Wir überwinden Grenzen

Analyzing and treating the consequences of genetic changes - that is the goal of the "Institute for Disease Modeling and Targeted Medicine" (IMITATE) at the University of Freiburg and the Medical Center - University of Freiburg. An application for funding for the construction and equipment has been recognized as eligible by the German Council of Science and Humanities. The Joint Science Conference must finally approve the project on June 24, 2016. "We are delighted that the project has been positively evaluated and has prevailed against tough competition. We hope that the GWK will make the appropriate decision shortly. With so much federal money, we will certainly also make our contribution from the state side," said Science Minister Theresia Bauer. The plan is for the federal government and the state of Baden-Württemberg to fund IMITATE with around 57 million euros over the next five years. The research building on Breisacher Strasse should be ready for occupancy in 2022.

"At IMITATE, scientists from various disciplines work together under one roof to develop tailored therapies for patients. With the new research building, we are creating excellent working conditions for our outstanding life sciences," says Prof. Dr. Dr. h.c. Hans-Jochen Schiewer, Rector of the University of Freiburg.

Thanks to technical advances, thousands of human genomes are decoded every day. However, researchers have rarely been able to find out which genetic alterations actually cause disease and how they can be treated. The IMITATE scientists want to close the gap between the enormous amounts of genome data and the lack of applicability at the patient's bedside and extract precisely the information that is crucial for an individual patient and their treatment. Around 165 employees from various faculties at the University of Freiburg and different departments at the Medical Center - University of Freiburg, including six junior research groups, will work together on three main research areas: 1) data analysis and modelling of genetic and epigenetic diseases, 2) imaging and characterization of the models and 3) the search for individual therapies.

According to the current state of research, in order for genetic changes to be classified as harmful with sufficient certainty, they must be reproduced in an animal model - so far almost always in mice. IMITATE wants to break new ground here. Preferably zebrafish and frog larvae, but also flies and threadworms will be used to elucidate complex genetic and epigenetic diseases in humans. Although humans are separated from these organisms by around 400 million years of evolution, many gene functions have remained the same. "For example, kidney function in these animal models can be investigated just two to three days after fertilization of the eggs," said Prof. Dr. Gerd Walz, Medical Director of the Department of Medicine IV at the Medical Center - University of Freiburg and spokesperson for IMITATE. "At this stage, the larvae are only a few millimetres in size, largely transparent and are particularly suitable for high-resolution microscopy methods."

For this reason, IMITATE is being equipped with the latest confocal fluorescence and electron microscopes, which are so sensitive that streetcars, cars and even bicycles affect their precision, at a cost of almost seven million euros. Extensive architectural and technical precautions have to be taken to ensure that the devices work perfectly.

To replicate genetic diseases in animal models, IMITATE researchers will use genome editing techniques such as the CRISPR/Cas system, which bacteria use to defend themselves against intruders. With this bacterial defense system, genomes can be modified in a very short time. Ideally, researchers will not only be able to reproduce potentially disease-causing genetic changes, but also correct diseased genes. Recently, this has also been possible in frog larvae, which are particularly suitable for studying developmental processes. However, in order for frogs to lay the eggs used in the experiments, perfect temperature and environmental conditions are crucial, for which IMITATE will create the appropriate conditions.

Before drugs can be used in humans and investigated in studies, ethics committees and regulatory authorities require proof that the active ingredients are effective and tolerable in at least one mammal. Mice are usually used here. Here too, IMITATE wants to break new ground and avoid unnecessary experiments. Thanks to efficient genome editing methods, complex genetic diseases can be represented in the mouse model in the shortest possible time, eliminating the need for lengthy crossbreeding.

"In order to minimize the number of necessary experiments, a state-of-the-art mouse hospital with MRI, CT, ultrasound and bioluminescence equipment is being set up," explains Prof. Walz. In this way, mice can be repeatedly examined under ideal environmental conditions in perfectly air-conditioned rooms and disease manifestations can be detected as early and precisely as possible. Thanks to these innovations, the planned "Specified Pathogen-Free (SPF)" facility is comparatively small, with around 3,000 cages for a maximum of 10,000 mice - such facilities are normally three to four times as large.

IMITATE will generate enormous amounts of data. However, without appropriate processing, high-dimensional data ("big data") is "big chaos". IMITATE therefore integrates various groups from the fields of bioinformatics, image recognition and genetic epidemiology in order to translate this data into patient-relevant information. Neural network programs help, for example, to evaluate videos recorded during zebrafish or frog development using high-resolution confocal microscopy. Other computer programs are designed to optimize data acquisition during evaluation so that experiments do not have to be repeated unnecessarily. Ultimately, the aim of IMITATE is to use the extensive data to develop potential targets for new drugs or to create the knowledge to use existing drugs in a targeted manner.

Background genome analysis

The human genome comprises around three billion DNA base pairs, which code for 20,000 genes or proteins. This means that only just under ten percent of the genome's potential storage capacity is used. Technical advances have reduced the cost of sequencing a human genome from several billion to a few hundred euros. The resulting mass sequencing has shown that almost every second gene has deviations. These deviations usually go unnoticed, as there are two gene copies for most proteins: the variant inherited from the father and the variant inherited from the mother. Deviations are usually compensated for by the second gene copy. The researchers were surprised to find that an average of five to 20 genes are completely missing in each person without any noticeable consequences.

Patient example

35-year-old Helga K. has a problem. Her GP has diagnosed a restriction in her kidney function. She has not noticed anything so far and is very active as a businesswoman and mother of two healthy children. However, she is concerned that her father had to have a kidney transplant at the age of 55. And her grandfather also died unexpectedly at the age of 60 - allegedly due to a kidney problem. Obviously there is a genetic strain in the family. Helga K. decided to have her entire genome sequenced. The result is frustrating: no one can say whether her disease is genetic.

The reason for this lies in the complex structure of the human genome. Three billion DNA base pairs code for 20,000 genes. In Helga K.'s case, sequencing does not reveal a single disease-causing gene, but rather changes in several different kidney genes. It is currently unknown whether it is precisely these changes that can lead to kidney failure.

What is even worse for Helga K. is that she does not know whether she has passed her disease on to her two children. Classical genetic diseases are caused by mutations in a gene and follow a typical inheritance pattern that was discovered by the religious priest Gregor Mendel back in 1866. However, many human diseases such as blood sugar or high blood pressure are caused by several genes at the same time and are also influenced by environmental factors such as diet. This probably also applies to Helga K.'s kidney disease. As she has a healthy brother, obviously not every member of the family suffers from the disease.

In the event that the kidney disease is not genetic, but was triggered by a dysregulation of the immune system, Helga K. is recommended high-risk chemotherapy. In order to clarify whether she could benefit from this, her genome, including the altered genes, must be replicated in zebrafish using the CRISPR/Cas method. This allows the consequences of the changes to be investigated. Within a few months, it can be shown whether Helga K. suffers from a genetic kidney disease - and whether chemotherapy would therefore be pointless. At the same time, the model can be used to investigate why the kidney disease occurs in the first place and what a targeted, individualized therapy for Helga K. would have to look like.