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Vision paper for a third funding phase of HepatoSys: "Bridging the Scales"
The Project Committee
July 2008
The liver plays a central role in metabolism, protein synthesis, storage and detoxification.
Exceptionally high capacity of regeneration ensures liver functionality despite continuous
exposure to toxic substances. The diverse functions of the liver require the precisely
regulated interplay of mainly hepatocytes with endothelial cells lining blood sinosides as
well as bile duct cells but also with stellate (Ito) cells and immunological cells such as
Kupffer cells. World wide chronic inflammation of the liver with a link to metabolic
syndrome and cancer pose a major health burden. Therefore the establishment of an In
Silico-Liver developed from interlinked models at different scales and based on highquality quantitative data will provide a highly innovative tool to unravel underlying
mechanisms facilitating liver functions, to address emergent properties and to
quantitatively predict the consequences of perturbations caused by genetic variability or
disease promoting alterations. Most evidently, the establishment of an In Silico-Liver
capturing essential liver functions is a long-term process that requires the steady
development of data-based models at all scales and progressive model integration.
However, already working towards this highly ambitious long-term goal will have a major
impact on cost effective drug discovery, risk assessment and personalized medicine.
Approaching this long-term goal HepatoSys focuses on four major areas “regeneration”,
“metabolism”, “iron storage” and “detoxification”. In the first funding phase “Getting
Started” of HepatoSys the infrastructure, standard operating procedure, and the basis of
the data management system were established. Currently, in the second phase of
HepatoSys
termed
“Integration”,
biological
processes
of
signalling,
detoxification/metabolism, endocytosis and iron metabolism are investigated and first
efforts are underway to link submodule models. In order to take the next step, we propose
for the third funding period “Bridging the scales” as the central theme:
(i) Bridging the spatial scales: Single Molecule - Intracellular - Supracellular
Hepatocytes constitute 90% of the liver volume and significantly contribute to the diverse
functions of the liver. Currently, entirely different modelling strategies are employed to
examine essential functions of the liver such as regeneration is studied by dynamic
modelling of signalling pathways, metabolism/detoxification by flux based analysis and
endocytosis by spatio-temporal modelling. However, to gain access to mechanisms
regulating the intricate interplay of e.g. signalling networks, endocytosis and metabolism
during regeneration it is essential to bridge these differences and successively generate
an integrated model. A possible strategy could be to simultaneous quantified by mass
spectrometry metabolites and alterations in signalling components. Furthermore, in the
liver lobulus the characteristically polarized hepatocytes are organized in single-cell plates
and are exposed to periportal to pericentral gradients for oxygen, food and information
supply. Thus hepatocytes differ significantly depending on their position in the liver lobulus.
To quantitatively examine these effects it will be important to monitor organ explants or
events in the liver of whole animals by advanced imaging techniques and employ
biosensors as well as fluorescent-probes or reporter strains expressing fluorescent-tagged
components. At the single cell level these tools should facilitate the quantitative
examination of dynamic changes in the organization and localization e.g. of signalling
complexes or target gene induction and the dynamics of transport processes and thereby
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contribute significantly to advance spatial-temporal models.
A further important aspect determining liver functions is cell-cell communication.
Hepatocyte not only self-interact to from bile ducts, but in addition interact with cells lining
the blood sinusoids as well as the bile duct, hepatic stellate cells and liver macrophages
(Kupffer cells). Major mediators of cell-cell communication are cytokine-networks. Thus it
will be important to identify relevant cytokines, quantify dynamic changes in the networks
and include these into models.
Furthermore, fluidic flow in the liver such as blood flow, bile excretion etc. have to be
quantified by advancing and adapting techniques of medical imaging and linked to events
at the single cell level to step-by-step develop multi-scale models.
(ii) Bridging the time scales: Seconds - Minutes – Hours – Days - Years
Major functions of the liver operate on entirely different time scales. Metabolites are
converted with in seconds whereas ligand induced activation of signalling pathways can
take minutes to hours. Conversion into alterations in gene regulatory networks then takes
from minutes to days which subsequently results in coordinated biological responses. For
example the entire process of regeneration from partial hepatectomy to full reconstitution
of the liver takes approximately 2 weeks. Disease relevant alterations can accumulate over
a time frame of years resulting in progressive disease development. Inflammatory
responses can lead to chronic inflammation of the liver resulting in hepatic fibrosis which
becomes irreversible leading to hepatic cirrhosis and finally fostering the onset of
hepatocellular carcinoma formation. Thus, it will be important to establish models covering
the different time scales and facilitating predictive extrapolation for time points beyond the
experimentally measured time frame.
(ii) Bridging research areas: Basic – Translational – Applied
Liver regeneration can be severely impaired by inflammatory processes leading to tissue
destruction and replacement of functional hepatic tissue by scar tissue. Development of
hepatic fibrosis and cirrhosis occurs as a consequence of different causes such as
alcohol-induced liver disease, chronic viral hepatitis, non-alcoholic steatohepatitis (NASH),
drug-induced liver damage, auto-immune hepatitis or storage diseases. Cirrhosis in turn is
an important prerequisite for the pathogenesis of primary hepatocellular carcinoma (HCC)
which develops in more than 80 % of all cases at the bottom of cirrhosis. The observation
that HCC-development requires precedent cirrhosis strongly suggests that deregulation of
hepatocyte proliferation and differentiation in the environment of chronic inflammation may
be an important pathogenetic factor for the development of HCC. Data-based modelling of
signalling pathways involved in liver regeneration has already provided insights into
mechanisms that could foster the process. Therefore establishing interlinked models of
increasing complexity will facilitate insights into key properties and help to predict
strategies for early intervention.
Multifactorial diseases such as metabolic syndrome are characterized by alterations in
metabolic processes, insulin resistance and obesity. Perturbation of signalling pathways
such as insulin resistance results in metabolic disturbance and can trigger inflammatory
processes and inflammatory processes may interfere with signalling resulting in insulin
resistance demonstrating the tight interrelation of inflammation, fibrosis development,
metabolic abnormalities and hepatocyte regeneration. To untangle these relations and
establish possibilities for targeted intervention and possibly prevention it is important to
integrate models capturing regulation of metabolic processes, signalling and gene
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regulatory networks and link these with mechanistic models at the organ level.
For drug discovery toxicity of substance under development is a major problem. The liver
has evolved sophisticated mechanisms to detoxify substances however due to
polymorphisms and genetic variability in the human population the effects are frequently
difficult to predict.
Animal testing (ethical issues) link to relevance for humans (generate proliferating
hepatocytes)
from fundamental understanding to specific prediction
prediction of toxiticity, polymorphism,
model based finger-printing, personalized medicine
(iv) Bridging technologies: Improving Sensitivity and Precision
live cell imaging
imaging of organ explants
imaging of whole animals
single molecule spectroscopy
development of biosensor/fluorescent probes
development of reporter strains
quantitative mass spectrometry with enhanced sensitivity (proteomics, metabolomics)
(iiv) Bridging the disciplines: Systems Biology Education
(iiiv) Bridging efforts: From national to international
EU FP 7 funded STREP CancerSys BMBF funded HepaChip
Boogle (UK), Hook (USA), Virtual Liver (USA)
(iiv)
Bridging the scales requires that the foundation is solid. Therefore, while reaching out for
higher scales, solid work on the lower scales will continuously be necessary.
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