched functional pathwayaccording to their p-value and FDR values
wasinterleukin-17 signaling pathway representedin Table 3. The up-regulated protein interleukin-17 receptor E (IL17RE) and interleukin-25 (IL25)(Table 3) was predicted to be involved in thisfunction. The differentially expressed proteinswhich included in top 20 enriched functionalpathways comprised 11 up-regulated and 14down-regulated proteins upon PAR2 activation.
DiscussionIn the present study, we determined the
secretory proteins involved in inflammatoryprocess upon PAR2 activation by PAR2-AP insmooth muscle cells using LC-MS/MS basedmethod. Rabbit gastric smooth muscle was usedbecause human tissue was not readily available.It is best known that smooth muscle can changeits appearance and its function in response to awide array of stimuli. This is referred to as thephenotypic plasticity (26). Smooth muscle canlose its contractile apparatus and become asecretory cell in response to the right stimuli. Ithas been shown that smooth muscle cellssecrete highly active signaling proteins (14),indicating the validity of the approach taken. Wedemonstrate that the PAR2 activation inducesrobust protein secretion in smooth muscle cells.A total of 310 peptides were detected and foundto correspond to 275 proteins. This approachidentified 160 proteins with a 2-fold change intreated sample as compared with untreatedsample. These proteins could be classified bytheir functions in inflammation, cytokinesis andcell cycle, regulation of apoptosis, developmentalprocess and response to stress.
Although many of the altered proteins weremainly related to regulation of small G-proteinsignaling, developmental process, cell cycle andapoptosis, and response to stress, more recentwork has focused on the ability of muscle toinfluence immune function through cytokine andgrowth factor production. Growing evidence hasshown that smooth muscle cells secrete highlyactive signaling proteins (14). Nonetheless,results are limited at this point to a few cytokinesand chemokines such as IL-1 beta (27), IL-8 andIL-6 (20), and monocyte chemotactic protein
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-2.8
40
Tab
le 1
: Id
entif
ied
prot
ein
from
sm
ooth
mus
cle
secr
etom
e an
d re
lativ
e ex
pres
sion
rel
ativ
e ab
unda
nces
of p
eptid
es. P
rote
in n
ames
whi
ch w
ere
iden
tifie
d to
be
sign
ifica
ntly
upr
egul
ated
or
dow
nreg
ulat
ed b
y pr
oteo
mic
exp
erim
ent
wer
e sh
own.
Ana
lysi
s fo
cuse
d on
pro
tein
s w
hose
exp
res-
sion
cha
nged
at
leas
t ±
2 fo
ld in
tre
ated
sam
ple
com
pare
d w
ith c
ontr
ol s
ampl
e. T
he r
elat
ive
abun
danc
es o
f pe
ptid
es w
ere
expr
esse
d as
log2
inte
nsiti
es.
Current Trends in Biotechnology and PharmacyVol. 10 (3) 194-221 July 2016, ISSN 0973-8916 (Print), 2230-7303 (Online)
204D
DB
1- a
nd C
UL4
-ass
ocia
ted
fact
or 5
Q96
JK2
AG
TS
HK
06.
396.
390
Deh
ydro
gena
se/r
educ
tase
SD
R f
amily
mem
ber
9Q
9BP
W9
TF
DE
K0
3.47
3.47
0D
elet
ed in
mal
igna
nt b
rain
tum
ors
1 pr
otei
nQ
9UG
M3
YT
RIP
SR
5.91
4.8
-1.1
10D
eoxy
guan
osin
e ki
nase
, m
itoch
ondr
ial
Q16
854
MA
AG
R7.
910
-7.9
10D
eoxy
nucl
eotid
yltr
ansf
eras
e te
rmin
al-in
tera
ctin
g pr
otei
n 1
Q9H
147
AT
GG
K3.
181
-2.1
80D
NA
rep
licat
ion
licen
sing
fac
tor
MC
M5
P33
992
AG
ITT
TLN
SR
6.28
8.31
2.03
0D
naJ
hom
olog
sub
fam
ily B
mem
ber
2P
2568
6A
GT
QG
GA
RG
DA
AE
R3.
360.
99-2
.370
Dua
l sp
ecifi
city
mito
gen-
activ
ated
pro
tein
kin
ase
kina
se 5
Q13
163
NQ
QG
PP
9.11
2.27
-6.8
40D
ystr
ogly
can
Q14
118
AP
ITR
4.98
0-4
.980
E3
SU
MO
-pro
tein
liga
se E
GR
2P
1116
1N
GV
AG
DG
MIN
IDM
TG
EK
2.77
4.44
1.67
0E
chin
oder
m m
icro
tubu
le-a
ssoc
iate
d pr
otei
n-lik
e 3
Q32
P44
VA
SG
QTA
GV
DK
8.8
1.33
-7.4
70E
cto-
NO
X d
isul
fide-
thio
l ex
chan
ger
2Q
1620
6D
ME
EA
KE
K5.
894.
85-1
.040
Eto
posi
de-in
duce
d pr
otei
n 2.
4 ho
mol
ogO
1468
1A
TAG
H2.
360
-2.3
60E
ukar
yotic
tra
nsla
tion
initi
atio
n fa
ctor
3 s
ubun
it B
P55
884
DR
LSQ
SK
7.28
4.71
-2.5
70F
ER
M,
Rho
GE
F a
nd p
leck
strin
dom
ain-
cont
aini
ng p
rote
in 2
O94
887
ALT
AD
LPR
10.2
37.
41-2
.820
Fla
p en
donu
clea
se G
EN
hom
olog
1Q
17R
S7
VD
TE
AS
K5.
636.
941.
310
For
khea
d-as
soci
ated
dom
ain-
cont
aini
ng p
rote
in 1
B1A
JZ9
LYLD
MS
K2.
36.
574.
270
Gam
ma-
amin
obut
yric
aci
d re
cept
or s
ubun
it ga
mm
a-1
Q8N
1C3
GK
VLA
AR
5.74
7.72
1.98
0G
amm
a-am
inob
utyr
ic a
cid
rece
ptor
sub
unit
rho-
2P
2847
6V
FP
DG
HV
LYS
MR
4.81
6.16
1.35
0G
lyci
ne r
ecep
tor
subu
nit
alph
a-2
P23
416
GR
TS
GY
DA
R7.
060
-7.0
60G
olgi
n su
bfam
ily A
mem
ber
2Q
0837
9S
EE
TR
5.9
7.48
1.58
0H
isto
ne H
2AX
P16
104
AP
SG
GK
6.56
4.1
-2.4
60H
omeo
box
prot
ein
Hox
-A2
O43
364
RV
EIA
ALL
DLT
ER
5.56
0-5
.560
Hyc
cin
Q9B
YI3
QG
HS
K2.
140
-2.1
40E
ukar
yotic
tra
nsla
tion
initi
atio
n fa
ctor
4 g
amm
a 1
Q04
637
GG
PG
GE
LPR
6.47
0.6
-5.8
70In
ter-
alph
a-tr
ypsi
n in
hibi
tor
heav
y ch
ain
H3
Q06
033
AV
SQ
GK
TAG
LVK
4.7
0.47
-4.2
30In
terle
ukin
-17
rece
ptor
EQ
8NF
R9
VA
SD
AS
GLQ
R5.
427.
061.
640
Inte
rleu
kin-
25Q
9H29
3A
SE
DG
PLN
SR
1.39
4.05
2.66
0Ju
ncto
phili
n-3
Q8W
XH
2LG
AR
AE
PR
1.41
4.43
3.02
0K
alir
inO
6022
9E
TS
ER
0.49
4.32
3.83
0K
AT
8 re
gula
tory
NS
L co
mpl
ex s
ubun
it 3
Q9P
2N6
IPT
LID
R5.
817.
041.
230
Ker
atin
ocyt
e pr
olin
e-ric
h pr
otei
nQ
5T74
9V
GG
PR
3.53
5.53
2.00
0K
ines
in-li
ke p
rote
in K
IF18
BQ
86Y
91LQ
AE
VA
ALR
4.18
1.13
-3.0
50Le
iom
odin
-3Q
0VA
K6
ISK
LDP
KK
6.59
4.19
-2.4
00F
-act
in-u
ncap
ping
pro
tein
LR
RC
16A
Q5V
ZK
9E
FIF
V7.
350
-7.3
50Le
ucin
e-ric
h re
peat
-con
tain
ing
prot
ein
42Q
9Y54
6T
PM
AA
EP
R4.
085.
191.
110
Pro
tein
Nam
eU
niP
rot
Pep
tid
eC
on
tro
lP
AR
2L
og
2 F
old
Acc
essi
on
Ch
ang
e
Activation in Gastrointestinal Smooth Muscle Cells
Current Trends in Biotechnology and PharmacyVol. 10 (3) 194-221 July 2016, ISSN 0973-8916 (Print), 2230-7303 (Online)
205Le
ucin
e-ric
h re
peat
-con
tain
ing
prot
ein
47Q
8N1G
4A
DG
ER
05.
035.
030
Leuc
ine-
rich
repe
at-c
onta
inin
g pr
otei
n 7
Q96
NW
7A
SM
TK
2.67
0-2
.670
Lim
bin
Q86
UK
5A
TR
AA
AV
DR
3.59
0-3
.590
Low
-den
sity
lip
opro
tein
rec
epto
r-re
late
d pr
otei
n 6
O75
581
QA
VV
K4.
760
-4.7
60Ly
sine
-spe
cific
dem
ethy
lase
5A
P29
375
ATA
AK
05.
665.
660
Lysi
ne—
tRN
A l
igas
eQ
1504
6A
SG
GK
1.51
3.03
1.52
0M
ajor
fac
ilita
tor
supe
rfam
ily d
omai
n-co
ntai
ning
pro
tein
4A
Q8N
468
ED
AS
SLP
R9.
196.
41-2
.780
Mel
anom
a-as
soci
ated
ant
igen
B1
P43
366
AG
SS
QV
SLR
6.57
3.69
-2.8
80M
etal
tra
nspo
rter
CN
NM
2Q
9H8M
5M
IVG
EE
KK
7.21
5.64
-1.5
70M
ethy
lcyt
osin
e di
oxyg
enas
e T
ET
3O
4315
1G
DE
GR
5.14
2.89
-2.2
50M
inor
his
toco
mpa
tibili
ty a
ntig
en H
13Q
8TC
T9
FF
PA
NF
PN
R3.
470
-3.4
70M
itoge
n-ac
tivat
ed p
rote
in k
inas
e-bi
ndin
g pr
otei
n 1
O60
336
LFS
GV
AN
AR
3.98
0.79
-3.1
90M
utS
pro
tein
hom
olog
5O
4319
6A
AV
LSR
3.58
2.43
-1.1
50N
-ace
tylg
luta
mat
e sy
ntha
se,
mito
chon
dria
lQ
8N15
9G
TG
GS
R6.
485.
12-1
.360
NA
CH
T, L
RR
and
PY
D d
omai
ns-c
onta
inin
g pr
otei
n 9
Q7R
TR
0M
KG
VA
L2.
540.
98-1
.560
NA
DH
deh
ydro
gena
se [
ubiq
uino
ne]
1 al
pha
subc
ompl
ex s
ubun
it 6
P56
556
EA
GG
VX
GD
CLR
K6.
154.
94-1
.210
Nan
ce-H
oran
syn
drom
e pr
otei
nQ
6T4R
5D
SG
DM
SV
R5.
410
-5.4
10N
euro
geni
c lo
cus
notc
h ho
mol
og p
rote
in 3
Q9U
M47
AP
EG
GG
GR
5.25
3.38
-1.8
70N
euro
tryp
sin
P56
730
SV
TK
L5.
360
-5.3
60O
lfact
ory
rece
ptor
4F
3/4F
16/4
F29
Q6I
EY
1K
MK
VA
MQ
RLV
SK
6.67
8.3
1.63
0O
lfact
ory
rece
ptor
6C
3Q
9NZ
P0
NQ
QV
KQ
AF
K0
3.82
3.82
0O
lfact
ory
rece
ptor
6N
1Q
8NG
Y5
TG
ILG
05.
215.
210
PD
Z d
omai
n-co
ntai
ning
pro
tein
8Q
8NE
N9
DTA
LTR
5.81
2.91
-2.9
00P
H a
nd S
EC
7 do
mai
n-co
ntai
ning
pro
tein
1A
5PK
W4
HG
SE
PR
3.44
4.54
1.10
0P
HD
fin
ger
prot
ein
3Q
9257
6M
MG
PLS
QA
SR
04.
094.
090
Phe
nyla
lani
ne—
tRN
A l
igas
e, m
itoch
ondr
ial
O95
363
TIG
GD
LVE
K2.
015.
353.
340
Phe
nyle
than
olam
ine
N-m
ethy
ltran
sfer
ase
P11
086
TAV
GV
1.11
4.92
3.81
0P
leck
strin
hom
olog
y do
mai
n-co
ntai
ning
fam
ily G
mem
ber
4BQ
96P
X9
RA
DLD
GP
R4.
941.
43-3
.510
Ple
ckst
rin h
omol
ogy
dom
ain-
cont
aini
ng f
amily
H m
embe
r 1
Q9U
LM0
AP
GT
PR
4.94
0-4
.940
Ple
xin-
B3
Q9U
LL4
QV
TLS
VP
R9.
227.
58-1
.640
Pol
ypep
tide
N-a
cety
lgal
acto
sam
inyl
tran
sfer
ase
11Q
8NC
W6
MM
GS
VT
VR
07.
337.
330
Pot
assi
um v
olta
ge-g
ated
cha
nnel
sub
fam
ily G
mem
ber
2Q
9UJ9
6LR
CC
AP
VR
5.28
0-5
.280
pre-
rRN
A p
roce
ssin
g pr
otei
n F
TS
J3Q
8IY
81G
VG
RK
1.11
0-1
.110
Pro
babl
e A
TP
-dep
ende
nt R
NA
hel
icas
e D
DX
60Q
8IY
21IA
SK
K3.
640
-3.6
40P
rote
in E
RG
IC-5
3P
4925
7M
AG
SR
02.
762.
760
Pro
tein
Nam
eU
niP
rot
Pep
tid
eC
on
tro
lP
AR
2L
og
2 F
old
Acc
essi
on
Ch
ang
e
Sorratod Bosuwan et al
Current Trends in Biotechnology and PharmacyVol. 10 (3) 194-221 July 2016, ISSN 0973-8916 (Print), 2230-7303 (Online)
206P
rote
in F
AM
24A
A6N
FZ
4LS
SS
YD
FAR
3.75
2.52
-1.2
30
Pro
tein
FA
M60
AQ
9NP
50A
GP
SLK
TT
LKP
KK
6.37
4.33
-2.0
40
Pro
tein
KIB
RA
Q8I
X03
SM
SS
LSP
R4.
642.
88-1
.760
Pro
tein
sal
vado
r ho
mol
og 1
Q9H
4B6
LSA
PS
YLA
R6.
397.
791.
400
Pro
tein
SE
TQ
0110
5S
AP
AA
K2.
060.
34-1
.720
Put
ativ
e he
licas
e M
OV
-10
Q9H
CE
1M
KP
GS
EIS
K2.
780
-2.7
80P
yruv
ate
kina
se P
KLR
P30
613
AA
LGP
K0
4.6
4.60
0
Ral
GT
Pas
e-ac
tivat
ing
prot
ein
subu
nit
alph
a-1
Q6G
YQ
0A
TM
LTD
K1.
570
-1.5
70
Rap
gua
nine
nuc
leot
ide
exch
ange
fac
tor
2Q
9Y4G
8S
SF
GK
07.
117.
110
Ras
-rel
ated
pro
tein
Rab
-4A
P20
338
RD
LDA
ER
2.78
7.5
4.72
0
Reg
ulat
or o
f G
-pro
tein
sig
nalin
g 3
P49
796
AG
GS
R4.
270
-4.2
70
Rem
odel
ing
and
spac
ing
fact
or 1
Q96
T23
AA
AA
R4.
312.
92-1
.390
Ret
inal
-spe
cific
AT
P-b
indi
ng c
asse
tte t
rans
port
erP
7836
3G
NG
FAG
EG
KG
VA
4.61
1.89
-2.7
20
Rho
gua
nine
nuc
leot
ide
exch
ange
fac
tor
11O
1508
5M
IHE
GP
LTW
R6.
084.
87-1
.210
Rho
gua
nine
nuc
leot
ide
exch
ange
fac
tor
17Q
96P
E2
LAD
VLS
PR
8.42
10.7
32.
310
Rho
mbo
id d
omai
n-co
ntai
ning
pro
tein
3Q
9Y3P
4G
PG
PP
03.
423.
420
RIN
G f
inge
r pr
otei
n 17
Q9B
XT
8M
MN
EIQ
K0
5.52
5.52
0S
cave
nger
rec
epto
r cy
stei
ne-r
ich
type
1 p
rote
in M
130
Q86
VB
7Q
LGC
GS
ALK
1.47
0-1
.470
Sec
rete
d fr
izzl
ed-r
elat
ed p
rote
in 2
Q96
HF
1Q
GG
ELV
ITS
VK
2.54
1.36
-1.1
80
Sem
apho
rin-3
FQ
1327
5T
MT
ISS
K0.
963.
012.
050
Ser
ine/
thre
onin
e-pr
otei
n ki
nase
VR
K2
Q86
Y07
DP
VA
VQ
TAK
5.42
3.49
-1.9
30
Ser
ine/
thre
onin
e-pr
otei
n ph
osph
atas
e 2A
65
kDa
regu
lato
ry s
ubun
it A
bet
a is
ofor
mP
3015
4A
AK
GP
ALS
AA
CR
7.34
5.03
-2.3
10S
erin
e-pr
otei
n ki
nase
AT
MQ
1331
5A
AD
IR3.
662.
2-1
.460
Sm
ooth
elin
P53
814
SLS
VLS
PR
4.8
3.49
-1.3
10
Sod
ium
/hyd
roge
n ex
chan
ger
9B1
Q4Z
JI4
AT
VQ
G5.
463.
03-2
.430
Sod
ium
-dep
ende
nt s
erot
onin
tra
nspo
rter
P31
645
GV
AG
DK
6.21
3.9
-2.3
10
Sod
ium
/myo
-inos
itol
cotr
ansp
orte
r 2
Q8
WW
X8
FG
GS
R0
4.16
4.16
0
Str
uctu
ral
mai
nten
ance
of
chro
mos
omes
pro
tein
3Q
9UQ
E7
AA
TG
K4.
115.
981.
870
Syn
emin
O15
061
RS
PG
PG
SP
DR
4.29
3.01
-1.2
80
Pro
tein
Nam
eU
niP
rot
Pep
tid
eC
on
tro
lP
AR
2L
og
2 F
old
Acc
essi
on
Ch
ang
e
Activation in Gastrointestinal Smooth Muscle Cells
Current Trends in Biotechnology and PharmacyVol. 10 (3) 194-221 July 2016, ISSN 0973-8916 (Print), 2230-7303 (Online)
207TA
TA-b
indi
ng p
rote
in-a
ssoc
iate
d fa
ctor
172
O14
981
DA
VE
TN
EK
6.02
3.78
-2.2
40
Tetr
atric
opep
tide
repe
at p
rote
in 2
8Q
96A
Y4
DG
TS
SLP
R7.
556.
29-1
.260
Titi
nQ
8WZ
42N
AV
GV
SLP
R6.
425.
19-1
.230
Toll-
like
rece
ptor
2O
6060
3A
AIK
S2.
083.
181.
100
TO
X h
igh
mob
ility
gro
up b
ox f
amily
mem
ber
3O
1540
5A
IGE
K0.
123.
853.
730
Tran
scrip
tion
fact
or 1
5Q
1287
0R
AG
GA
GS
VV
VV
R3.
180
-3.1
80Tr
ansc
riptio
n fa
ctor
TF
IIIB
com
pone
nt B
’’ ho
mol
ogA
6H8Y
1E
EIG
LVE
K1.
480
-1.4
80
Tran
smem
bran
e pr
otea
se s
erin
e 11
DO
6023
5N
NA
AK
3.33
0-3
.330
Tran
smem
bran
e pr
otei
n 11
9Q
4V9L
6A
GG
PR
3.13
4.93
1.80
0Tr
inuc
leot
ide
repe
at-c
onta
inin
g ge
ne 6
C p
rote
inQ
9HC
J0Q
QE
QK
QLL
K0
9.97
9.97
0
Trip
artit
e m
otif-
cont
aini
ng p
rote
in 4
6Q
7Z4K
8A
GA
IK4.
60.
93-3
.670
Tum
or p
rote
in D
55Q
96J7
7LG
DV
KK
SA
TF
R0
7.76
7.76
0
Tyro
sine
-pro
tein
pho
spha
tase
non
-rec
epto
r ty
pe 1
P18
031
GV
VM
LNR
06.
136.
130
Ubi
quiti
n-co
njug
atin
g en
zym
e E
2 G
1P
6225
3R
KV
AR
CV
R0
2.21
2.21
0U
BX
dom
ain-
cont
aini
ng p
rote
in 1
0Q
96LJ
8T
RP
SLP
R2.
564.
011.
450
Ush
erin
O75
445
GV
IEK
4.38
0-4
.380
Vite
lline
mem
bran
e ou
ter
laye
r pr
otei
n 1
hom
olog
Q7Z
5L0
GN
AE
R3.
080
-3.0
80V
-set
and
im
mun
oglo
bulin
dom
ain-
cont
aini
ng p
rote
in 1
0Q
8N0Z
9S
LLN
LTV
AD
LPR
4.31
5.58
1.27
0
WD
rep
eat
dom
ain-
cont
aini
ng p
rote
in 8
3Q
9BR
X9
GH
AG
K0
3.85
3.85
0
YT
H d
omai
n-co
ntai
ning
pro
tein
1Q
96M
U7
LSS
SV
RA
VR
K5.
713.
61-2
.100
Zin
c fin
ger
FY
VE
dom
ain-
cont
aini
ng p
rote
in 1
Q9H
BF
4A
VP
SR
6.92
1.57
-5.3
50
Zin
c fin
ger
prot
ein
18P
1702
2G
MF
GD
EE
PG
R7.
290.
43-6
.860
Zin
c fin
ger
prot
ein
268
Q14
587
SN
LTD
HQ
R4.
850.
92-3
.930
Zin
c fin
ger
prot
ein
416
Q9B
WM
5H
CS
AK
DS
LR2.
10.
93-1
.170
Zin
c fin
ger
prot
ein
462
Q96
JM2
AR
IIK3.
865.
932.
070
Zin
c fin
ger
prot
ein
574
Q6Z
N55
AT
PT
K0
1.25
1.25
0Z
inc
finge
r pr
otei
n 65
8Q
5TY
W1
TAT
PK
7.45
1.24
-6.2
10
Zin
c fin
ger
prot
ein
717
Q9B
Y31
IHT
GG
KP
HG
CN
K7.
018.
931.
920
Zin
c fin
ger
X-c
hrom
osom
al p
rote
inP
1701
0E
VG
LP3.
315.
972.
660
Pro
tein
Nam
eU
niP
rot
Pep
tid
eC
on
tro
lP
AR
2L
og
2 F
old
Acc
essi
on
Ch
ang
e
Sorratod Bosuwan et al
Current Trends in Biotechnology and PharmacyVol. 10 (3) 194-221 July 2016, ISSN 0973-8916 (Print), 2230-7303 (Online)
208
Tab
le 2
. An
no
tati
on
clu
ster
s w
ith
sig
nif
ican
tly
enri
ched
GO
bio
log
ical
pro
cess
es a
nd
pat
hw
ays
in P
AR
2-A
P tr
eate
d s
amp
les.
Enr
ichm
ent
anal
ysis
was
per
form
ed f
or d
isea
se (
OM
IM_D
ISE
AS
E),
fun
ctio
nal
cate
gori
es (
CO
G_O
NT
OLO
GY
), G
O B
P (
PA
NT
HE
R_B
P_A
LL a
ndG
OT
ER
M_B
P_A
LL)
and
path
way
(K
EG
G a
nd R
eact
ome)
usi
ng D
AV
ID t
ools
(fu
nctio
nal
anno
tatio
n cl
uste
r).
Gen
es o
r te
rms
wer
e ra
nked
base
d on
the
p-v
alue
. O
nly
sign
ifica
nt a
nnot
atio
n te
rms
(p-v
alue
< 0
.05)
are
sho
wn.
FD
R:
fals
e di
scov
ery
rate
.
Cat
ego
ryTe
rmp
-val
ue
FD
R (
%)
Gen
es s
ymb
ols
Ann
otat
ion
Clu
ster
1E
nric
hmen
t S
core
: 2.
06
GO
TE
RM
_BP
_ALL
GO
:005
1056
Reg
ulat
ion
of s
mal
l G
TP
ase
0.00
11.
99O
9488
7, Q
6GY
Q0,
O60
229,
Q96
PE
2,
med
iate
d si
gnal
tra
nsdu
ctio
nQ
8WZ
42,
Q9Y
4G8,
Q96
PX
9, O
1508
5,A
5PK
W4
GO
TE
RM
_BP
_ALL
GO
:003
5023
Reg
ulat
ion
of R
ho p
rote
in0.
001
2.29
O94
887,
O60
229,
Q96
PE
2, Q
8WZ
42,
sign
al t
rans
duct
ion
Q96
PX
9, O
1508
5
GO
TE
RM
_BP
_ALL
GO
:004
6578
Reg
ulat
ion
of R
as p
rote
in0.
008
12.6
9O
9488
7, O
6022
9, Q
96P
E2,
Q8W
Z42
,
sign
al t
rans
duct
ion
Q96
PX
9, O
1508
5, A
5PK
W4
Ann
otat
ion
Clu
ster
2E
nric
hmen
t S
core
: 1.
34
GO
TE
RM
_BP
_ALL
GO
:003
5023
Reg
ulat
ion
of R
ho p
rote
in0.
001
2.29
O94
887,
O60
229,
Q96
PE
2, Q
8WZ
42,
sign
al t
rans
duct
ion
Q96
PX
9, O
1508
5
GO
TE
RM
_BP
_ALL
GO
:004
6578
Reg
ulat
ion
of R
as p
rote
in0.
008
12.6
9O
9488
7, O
6022
9, Q
96P
E2,
Q8W
Z42
,
sign
al t
rans
duct
ion
Q96
PX
9, O
1508
5, A
5PK
W4
Ann
otat
ion
Clu
ster
3E
nric
hmen
t S
core
: 1.
27
GO
TE
RM
_BP
_ALL
GO
:003
5282
Seg
men
tatio
n6.
80E
-04
1.09
Q13
315,
Q96
HF
1, P
1116
1, Q
1287
0, O
4336
4
GO
TE
RM
_BP
_ALL
GO
:000
3002
Reg
iona
lizat
ion
0.00
69.
54Q
1331
5, Q
96H
F1,
O75
581,
P11
161,
Q12
870,
O43
364,
Q9H
2X0
GO
TE
RM
_BP
_ALL
GO
:000
7420
Bra
in d
evel
opm
ent
0.01
015
.98
Q13
315,
O15
078,
P31
645,
P51
587,
P11
161,
O43
364,
Q9U
M47
, Q
9H2X
0
GO
TE
RM
_BP
_ALL
GO
:000
7389
Pat
tern
spe
cific
atio
n pr
oces
s0.
024
33.0
9Q
1331
5, Q
96H
F1,
O75
581,
P11
161,
Q12
870,
O43
364,
Q9H
2X0
GO
TE
RM
_BP
_ALL
GO
:000
9952
Ant
erio
r/po
ster
ior
patte
rn
form
atio
n0.
029
38.6
8Q
1331
5, Q
96H
F1,
O75
581,
Q12
870,
O43
364
GO
TE
RM
_BP
_ALL
GO
:000
1756
Som
itoge
nesi
s0.
032
41.4
7Q
1331
5, Q
96H
F1,
Q12
870
Activation in Gastrointestinal Smooth Muscle Cells
Current Trends in Biotechnology and PharmacyVol. 10 (3) 194-221 July 2016, ISSN 0973-8916 (Print), 2230-7303 (Online)
209
Ann
otat
ion
Clu
ster
4E
nric
hmen
t S
core
: 1.
18
GO
TE
RM
_BP
_ALL
GO
:004
8856
Ana
tom
ical
str
uctu
re0.
015
21.3
6Q
96H
F1,
Q9U
GM
3, P
2090
8, Q
8WZ
42,
deve
lopm
ent
O4
33
64
, Q
9B
PW
9,
Q1
31
63
, Q
6T
4R
5,
Q1
33
15
, O
15
07
8,
P5
38
14
, Q
9U
M4
7,
Q1
411
8,
A5
PK
W4
, Q
02
38
8,
O9
48
87
,P
2341
6, P
3164
5, P
3535
4, P
1116
1, O
7544
5,Q
9Y
5Q
5,
O6
02
29
, P
09
54
3,
O7
55
81
,Q
12
87
0,
P5
15
87
, Q
9H
2X
0,
Q9
NQ
Y0
,Q
1327
5, Q
9H29
3, O
1508
5G
OT
ER
M_B
P_A
LLG
O:0
0072
75 M
ultic
ellu
lar
orga
nism
al d
evel
opm
ent
0.02
836
.70
Q9
6H
F1
, Q
9U
GM
3,
P2
09
08
, Q
8W
Z4
2,
Q9
BP
W9
, O
43
36
4,
Q1
31
63
, Q
6T
4R
5,
Q1
33
15
, O
15
07
8,
P5
38
14
, P
29
37
5,
Q9
UM
47
, Q
14
118
, A
5P
KW
4,
Q0
23
88
,O
9488
7, P
2341
6, P
3164
5, P
3535
4, P
1116
1,Q
9U
LL
4,
O7
54
45
, Q
9B
XT
8,
Q9
Y5
Q5
,Q
9257
6, O
6022
9, P
0954
3, O
7558
1, Q
1287
0,P
5158
7, Q
9H2X
0, Q
1327
5, Q
9H29
3G
OT
ER
M_B
P_A
LLG
O:0
0325
02 D
evel
opm
enta
l pr
oces
s0.
038
46.1
7Q
96
HF
1,
Q9
UG
M3
, P
20
90
8,
Q8
WZ
42
,Q
9B
PW
9,
O4
33
64
, Q
13
16
3,
Q6
T4
R5
,Q
13
31
5,
O1
50
78
, P
53
81
4,
P2
93
75
,Q
9U
M4
7,
Q1
411
8,
A5
PK
W4
, Q
02
38
8,
O94
887,
P23
416,
P31
645,
P35
354,
P11
161,
O7
54
45
, Q
9U
LL
4,
Q9
BX
T8
, Q
9Y
5Q
5,
Q92
576,
O60
229,
P09
543,
O75
581,
Q12
870,
P5
15
87
, Q
9H
2X
0,
Q9
NQ
Y0
, Q
13
27
5,
O15
085,
Q9H
293
GO
TE
RM
_BP
_ALL
GO
:003
2501
Mul
ticel
lula
r or
gani
smal
pro
cess
0.04
249
.69
Q9
UG
M3
, Q
96
HF
1,
P2
09
08
, Q
8W
Z4
2,
P7
83
63
, O
43
19
6,
O6
02
35
, Q
9B
PW
9,
O4
33
64
, Q
8N
1C
3,
Q1
31
63
, Q
6T
4R
5,
Q9
NZ
P0
, Q
13
31
5,
O1
50
78
, P
53
81
4,
P2
93
75
, Q
9U
M4
7,
Q1
411
8,
A5
PK
W4
,P
1610
4, Q
0238
8, O
9488
7, Q
6IE
Y1,
P23
416,
P31
645,
P35
354,
P49
257,
P11
161,
O75
445,
Q9
UL
L4
, Q
9B
XT
8,
Q9
Y5
Q5
, Q
92
57
6,
O6
02
29
, Q
7Z
5L
0,
P0
95
43
, Q
8N
GY
5,
O7
55
81
, Q
12
87
0,
P5
15
87
, P
28
47
6,
Q9H
2X0,
Q13
275,
O15
085,
Q9H
293
Sorratod Bosuwan et al
Current Trends in Biotechnology and PharmacyVol. 10 (3) 194-221 July 2016, ISSN 0973-8916 (Print), 2230-7303 (Online)
210
Ann
otat
ion
Clu
ster
5
Enr
ichm
ent
Sco
re:
1.04
GO
TE
RM
_BP
_ALL
GO
:000
0910
Cyt
okin
esis
0.04
653
.20
P51
587,
Q9N
QY
0, O
1508
5
Ann
otat
ion
Clu
ster
6E
nric
hmen
t S
core
: 0.
94G
OT
ER
M_B
P_A
LLG
O:0
0071
26 M
eios
is0.
001
2.19
Q13
315,
P46
013,
O43
196,
P51
587,
Q9U
QE
7, P
1610
4G
OT
ER
M_B
P_A
LLG
O:0
0513
27 M
pha
se o
f m
eiot
ic c
ell c
ycle
0.00
12.
19Q
1331
5, P
4601
3, O
4319
6, P
5158
7, Q
9UQ
E7,
P16
104
GO
TE
RM
_BP
_ALL
GO
:005
1321
Mei
otic
cel
l cy
cle
0.00
22.
39Q
1331
5, P
4601
3, O
4319
6, P
5158
7, Q
9UQ
E7,
P16
104
GO
TE
RM
_BP
_ALL
GO
:000
7292
Fem
ale
gam
ete
gene
ratio
n0.
002
3.37
Q13
315,
Q7Z
5L0,
P35
354,
O43
196,
P51
587
GO
TE
RM
_BP
_ALL
GO
:000
6259
DN
A m
etab
olic
pro
cess
0.02
634
.58
Q13
315,
P33
992,
Q01
105,
Q99
828,
Q17
RS
7,O
4319
6, P
5158
7, Q
6VM
Q6,
Q9U
QE
7, P
1610
4G
OT
ER
M_B
P_A
LLG
O:0
0062
81 D
NA
rep
air
0.03
240
.77
Q13
315,
Q99
828,
Q17
RS
7, O
4319
6, P
5158
7,Q
9UQ
E7,
P16
104
Ann
otat
ion
Clu
ster
8E
nric
hmen
t S
core
: 0.
84G
OT
ER
M_B
P_A
LLG
O:0
0096
07 R
espo
nse
to b
iotic
stim
ulus
0.04
250
.10
Q9U
GM
3, P
3061
3, P
3535
4, O
4319
6,P
2568
6, O
6060
3, P
1885
0, Q
9H29
3
Ann
otat
ion
Clu
ster
9E
nric
hmen
t S
core
: 0.
78G
OT
ER
M_B
P_A
LLG
O:0
0069
17 I
nduc
tion
of a
popt
osis
0.01
825
.27
Q13
315,
O60
229,
Q13
625,
Q96
PE
2,O
1468
1, P
5158
7, O
6060
3, O
1508
5G
OT
ER
M_B
P_A
LLG
O:0
0125
02 I
nduc
tion
of p
rogr
amm
ed0.
018
25.6
0Q
1331
5, O
6022
9, Q
1362
5, Q
96P
E2,
cell
deat
hO
1468
1,
P51
587,
O60
603,
O15
085
GO
TE
RM
_BP
_ALL
GO
:004
3065
Pos
itive
reg
ulat
ion
of a
popt
osis
0.02
836
.52
Q13
315,
O60
229,
Q13
625,
Q96
PE
2,P
3535
4, O
1468
1, P
5158
7, O
6060
3, O
1508
5G
OT
ER
M_B
P_A
LLG
O:0
0430
68 P
ositi
ve r
egul
atio
n of
0.02
937
.57
Q13
315,
O60
229,
Q13
625,
Q96
PE
2,pr
ogra
mm
ed c
ell
deat
hP
3535
4, O
1468
1, P
5158
7, O
6060
3, O
1508
5G
OT
ER
M_B
P_A
LLG
O:0
0109
42 P
ositi
ve r
egul
atio
n of
cel
l de
ath
0.02
938
.28
Q13
315,
O60
229,
Q13
625,
Q96
PE
2, P
3535
4,O
1468
1,P
5158
7, O
6060
3, O
1508
5A
nnot
atio
n C
lust
er 1
3
Enr
ichm
ent
Sco
re:
0.69
GO
TE
RM
_BP
_ALL
GO
:000
6807
Nitr
ogen
com
poun
d m
etab
olic
0.02
129
.36
Q96
MU
7, Q
9BY
31,
O43
196,
Q96
L58,
proc
ess
Q9
HC
E1
, O
43
36
4,
Q
6V
MQ
6,
Q9
BW
M5
,Q
9BR
X9,
Q13
315,
A5Y
KK
6, Q
96JM
2, Q
17R
S7,
P17
022,
Q14
587,
Q01
433,
P29
375,
Q9U
QE
7,Q
3L8U
1, Q
9UM
47,
P16
104,
Q8N
159,
Q06
033,
Q01
105,
Q99
828,
Q5T
YW
1, Q
8IY
81,
P11
086,
Q0
46
37
, P
111
61
, A
6H
8Y
1,
P3
39
92
, Q
15
04
6,
Q92
576,
Q96
T23
, Q
6ZN
55,
O95
363,
P09
543,
P17
010,
Q12
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Sorratod Bosuwan et al
Current Trends in Biotechnology and PharmacyVol. 10 (3) 194-221 July 2016, ISSN 0973-8916 (Print), 2230-7303 (Online)
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(MCP) (18). These active signaling proteins aresuggested to be very important in cell proliferation(28) and the development of non-immunediseases with etiological origins in inflammatoryprocesses such as atherosclerosis (18) as wellas that of immune system disorders like asthma(20) and inflammatory bowel diseases (29,30).However, considering the variety of secretoryproteins that are available much less is knownconcerning the proteins that synthesize andsecrete from gastrointestinal smooth musclecells and their significance of these proteins inthe context of inflammatory processes, and thepresent discussion will therefore be restricted toproteins involved in inflammatory responses,growth and cell survival.
PAR2 influences the secretion of inflamma-tory molecules : Role of PAR2 in the regulationof inflammation is supported by several studies.Inflammatory mediators such as interleukin 1alpha, tumor necrosis factor alpha andlipopolysaccharide increased the expression ofPAR2 in cultured human umbilical veinendothelial cells (31). PAR2 activation alsostimulates the release of prostanoids inendothelial cells (32) as well as the release ofIL-6, IL-8 and PGE2 in fibroblasts (33). In thegastrointestinal tract, PAR2 has been reportedto be constitutively expressed in various cell typessuch as smooth muscle cells, interstitial cells ofCajal, and enterocytes (1,13, 34). Recentevidence has shown that activation of PAR2increase impairment of the epithelial barrier,neutrophil infiltration, and pro-inflammatorycytokines secretion (22, 35) which areparameters of inflammation.
In this study, the immune-related proteinsof smooth muscle cell in response to PAR2 havebeen characterized. In our quantitative secretomeanalysis, the secreted proteins released fromsmooth muscle cells during PAR2 activationincluding cytokine (IL-25) and receptors (IL-17REand TLR2).
IL-25 (also known as IL-17E) can stimulatethe production of IL-10 and inhibits production ofmucosal IFN-gamma in DSS-induced colitis (36).
IL-25 also promotes type 2 helper T (Th2) cellresponses (37). Type 2 responses assist with theresolution of cell-mediated inflammation.Recombinant IL-25 is able to significantly inhibitthe production of IL-1 beta, IL-6, and TNF-alphaby peripheral blood mononuclear cells from activeVogt-Koyanagi-Harada syndrome patients (38).Contrary to these findings, it has been shownthat IL-17E induces activation of NF-kB andstimulates production of the proinflammatorychemokine IL-8 in renal cell carcinoma cell lines(39).
IL-17RE is a specific receptor for IL-17C(40). Activation of IL-17RE stimulates toproduction of antibacterial peptides as well aspro-inflammatory molecules such as TNF and IL-1 betavia NF-kB and MAPK signaling pathway(40-43). In contrast to that IL-17 may play aprotective role depending on the state of disease.There is evidence shown that IL-17R-deficientmice are more susceptible to alveolar bone lossinduced by P. gingivalis (23). These protectiveeffects of IL-17 could be attributed to its ability toregulate COX-2 and PGE2 production.
In addition, we showed that TLR2 is presentin culture supernatant of smooth muscle cells,its levels is increased after PAR2 activation.Inagreement with our results, recent evidence hasidentified a linkage between PAR2 and TLR2.PAR2 is needed for TLR2 mRNA expression asdetermined by silencing PAR2 in culturedepithelial cells with subsequent bacterialstimulation (44).TLR over-activation may lead toend organ damage and serious acute and chronicinflammatory conditions. Therefore, TLRresponses must be tightly regulated to controldisease outcomes. A soluble form of TLR2(sTLR2) has recently been identified as aregulator of TLR2-mediated inflammatoryresponses to bacteria. sTLR2 acts as a decoymicrobial receptor and disrupts the interactionof TLR2 with its co-receptor, CD14. Therefore, itis capable of blunting immune responses withoutabrogating microbial recognition (45). Thepresent study shows that TLR2 is identified inculture supernatant of smooth muscle cell and
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assumed to be in its soluble from which mayparticipate in regulating the inflammatoryresponse. Taken together, PAR2 may contributeto protective role during inflammation sincePAR2-AP stimulates secretion of IL-25, IL-17RE,and TLR2 from smooth muscle cells.
Protein expression profiling of culturesupernatant revealed down-regulation ofprostaglandin G/H synthase 2 (PTGS2), sCD93,and CD163 during PAR2 activation.PTGS2 (alsoknown as cyclooxygenase-2 or COX-2) convertsarachidonate to prostaglandin H2 (PGH2) whichcan then be metabolized to several products withdiffering biologic activities, including prostacyclin,thromboxane, prostaglandin D2, prostaglandinE2, and prostaglandin F2a. Prostanoids exertboth pro-inflammatory and anti-inflammatoryactions not only by acting as mediators of acuteinflammation but also by regulating geneexpression in mesenchymal and epithelial cellsat inflammatory site. The present study showsthat the smooth muscle cells secrete COX-2either constitutively or after stimulation withPAR2-AP. Cox-2 is an endoplasmic reticulum-resident enzyme and its expression is inducible(46). In agreement with our results, COX-2 iscapable of secreting from goblet cells into theintestinal lumen along with mucins. High mucinCOX-2 from goblet cells may increase luminalprostaglandin synthesis, alter epithelialpermeability, and modulate intestinal immuneresponses (47). Thus reduced level of COX-2after stimulation with PAR2-AP may lead to theanti-inflammatory effects.
sCD93 is a receptor for complement C1q,mannose-binding lectin (MBL2), and pulmonarysurfactant protein A (SPA) (48-50). The functionof sCD93 is involved in removal or destruction ofpathogens and immune complexes mediated bymonocyte and macrophage phagocytosis (50).A soluble form of CD93 (sCD93) has recentlybeen identified (51). It was demonstrated thatsCD93 level is increased during inflammation invivo (52). Serum level of sCD93 is increased inasthmatic patients compared to healthy controls(53). High level of sCD93 in peritoneal lavage
fluid from wild-type mice significantly enhancesengulfment of apoptotic cells in vitro whencompared to inflammatory fluid from sCD93-deficient mice[52].Consistent with the previousobservation that sCD93 induced monocyteadherence and enhanced phagocytosis (54) .Thus, reduced level of sCD93 after PAR2activation may lead to defective clearance ofapoptotic cells. To our knowledge, this is the firstreport to identify the smooth muscle cells as asource of sCD93.
CD163 is a cell surface glycoprotein thatis required for clearance and endocytosis ofapoptotic cells or hemoglobin/haptoglobincomplexes by macrophages (55). Recentlysoluble form of CD163 (sCD163) has beenidentified. Soluble CD163 is a normal plasmaprotein with normal level to be in the range of0.7–4.69 ìg/ml (56). sCD163 actively inhibitsphorbol-ester-induced proliferation oflymphocytes (57). Only the soluble form of theCD163 participates in anti-inflammation byinhibition of activated T-lymphocyte,whereas theclearance of hemoglobin uses CD163 in its cell-bound form (58). These observations confirm thatsCD163 participates in the anti-inflammatoryprocess, through the reduction of immuneresponse. Thus, reduced level of sCD163 afterPAR2 activation may lead to the reduction of anti-inflammatory response.
Taken together, our data support previousstudies that PAR2 is capable of regulatinginflammation through not only on upregulationof pro-inflammatory mechanisms but also onsuppression of the anti-inflammatory responseby smooth muscle cells.Activation of PAR2stimulates the release of cytokine and solubleproteins such as IL-25, IL-17RE and TLR2 whichfurther stimulatethe production of pro-inflammatory cytokines and immunoregulatingcytokines. In addition, activation of PAR2attenuates an anti-inflammatory program throughsuppression of sCD93,sCD163,and COX-2secretion.Further studies are needed to addresshow IL-25, IL-17RE, TLR2, COX-2, sCD93, andsCD163 fit into the existing network of the
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numerous inflammatory and anti-inflammatoryproteins.
PAR2 positive regulation of apoptosis andcell cycle : Apoptosis is a physiologicalphenomenon. The significance of apoptosis isto remove senescent cells (59) and the overfunctional cells. Deregulation of apoptosis isassociated with the pathogenesis of a numberof disorders, such as tumor cell growth.Interestingly, differentially expressed proteinsrelated to apoptotic process were found uponactivation of PAR2. In our quantitative secretomeanalysis, the secreted proteins identified includedserine-protein kinase ataxia telangiectasiamutated (ATM), breast cancer type 2susceptibility protein (BRCA2), and apoptosis-stimulating of p53 protein 2 (ASPP2).
ATM is a serine protein kinase implicatedin cell cycle regulation and DNA repair (60).UponDNA damage, eukaryotic cells activate multipleevents such as ATM-Chk2 and/or ATR-Chk1checkpoint to arrest the cell cycle and initiate DNArepair (61). If damage is beyond repair, ATMkinase employs apoptosis to remove excessivelydamaged cells and stimulates cytokine secretionto alert neighboring cells. A defect in ATM kinasehas severe consequences in repairing certaintypes of damage to DNA. All ataxia telangiectasia(AT) patients contain mutations in the ATM gene.ATM kinase is the DNA repair gene shown to beinvolved in cancer predisposition. Leukemia andlymphoma is the most frequently malignancyfound in 38% of AT homozygotes (62). ATMkinase alterations are present at diagnosis inabout 25% of individuals with chronic lymphocyticleukemia. These alterations are associated witha poor prognosis (63). The mutated ATM genespredispose to breast cancer development andadverse radiotherapy responses (64). ATMkinase augments cell survival by activating NF-kappaB (65,66).ATM kinase is also able topromote the phosphorylation of cyclin D1 Thr286(67). Phosphorylation of cyclin D1 promotes thenuclear-to-cytoplasmic redistribution of cyclin D1during S phase of the cell cycle and inhibits the
process of cell division (68). Therefore, ATMkinase appears essential for regulated celldivision. There has thus far, been one report inwhich activation of PAR2 promoted DNAsynthesis, upregulated Cyclin D1 activity, andincreased colonic cancer cell proliferation (69).The present study shows that activation of PAR2promotes ATM kinase secretion by smoothmuscle cell. This result implies possible role ofPAR2 in the regulation of cell division and mayinvolve in the manipulation of cell survivaloutcomes after cell stress.
Breast cancer type 2 susceptibility protein(BRCA2) is a human tumor suppressor gene andresponsible for repairing DNA. BRCA2 proteinhas been shown to be able to bind to RAD51,p53, and p21WAF-1/CIP1 proteins. It has been shownthat BRCA2-defective cancer cells are unable torepair the double-strand DNA breaks induced byionizing radiation (70). Deficiency of eitherRAD51 or BRCA2 protein in embryonic miceleads to extreme sensitivity to irradiation,suggesting a role in double-stranded DNA breakrepair (71). Both p21WAF-1/CIP1 and p53 protein areknown to cause cell cycle arrest, implicatingBRCA2 in the DNA repair process. BRCA2protein is associated with high risks of breastcancer.BRCA2 is a nuclear protein and is inducedin late G1/earlyS phase, before DNA synthesis(72,73). In spite of this BRCA2 protein hassequence homology and biochemical analogy tothe granin family of secreted proteins, suggestingBRCA2 is a secreted protein (74). Bernard-Gallon et al. (75) demonstrated that BRCA2proteins are localized in the cytoplasm and cellnuclei of normal mammary tissues, ofcarcinomas in situ, and of invasive carcinomasas well as in secretions inside the ducts ofmammary tissue. However, the breast is anexocrine gland, thus becoming secretory innature. Surprisingly, we identify BRCA2 proteinfrom supernatant of primary cultured smoothmuscle cell using LC-MS/MS method. Althoughthe primary role of smooth muscle cells iscontraction, they exhibit their specializedsecretory function. Our finding suggests that
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BRCA2 protein is secreted in the secretome ofsmooth muscle cell and the secretion isdecreased in the presence of PAR2-AP. Reducedlevels of BRCA2 protein in cells may allow theaccumulation of unrepaired DNA damages andcan lead to increased mutations. Some of thesemutations can cause cells to divide in anuncontrolled way and form a tumor.To ourknowledge, this is the first report to identify thesmooth muscle cells as a source of BRCA2protein.
Apoptosis-stimulating of p53 (ASPP)protein 2 (also called ASPP2) is a pro-apoptoticregulator that belongs to a member of ASPPfamily of p53 interacting proteins. ASPP2regulates apoptosis and cell growth throughinteractions with other regulatory moleculesincluding members of the p53 family.ASPP2induces apoptosis via stimulation the apoptoticfunction of p53 but not cell cycle arrest (76). Co-expression of ASPP2 with p53 significantlyenhanced the transactivation function of p53 onpromoters of proapoptotic genes, such as Baxand PIG3 (76).The expression of ASPP2 isfrequently suppressed in many cancers (77-79).Here, we identify ASPP2 from supernatant ofprimary cultured smooth muscle cells. Theprotein level of ASPP2 is absent in cellsstimulated with PAR2-AP but increases inuntreated samples. In pathological conditions, theexpression of ASPP2 can suppress tumor growthand confer cellular sensitivity to treatments. Lackof costimulators of p53, as in case of PAR2-activation, could also account for the loss of thetumor suppressor function of p53 which maycontribute to increase cell survival. Hence, PAR2may inhibit the apoptotic function of p53 by lowerASPP2 protein level.
Proteases activate PARs by irreversiblecleavage, so that the exposed tethered ligand isalways available to interact with the cleavedreceptor. Thus activation would result insustained signaling unless there were efficientmechanisms to terminate the signal.Nonetheless, during normal physiologicalcondition, signaling by PAR2 is efficiently
terminated by receptor phosphorylation andassociation with β-arrestins (80). In addition, theaction of protease can be terminated by itsremoval from the vicinity of the receptor. Alteredendothelial or epithelial integrity is thought toexpose the underlying smooth muscle cells toproteases that derive from the circulation,inflammatory cells, and from intestinal lumen.Thus proteases are always available for receptoractivation. Prolonged activation of PAR2 altersprotein secretion patterns in gastrointestinalsmooth muscle cells. Here we reported that manyof the altered proteins were mainly related toregulation of small G-protein signaling,developmental process, cell cycle, apoptosis, andresponse to stress. Interference with the normalsignaling by prolonged activation of PAR2 canalter the balance among the different pathwaysresponding to that signal, thus generatingfunctional heterogeneity that may affectproliferation, quiescence, survival, apoptosis, orinflammation.Many proteases that activate PARsare produced during inflammation. Theseproteases derive from inflammatory cells, thecoagulation cascade and other sources. Besideexpression of PARs themselves are also elevatedduring inflammation (31). PAR2 agonists activatethe NF-kappa B pathway in keratinocytes (81)and endothelial cells (82). NF-kappa B is knownto regulate the expression of many genesincluding immune-mediating genes andinflammatory genes, anti-apoptotic genes, cellproliferation regulation genes, and genesencoding negative regulators of NF-kappa B(83).These observations indicate that NF-kappa Bmay play a critical role in the pathogenesis ofchronic inflammation. Recent evidences havesuggested that NF-kappa B is a key regulator ofinflammation-induced tumor development (84).NF-kappa B stimulates cell proliferation andactivates the expression of growth factor genes,proto-oncogene c-MyC (85), and cyclin D1 (86),suggesting that NF-kappa B contributes to cancerdevelopment. PAR2 antagonists can also reduceinflammation, emphasizing the importance ofPAR2 in inflammation. Growing evidencesuggests that PAR2 play important roles in
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pathogenesis of chronic inflammation, such asinflammatory bowel disease (29). In addition,PAR2 may also contribute to tumor formation andmetastasis since PAR2-AP stimulatesproliferation of colon tumor cell lines (69,87).PAR2 is expressed by a wide range of tumor cells(1, 87, 88). These observations emphasize theroles in chronic inflammation and tumor growth.
ConclusionsIn summary, the study successfully
identified proteins that are differentially secretedby smooth muscle cells upon activation by PAR2activating peptide. The results of this studyprovide the first overview of alterations in thesecretome of culture smooth muscle cells uponactivation with PAR2-AP. Such secreted proteinsmay be of pathological significance in the role ofPAR2 in regulation the inflammation, proliferation,and apoptotic process. Combining candidatesecreted proteins with the actual abundance andfunction of these proteinsprovides insights intotheir biological importance in physiological andpathological states. Secreted proteins derivedfrom smooth muscle cells during pathologicalstates may contribute to chronic inflammation orcancer prevention. However, more studies arerequired to elucidate the mechanisms by whichPAR2 mediate its secretory effects on smoothmuscle cell in inflammation orcancer. Additionalevaluation of diseased tissues or tumorsamples with LC-MS/MS may also help identifycellular proteins biologically important for thedevelopment and progression of human disease.
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