Modeling and Controlling TGF- Pathway Using

Standard Petri Nets

Niloofar Nickaeen, Jafar Ghaisari, IEEE Senior Member

Yousof Gheisari, Shiva Moein

Dept. of Electrical and Computer Eng.

Isfahan University of Technology
Isfahan, 84156-83111, Iran
Email: ghaisari@cc.iut.ac.ir

Regenerative Medicine Lab, Isfahan Kidney Diseases

Research Center, Isfahan University of Medical Sciences
Isfahan, Iran
Email: ygheisari@gmail.com

AbstractCell growth is controlled by some factors known as

growth factors. One of these growth factors is a substance called
TGF-. Any malfunction in the system which growth factors
perform in, results in drastic cell growth thus cell death. The aim
of this study is to control the system of TGF- growth factor in
the case of fibrosis, a condition created by malfunction in the
pathway of TGF-. A model of TGF- pathway is proposed using
standard Petri Nets. Then a control is proposed not only to
control the amount of TGF- in the pathway but also to observe
the law of conservation of matter as the absolute rule in
biological systems. The results clearly show the control of TGF-
concentration in the pathway. The research may provide a basis
for drug design and determination of target reactants to control
fibrosis.

(ODE). A search was done in the parameter space in order to

identify the most important factors involved in oscillatory
responses of the pathway. In [2], authors modeled the pathway
using ODEs and estimated series of parameters to create
certain types of outputs e.g. oscillatory responses. In [3], again
an ODE model of TGF- pathway was constructed and
robustness analysis was done using the model. In [4], an ODE
model of the TGF- pathway is developed and the importance
of negative feedback motifs in the pathway is investigated. [14] study the dynamic behavior of TGF- pathway using the
models constructed based on the literature. Yet, neither has
tried to use mathematical approaches to determine the target
substances to control malfunctions in this pathway which
usually results in drastic conditions.
In this paper, the TGF- pathway is modeled using
standard Petri Nets. Gathering data from literature, a more
sophisticated model is presented. Several reactions involved in
TGF- pathway which have not been noticed in previous
studies have been used in this modeling. To decrease the
effects of malfunctions in the pathway, a control based on the
biological network structure is proposed. The control consists
of adding a place representing a drug to the pathway such that
a P-invariant is created in the new net. Using this P-invariant,
the control is applied to the system. As a result of the control,
TGF- density stays under a limited boundary.

Keywords TGF-; Ptri Nets; Fibrosis; Biological Networks;

Biological Modeling; P- invariants.

I.

INTRODUCTION

Particularly, in the last two decades, engineering and

applied mathematics have been widely used in modeling and
analysis of biological networks. A pathway is defined by some
chemical reactions occurring sequentially so that the product
of each reaction is the reactant for the upcoming reaction.
TGF- pathway is a pathway responsible for many behaviors
of the cell such as cell growth or differentiation. TGF- is a
growth factor, a factor which results in the cell growth. If as a
result of a malfunction in the pathway the amount of growth
factors increase upon some limits, the infected cell grows
dramatically until death. One of the malfunctions which may
result in this phenomenon is known as fibrosis. In the case of
fibrosis, a positive feedback happens in the following way,
resulting in cell death: TGF- initializes a pathway which
eventually results in a gene being expressed. One of the
productions of the very same gene is TGF- itself. Therefore if
the cell does not function properly, the amount of TGF-
increases with time resulting in the more of the gene being
expressed and more of TGF- being produced. So with the
increasing amount of TGF-, the cell grows more and more
until it dies. Many have tried to model and analyze the
behavior of TGF- pathway [1-4]. In [1], authors proposed a
model for this system using Ordinary Differential Equations

II.

MATERIAL AND METHODS

A. Petri Nets
Standard Petri Nets (PNs) are a modeling language
especially used to model asynchronous, concurrent and
distributed systems. Different biological systems have been
modeled by various types of PNs [5-7] where each type
emphasizes on a special characteristic of a biological system.
For example in [5], a pathway is modeled using standard PNs.
Then the model is upgraded to timed PNs by attributing
reaction speed to its transitions. The same approach of
modeling via standard PNs is used in this paper but the goal
here, is controlling the pathway.
Formal definition of PNs is as follows:
PNs are five tuple set of PN = (P, T, A, W, M0) where:

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P = { p1, p2, ..., pn } is a finite set of places

T = { t1, t2, ..., tm } is a finite set of transitions

A (PT) (TP) is a set of arcs

W : A { 1, 2, ... } is a weight function

M0 : P { 0, 1, 2, ... } is the initial marking

P T = and P T =

There are two sets of nodes present in a PN: places and

transitions. Places are shown by circles. They represent
system states or conditions. In the modeling of biological
systems, places may represent proteins, species, organism,
ions, temperature and PH value. Transitions which are
illustrated by squares describe the process or the event by
which system states change. In biological models they refer to
biochemical reactions.
Tokens which are illustrated by dots or numbers within a
place, quantify the models. They represent the value of a state
or condition. In biological systems, they refer to
concentrations of different species, temperature and PH value
[8].
A transition has to be executed for the system to change
state. The execution of a transition is known as firing the
transition. A set of firing rules have been defined for PNs. The
rules are as follows:
A transition "t" is enabled in a marking "m" if
p t : f (p, t) m(p). p t refers to all the input
places of transition t. f (p, t) is the arc weight between
place "p" and transition "t".
A transition "t", which is enabled in "m", may fire. When
"t" in "m" fires, a new marking " m' " is reached, with
p P: m' (p) = m (p) f (p, t) + f (t, p).
Where f (p, t) represents the weight of the arc linking
place "p" to transition "t" and f (t, p) is the weight of the
arc linking transition "t" to place "p".
The firing itself is timeless and atomic [9].
The first step to model TGF- pathway using PNs is to
determine transitions, places, arcs and their equivalents in the
TGF- pathway. To accomplish this purpose, the biological
structure of TGF- pathway needs to be studied.
B. TGF- Pathway
As it was mentioned, pathways are several chemical
reactions which happen sequentially. One of many pathways
functioning in the cell is TGF- pathway. It is a rather
important pathway due to its critical functions such as
differentiation (that is a process during which a specialized
cell is developed from a basic one) or cell growth. The
pathway functions as follows: TGF- as the initializing

element of the pathway, binds to a dimmer of its type two

receptor, TGF-R2. The structural formation of the complex
induces the recruitment of TGF- type one receptor, TGFR1. In this complex, TGF-R2 phosphorylates TGF-R1.
The activated TGF-R1 then phosphorylates certain proteins
called SMAD2 and SMAD3. Two phosphorylated SMADs
then bind to a protein known as SMAD4 resulting in a nuclear
complex. This trimmer binds to a specific DNA sequence and
result in the target gene being expressed. A more detailed
description will be presented in the next section including a
list of involved reactions [10, 11].
III.

MODELING THE TGF- PATHWAY

The first step to control the TGF- pathway includes

modeling the pathway. PNs were chosen as the modeling
method due to their ability to model certain properties of
biological pathways including concurrency and distribution.
In the proposed model, places represent substances which
function in the pathway. These substances were gathered from
the literature. Places used in the model along with their
equivalent substances are listed in table 1.
Model transitions represent chemical reactions of the
pathway. Their inputs are the reactants and their outputs are
products of each reaction. Transitions used in the model with
their equivalent reactions are listed in table 2. Transitions
number 20, 21 and 22 which illustrate the negative feedback
performance of the expressed gene, have not been noticed in
previous studies.
TABLE .
PLACES IN THE PN MODEL
places used in the model with their equivalent substances
Place

Substance

P1

TGF-

P2

TGF- Receptor2

P3

TGF- Receptor2/TGF- Complex

P4

TGF- Receptor1

P5
P6

TGF- Receptor1/ TGF- Receptor2/

TGF- Complex
Sara

P8

TGF- Receptor1/ TGF- Receptor2/

TGF- /Sara Complex
R-Smad

P9

phosphorilated R-Smad

P10

Cosmad

P11

R-Smad /Cosmad Dimmer

P12

R-Smad /Cosmad trimmer

P13

P300

P7

P14
P15
P16
P17

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R-Smad /Cosmad Dimmer/P300

Complex
R-Smad /Cosmad trimmer/P300
Complex
R-Smad /Cosmad Dimmer/P300/CBP
Complex
R-Smad /Cosmad trimmer/P300/CBP
Complex

transitions used in the model with their equivalent

reactions

places used in the model with their equivalent substances

Place

Substance

Transition

P18

GENE expression

P19

Inactive Rsmad

P20

Smurf

P21

Smad6/7

P22

Snon/c-ski

20

P23

Inhibited Smad6/7

21

P24

Inactive Cosmad

22

P25

Inactive TGF- Complex

23

P27

SHC_GRB2_SOS_RAS_RAF_MEK1_
MEK2_ERK1_ERK2
Inactive Rsmad_cosmad_trimmer

P28

Inactive Rsmad_cosmad_Dimmer

P29

Inactive R-Smad (Rsmad degradation)

P26

P30
P31
P32

Inactive Sara/ TGF- Complex (Sara/

TGF- Complex _degradation)
Inactive Sara/ TGF- Complex (Sara/
TGF- Complex _degradation)
(in another location of net other than P30
)
CBP

TABLE .
TRANSITIONS IN THE PN MODEL
transitions used in the model with their equivalent
reactions
Transition

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17

Reaction

TGF- +2 TGF-R2 TGF- - TGF-R2

TGF- + TGF- R2+2 TGF- R1 TGF-
complex
Sara + TGF- complex Sara_ TGF-
complex
Smurf+Smad6/smad7+ TGF- complex
inactive TGF- complex
Rsmad+SmurfRsmad degradation
Sara_ TGF- complex + Rsmad
Phosphorilated Rsmad
Phosphorilated Rsmad+ Cosmad
Rsmadcosmad dimmer
Phosphorilated Rsmad+2 Cosmad
Rsmadcosmad trimmer
Snon/ski+ Rsmadcosmad dimmer
(degradation)
Snonski+Rsmadcosmad trimmer
(degradation)
Snon/ski+ phosphorilated Rsmad + smurf
(degradation)
P300+Rsmadcosmad dimmer
Rsmad_Cosmad_Dimmer_P300
P300+Rsmadcosmad trimmer
Rsmad_Cosmad_trimmer_P300
Rsmad_Cosmad_Dimmer_P300+CBP
Rsmad_Cosmad_Dimmer_P300_CBP
Rsmad_Cosmad_trimmer_P300+CBP
Rsmad_Cosmad_trimmer_P300_CBP
Rsmad_Cosmad_Dimmer_P300_CBP
GENEexpression+ Snon/ski + Rsmad
+Cosmad+ Smad6/7 + TGF-+ P300+CBP
Rsmad_Cosmad_trimmer_P300_CBP

Reaction

18

GENEexpression+ Snon/ski + Rsmad

+Cosmad+ Smad6/7 + TGF-+P300+CBP
TGF- ; (degradation)

19

GENE products; (degradation)

GENEexpression+ Sara_ TGF- complex
Sara_ TGF- complex degradation
GENEexpression + Rsmadcosmad dimmer
Rsmadcosmad dimmer degradation
GENEexpression + Rsmadcosmad dimmer
Rsmadcosmad trimmer degradation
Cosmad+ Smad6/7 inactive Cosmad

25

Sara_ TGF- complex+ Smad6/7 Inactive

Sara_ TGF- complex
Smurf (Smurf Production)

26

Smurf + Smad6/7Inhibited Smad6/7

24

SHC+GRB2+SOS+RAS+RAF+MEK1+M
EK2+ERK1+ERK2 (production)
SHC+GRB2+SOS+RAS+RAF+MEK1+ME
K2+ERK1+ERK2 +Rsmad Rsmad
degradation

27
28

Using the proposed places and transitions, a model of the

pathway is constructed in a software specially designed to
model biological systems known as SNOOPY [12]. The model
is represented in Fig. 1.
In biological systems, a substance can affect different parts
of the system simultaneously. Thus, to avoid repeating the
same place in the model, some places known as logic places
are used. Logic places are illustrated by grey circles. Different
logic places with the same name are actually the same
substance performing in different parts of the system. Also for
the pathway to function, some substances must be present.
Therefore initial conditions were attributed to these places.
IV.

CONTROLLING THE PATHWAY

The first step to control the cell growth is controlling the

amount of TGF- as the initiator of the pathway. As it was
explained previously, based on the structure of the pathway,
the more the amount of TGF- increases, the more the
pathway occurs.
Before controlling the pathway, we need to make sure that
the applied control does not contrast with the law of
conservation of matter which is the absolute rule in biological
systems. Thus the same approach as [13] was chosen as the
control mechanism. In [13], an arbitrary standard PN is
considered and a control method based on P-invariants is
proposed for the PN. P-invariants are a subset of places in
which the weighted sum of tokens is constant. As the tokens
represent the amount of matter involved in reactions, Pinvariants indicate the law of conservation of matter in a
biological system. So using P-invariants as the control
approach guarantees the preservation of matter in a system.

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Fig. 1 . The Petri net model of TGF- pathway.

Therefore the method illustrated in [13] was considered to be

appropriate for controlling TGF- pathway.
Suppose that the limit value of TGF- is given by:
L*p b

(1)

b is a vector which its elements bi1 represent the limit which

needs to be set on the place i of the system. P is a vector [p1,
p2, , pn] in which pi represents place i. The coefficients of
equations summarized in (1) are the elements of a matrix L.
Adding C as the control places, we have
L*p +c=b

[2 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 1 0 0 0]

(3)

First, a limit must be set on the number of tokens in the

place representing TGF-. Defining b, L will be calculated
using (1). The incidence matrix of the controlled system is
calculated from (3), defining the structure of the system with
control applied on TGF-. To simulate the output, a limit of
500 tokens is defined as the limit on TGF- concentration.
Using a software called CHARLI, the incidence matrix of the

0 0 -100 -100

Element i of MC represents the connection between the added

control place and transition i in the system. The new arcs were
added using these four nonzero coefficients as the arc weights.
The model with control added, is illustrated in Fig. 2.
The initial condition of the control was calculated using (4),
C0=b-L*P0

(2)

Defining M as the incidence matrix of the system, it is proved

that the incidence matrix of the controlled system is
Mc=-L*M

Petri model was calculated. Mc then was calculated using (3).

Calculated Mc had four nonzero elements indicating four arcs
connecting the added control place to the transitions of the net.
Mc =

(4)

where P0 is the initial marking of the system. C0 is calculated

to be 400 tokens.
Applying the control, four new connections are formed in
the system. The following four stoichiometric reactions
represent changes according to the control place added.
(5)
2TGF-+2ReceptorTGF-/Receptor Complex+2X
(6)
TGF- TGF- Degradation +X
(7)
Trimmer-P300-CBP+100XGeneExpression
(8)
Dimmer-P300-CBP+100XGeneExpression
The control place represents an anonymous substance which

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Fig. 2 . The Petri net model of the TGF- pathway with the control added. The control is specified by the cycle around it.

controls the pathway. X is the anonymous factor which

stabilizes the system if it participates in the pathway with the
calculated stoichiometric coefficients. Because of the law of
conservation of matter, substance X must be made of chemical
units involved in the reactions with X. So the chemical
structure of X is known to some level.
As illustrated in Fig. 3 and Fig. 4, in the system with no
control, number of tokens in the place representing TGF-
breaks the 500 threshold in step 50 whereas in the controlled
system the number of tokens stays within the range.
In summary, one approach of drug design may be focused
on determining the X factor which participates in (5) to (8)
with the calculated stoichiometric coefficients. This factor
along with a specified initial condition may control the
pathway. The process may be applied to any of the key
elements in the pathway which may halt the pathway in their
absence.
At last, some points are worth noting. The amount of gene
expression differs due to different conditions of the cell. A
variety of factors may affect gene expression. To model these
factors, the weights of input arcs of the place which represents
gene expression may differ due to cell conditions. For this
study, the arc weights resulting in gene expression and thus
reproduction of TGF- were set in a way so that to make sure
the amount of TGF- increases drastically thus recreating
fibrosis condition. This way the function of the applied control

mechanism becomes clear. To fulfill this condition, the

weights of two input arcs of the place representing gene
expression were set to 100 each.
V.

CONCLUSION

Due to the importance of TGF- pathway activities,

malfunctions result in disastrous effects. Therefore controlling
the pathway in the case of malfunction is substantial.
In this paper, a PN based model was proposed for TGF-
pathway. Several new reactions, compared to prior models,
were also included. The model parameters were set in a way
so that the output increases dramatically, as it happens in
fibrosis condition. A control based on P-invariants was set on
the system in order not only to control the pathway but also to
observe the law of conservation of matter. The simulation
results illustrate the efficiency of this approach. The control
was translated to stoichiometric equations; thus describing the
structure of the anonymous matter which is able to control the
pathway in the case of fibrosis. The results are considered as a
basis for drug design and determination of target substances
for halting the pathway. A method for selecting target
substances to apply this control approach on, may be
addressed in future works.

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Fig. 3. Number of tokens representing TGF- density in a pathway with

malfunction and no control.

Fig. 4 . Number of tokens representing TGF- density in the

controlled pathway.

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