# Modelling hepatic stellate cells activation by TGFB1 using Kappa language

Matthieu Bouguéon, Pierre Boutillier, Jerome Feret, Octave Hazard, Nathalie Theret

<figure><img src="image_1.png" /></figure>

## To cite this version:

Matthieu Bouguéon, Pierre Boutillier, Jerome Feret, Octave Hazard, Nathalie Theret. Modelling hepatic stellate cells activation by TGFB1 using Kappa language. 2021, pp.1-23. [hal-03545569](https://hal.inria.fr/hal-03545569)

HAL Id: hal-03545569

https://inria.hal.science/hal-03545569

Submitted on 27 Jan 2022

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

<figure><img src="image_2.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
A Kappa model for
hepatic stellate cells
activation by TGBF1

GT Bioss 2021

Matthieu Bougueon, Pierre Boutillier, Jérôme Feret, Octave Hazard and Nathalie Theret.

irset
Institut de recherche en santé, environnement et travail

DyLiss

UNIVERSITÉ DE
RENNES 1

Inserm

Inria
Inventors for the digital world

ENS

PSL

<figure><img src="image_3.png" /></figure>

<figure><img src="image_4.png" /></figure>
# Liver Fibrosis

* Multiples causes

* Extracellular matrix (ECM) accumulation

* Reversible

<figure><img src="image_5.png" /></figure>
<figure><img src="image_6.png" /></figure>

# Hepatic Fibrosis

Liver injury induces inflammatory response leading to release of TGFB which activates quiescent qHSC towards a MFB phenotype promoting tissue repair

MFB are eliminated either by apoptosis/senescence pathways or by inactivation towards an inactivated HSC state.

The inactivated iHSC can be reactivated upon TGF-b stimulation in a faster manner

Upon chronic injuries, the dynamics of the system is modified and MFB escaped to the elimination pathways leading to ECM accumulation
# Objectives

A) Develop a Kappa-based model to analyze the dynamics of hepatic stellate cells upon TGF-beta stimulation

B) Identify the regulators of equilibrium between repair and fibrosis by integrating the matrix environment

C) While the equilibrium breaking is clearly the fibrosis threshold, founding target inhibiting TGF-β is the final aims of this project
Kappa

Walter Fontana

Pierre Boutillier

Jerome Feret

Jean Krivine

<figure><img src="image_7.png" /></figure>

HARVARD
MEDICAL SCHOOL

<figure><img src="image_8.png" /></figure>

ENS DE LYON

<figure><img src="image_9.png" /></figure>

<figure><img src="image_10.png" /></figure>

<figure><img src="image_11.png" /></figure>

université
PARIS
DIDEROT
PARIS 7

<figure><img src="image_12.png" /></figure>

ENS

<figure><img src="image_13.png" /></figure>

PSL
RESEARCH UNIVERSITY PARIS

**Kappa Language**

A rule-based language for modeling interaction networks

https://kappalanguage.org/
<figure><img src="image_14.png" /></figure>

# Kappa

Rules based language created in 2004
(V. Damos)

Rules describe agent behavior
modifying state of site of this agent.

## Exemple:

A site of the agent A will become red
and the site r will be bound to the
site x of B.
<figure><img src="image_15.png" /></figure>

# Kappa

Rules based language using agent

Rules based VS Agent Based

only information
on the modified
part

all conformations
of the agents or
the processus
must be describe
# Kappa

Kappa is a graphs rewriting language, meaning a model is a graph where Agent are nodes and interaction are edges

A model is a graph composed of multiple graphs modified each time a rules is fired

Chemistry syntaxe:

$$A + B -> C + D$$

<figure><img src="image_16.png" /></figure>
# Kappa rules

Rule describing TGFB binding to quiescent cell.

Interaction possible only if occurrences of HSC have their receptors in a membrane state and free.

<figure><img src="image_17.png" /></figure>

'HSC(state{quiescent} TGFBR1_2{membrane}[.]), TGFB1(cell[.] state{active})
-> HSC(state{quiescent} TGFBR1_2{intern}[1]), TGFB1(cell[1] state{active}) @ 'Ka'
Kappa Tools

KaSim

Stochastic Simulator
using Gillespie
algorithm.

KaSa

Static analyzer gives
informations on:

- link between agents,

- Impact of the state of
  site on link

- double link formation

Causality Analyzer

Understanding the
impact between rules,
what conditions must
be met to allow
another rule to be
triggered.

Spatial Kappa

Extension introducing
spatial information
and
compartmentalization
in Kappa
<figure><img src="image_18.png" /></figure>

Apoptosis/Senescence

~ 50%

Xiao Liu & al.2013

In vivo
# Model

* 1 Agent HSC with 7 state (quiescent, activated ...) and 1 site (TGFBR)

* 73 rules

## Parameters:

<table><tr><td>Environnement</td><td>Activation</td><td>Receptor</td></tr><tr><td>Number of HSC: 100</td><td>qHSC -> aHSC: 84h</td><td>Recycling rate: 30 min</td></tr><tr><td>Number of receptor: 10000</td><td>aHSC -> MFB : 84h</td><td>Receptor production Rate: 4 min</td></tr><tr><td>qHSC</td><td>MFB</td><td>Constitutive degradation rate: 36min</td></tr><tr><td>half life: 54.93d</td><td>half-life: 3.76d</td><td>Ligand induced degradation rate :4 min</td></tr><tr><td>activation speed: 1h</td><td>Inactivation: 5d</td><td></td></tr><tr><td>Proliferation</td><td>iHSC</td><td>TGFB</td></tr><tr><td>HSC proliferation half-time: 13.75h</td><td>reactivation: 42h</td><td>TGFB1 half life 3min</td></tr><tr><td>MFB proliferation half-time: 886.9h</td><td>iHSC half life: 54.93d</td><td>TGBF wave: 5000 * number of HSC</td></tr></table>
# Simulations protocol

Perform multiple simulations to
test the impact of the input

* TGFB concentration

* Frequence of TGFB input

* Number of TGFB input

<figure><img src="image_19.png" /></figure>
# Simulations

Parameters:

[TGFB]: 5000

number of input: 8

dT: 90h and 24h

<figure><img src="image_20.png" /></figure>

<figure><img src="image_21.png" /></figure>
# Simulations

Parameters:

[TGFB]: 5000

number of input: 8 and 16

dT between input: 90h

<figure><img src="image_22.png" /></figure>

<figure><img src="image_23.png" /></figure>
# Simulations

Parameters:
[TGFB]: 5000 and 1000
number of input: 8
dT between input: 90h

<figure><img src="image_24.png" /></figure>

<figure><img src="image_25.png" /></figure>
Simulations

<figure><img src="image_26.png" /></figure>

Parameters: [TGFB]: 5000, number of input: 8, dT between input: 90h

2 stimulations separate by 6 months
Analysis

- Despite the heterogeneity of the different source of data, we observed a recovery time consistent with the experimental data

- Chronic TGFb stimulation did not lead to accumulation of MFB that promote fibrosis

- Hypothesis; The extracellular matrix produced by activate hepatic stellate cells might contribute to the disequilibrium towards fibrosis
<figure><img src="image_27.png" /></figure>

Source: Michael W. King: Integrative Medical Biochemistry Examination and Board Review, www.accesspharmacy.com Copyright © McGraw-Hill Education. All rights reserved

# Extracellular Matrix

- provides physical support for cells

- establishes separation and maintenance of differentiated tissues

- regulates growth factors and receptor abundance

- maintains the level of hydration and the pH of the local environment
<figure><img src="image_28.png" /></figure>

Source: Michael W. King: Integrative Medical Biochemistry Examination and Board Review, www.accesspharmacy.com Copyright © McGraw-Hill Education. All rights reserved

# Extracellular Matrix

The components of ECM
- are mainly secreted by activated hepatic stellate cells

- the stiffness of ECM promotes activation of HSC

- the remodeling of ECM depends on protease activities also secreted by activated HSC

- increased stiffness of liver tissues is associated with the progression of fibrosis from stage 1 to stage 4
Perspectives

A) Integration of the mechanical effect of ECM on HSC activation by introducing the main driver of stiffness, the type I collagen that is produced by activated HSC and MFB

B) Comparative study of the use of molecules (TGFbeta receptor, collagen) as groups (token) or as individual agent. Computational challenge ?
# Acknowledgements

<figure><img src="image_29.png" /></figure>

## My supervisors

Nathalie Theret; Irset, Inserm

Anne Siegel; Irisa, Inria

Jérôme Feret; Team Antique, Inria

This work was supported by a travel grant by the SFBI

Pierre Boutillier; Nomadic Lab

Octave Hazard; Team Antique, Inria
Thank you!

Any questions?

<figure><img src="image_30.png" /></figure>

Matthieu Bougueon | matthieu.bougueon@irisa.fr