Medicines that are usually effective in treating diseases can sometimes be associated with severe adverse effects. This can occur when the liver, which normally metabolizes drugs and renders them harmless, becomes overburdened and even collapses completely. Prof. Dr. Jens Timmer from the University of Freiburg and Prof. Dr. Ursula Klingmüller from the German Cancer Research Center (DKFZ) in Heidelberg have joined forces in a huge European research project aimed at finding ways to enable the early identification of drug candidates with a potential toxic effect on the liver. The project could help the pharmaceutical industry save billions of euros. However, the researchers first need to obtain an understanding of the highly complex molecular networks in the liver cells. Timmer and Klingmüller are role models of a perfect symbiosis between biological and theoretical researchers, and have been working together for around fifteen years now.
The liver, which usually metabolizes drugs and converts them into forms that can be readily eliminated from the body, is sometimes unable to keep up. Some drugs are toxic to the liver; in some cases, drug-induced liver injury is very serious; the liver may fail completely, which can have fatal consequences for patients, or lead to the need for a transplant. As potential toxic effects are often not detected until a drug is on the market, pharmaceutical companies might be forced to withdraw from the market compounds that have otherwise shown a healing effect. It usually takes around ten years to develop a drug, including preclinical and clinical trials, so the removal of drugs from the market is associated with financial losses that can amount to billions of euros. Losses like these could be prevented if tests, using cell cultures for example, were available for companies to be able to test drugs for potential adverse effects on the liver early on in the drug discovery process.
“Pharmaceutical companies are usually under competitive pressure with numerous companies competing for a piece of the same pie,” said Prof. Dr. Jens Timmer, head of the Department of Data Analysis and Modelling of Dynamic Processes in the Life Sciences at the Institute of Physics at the University of Freiburg and director of the Freiburg Institute for Advanced Studies (FRIAS). “All these companies have found themselves in the same boat, which is why they have now joined forces and developed this huge cooperative project together with ourselves as basic researchers.”
The “Mechanism-Based Improved Systems for the Prediction of Drug-Induced Liver Injury (MIP-DILI)” initiative is being funded by the European Union and the European Federation of Pharmaceutical Industries and Associations (EFPIA) with 34.7 million euros for a period of five years. The majority of the money required for the research is being provided by the pharmaceutical companies involved in the project, including big players such as Merck and AstraZeneca, small- and medium-sized companies and numerous universities and scientific institutions. The partners are aiming to develop new test methods that will help researchers to detect potential liver toxicity issues much earlier on in the development process, thus reducing the number of cases of drug-induced liver injury or failure. The partners will focus mainly on cultures of liver cells in two- and three-dimensional configurations that mimic human liver physiology. However, an even more urgent issue is the need to gain a profound understanding of the underlying biology.
So when it comes to the black sheep among the drugs, the question is: what do they actually do in the liver cells? So far, researchers have only found an approximate answer to this question: they kill the liver cells and in some cases the surrounding liver tissue becomes massively inflamed. “Up until now, the major problem has been that the molecular mechanisms that lead to drug-induced liver injury are unknown,” said Prof. Dr. Ursula Klingmüller from the German Cancer Research Center (DKFZ) in Heidelberg, who is a specialist in systems biology studies of the signal transduction processes in liver cells and other model systems. Klingmüller and Timmer have been pooling their expertise for around fifteen years now. The signalling networks in liver cells that can be negatively affected by medicines are highly complex and can only be understood in detail using a systems biology approach that combines experimental biology and mathematical theory.
When Timmer and Klingmüller started working together in 1999, they initially focused on the Jak/STAT signalling cascade, a system consisting of three main components located in and below the membrane of blood precursor cells. This molecular signalling network is activated by the hormone erythropoietin (EPO), which is produced in the kidneys and induces the maturation of blood precursors into red blood cells. As they worked together using the experimental data produced in Klingmüller’s laboratory (who was then still at the Max Planck Institute of Immunobiology in Freiburg), the theoretician Timmer managed to successfully develop a mathematical model that described the temporal course of the individual reactions in the molecular signalling network much better than the biological models available at that time.
“Since then, the signalling systems we have investigated have become more and more complex,” said Klingmüller. “And now our two laboratories have areas of overlapping expertise. In our laboratory, for example, we are attempting to translate the conclusions gained from systems biology experiments into theoretical language.” And one of Timmer’s doctoral students is currently gaining initial experience in the systems biology methods that Klingmüller’s team use for their proteomic and genomic research.
The Jak/STAT signalling pathway is the simplest of all signalling pathways. Signalling pathways normally involve dozens of different molecules; the presence of numerous feedback loops makes them complex dynamic systems that can only be thoroughly understood by an iterative processing of information using experimental and theoretical systems biology. “The signalling processes of liver cells have a modular organization; some components, including the Jak/STAT cascade, are interconnected with each other on a second level,” said Timmer. “We hope that at some stage we will be able to bring these modules together in a theoretical model,” said Timmer, pointing out that this requires excellent experimental data, which is why the collaboration with Klingmüller is so fertile.The consortium still has a lot of work ahead of it, and the understanding of an individual liver cell might not turn out to be enough. “We believe that the toxic effect of some medicines is also associated with an overreaction of the innate and acquired immune systems,” Klingmüller said. “Therefore, we also need to understand which immune system messengers play a role and which individual patient dispositions we need to take into account when developing a drug test.” The broad cooperation with industry is of huge importance for the academic researchers: they are given access to reference compounds with known liver toxicity that are held by pharmaceutical companies and normally kept strictly confidential. In addition, laboratories in big companies have much greater technical capacities than university laboratories. And last but not least, the pharmaceutical companies have at their disposal pharmacokinetic models for their compounds that provide information on the quantities taken up by different organs. It can therefore be envisaged that the project will lead to a holistic understanding of drug effects: it goes without saying that complex problems are best solved in cooperation.