Business Unit 1

Medical Translational Research and Biomedical Technology: The Challenge of Innovative Diagnostics and Personalized Therapy

Overview

The therapeutic approaches for drug development and molecular genetics in the Fraunhofer Group for Life Sciences take into account the individual’s genotypic profile. To enable quick interaction between basic research and the clinical sector, optimal conditions for state-of-the-art translational medicine and personalized therapy are being created. Early clinical trials (first-inman und proof-of-concept in man) are performed in the Group’s own facilities that meet GCP standards. The pre-clinical research units in the Fraunhofer Group for Life Sciences, working in compliance with GLP guidelines, contribute with their innovative research approaches to substantial reduction of the cost and time required for developing novel diagnostics and medications. For some indication areas, the Fraunhofer Group for Life Sciences has the expertise to cover the whole process from the molecule up to the patient, regarding both research and registration. Fascinating solutions for the highly specialized equipment that is required are at the Group’s disposal: in fully equipped microarray facilities, the Group generates chips, for example for the analysis, recording, and comparison of gene expression profiles. The nONCOchip, which was developed as part of the research on non-coding RNAs (ncRNA), includes several tumor-relevant signaling pathways and is suitable for investigating a broad range of different tumor diseases.

Our experience in biohybrid test systems, in specific sensors for optical and acoustic imaging systems, in drug delivery systems based on nanoparticles, right through to prototype development for nebulizing systems is available to our clients. In compliance with Good Manufacturing Practice, the Fraunhofer Group for Life Sciences manufactures clinical investigational drug products – tissue engineering products, biologicals, and cellular therapeutics. Furthermore, the Group is well equipped for drug testing (pre-clinical and clinical). Complete phase-I and phase-II clinical trials, with a focus on respiratory diseases, are among the services we offer.

Many drugs and their metabolites are insufficiently degraded in even state-of-the-art sewage treatment plants. To prevent negative effects in downstream ecosystems, the Fraunhofer Group for Life Sciences offers services designed to meet real-life requirements: detection methods, bioaccumulation studies, and models for exposure assessment. The Group has developed a removal method based on nanostructured plastics for specifically removing pharmaceuticals from hospital wastewater. The ecologically compatible product design is particularly efficient and trendsetting. By making use of the Group’s consulting services at an early stage of the development work, clients can save substantial costs and may actually prevent environmental problems from occurring.

 

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Top-level: diagnostics for individualized treatment

Pharmacogenomics and pharmacogenetics

Chip-based technologies allow genome-wide gene expression profiles to be obtained. Based on the validated functions of these genes and their gene products, deductions can then be made about molecular changes in the organs, tissues, or cells under investigation. Completely equipped microarray facilities are available for this, so that biochips for this purpose can be developed in-house.

Using comparative gene expression profiles, the Fraunhofer Group for Life Sciences develops biomarkers that allow early assessment of pathogenesis, of the success of the intervention, and of unwanted side effects. Whether or not research should be continued can thus be decided at an early stage of drug development. The efficiency of clinical registration studies can be substantially enhanced by accurate and systematic stratification, as offered by the Group: as a result of different individual genetic situations, a drug product may induce unwanted side effects with different degrees of severity. Targeted screening measures allow those subjects to be excluded from the study in whom unwanted side effects are likely to occur. Both the number of clinical studies and the number of study participants can thus be reduced.

Whenever there are individual cases of serious side effects during non-stratified clinical studies, the scientists of the Fraunhofer Group for Life Sciences can even perform genomic analyses retrospectively using stored samples. Through comprehensive gene and protein analyses, they elucidate the mechanisms of action leading to these side effects. The insight gained from these analyses serves as a basis for ever more individualized treatment.

Recent studies have shown that in mammalian cells the transcriptomes – i.e. the total RNA transcripts in cells of a particular type or condition – are very complex. Particularly surprising was the result that at least 90% of the human genome is transcribed to RNA. Most of these RNAs do not include any signals for translation into proteins and are therefore referred to as non-coding RNA (ncRNA). This ncRNA represents an important cell-biological control level in complex organisms, which thus maps the condition of a cell or tissue very precisely. ncRNAs play an important role in particular in regulatory processes such as cell cycle control, cell differentiation, and cell death. It is, therefore, hardly surprising that a considerable number of different disease-associated and in particular tumor-associated ncRNAs have already been identified. Besides their role in cancerous diseases, ncRNAs seem to influence processes related to cell aging and immortalization.

Just like RNAs and transcribed proteins, ncRNAs represent important groups of potential diagnostic markers, which might enable the identification of subtypes of diseases and thus may provide important clues for personalized treatment. In addition, these molecules might also be potential drug targets. The Fraunhofer Group for Life Sciences is undertaking investigations in this direction, using methods of biomedicine and bioinformatics. The aim is to establish innovative platform strategies for the development of therapeutic targets and biomarkers and to translate these into clinical applications.

In-vitro diagnostic systems

On behalf of its clients, the Fraunhofer Group for Life Sciences develops both complete in vitro diagnostic (IVD) systems and specific assay units for the constituent steps of the drug development process by using biochips. A proprietary scanner platform is available for this. For specific applications, a user-friendly evaluation program is provided and interfaces to bioinformatics tools are integrated.

Chip systems developed by the Fraunhofer Group for Life Sciences include:

  • nONCOchip:

    The nONCOchip is a tailored microarray for screening ncRNA patterns. To support the search for novel biomarkers in tumor biology the nONCOchip has been equipped with 243,000 sensors. Of these, 60,000 are newly identified transcripts of ncRNAs which have been identified as relevant in transcriptome-wide studies on ncRNA expression in a large variety of oncological systems. Other customer-specific developments, for example for inflammatory diseases, are possible.
  • Deoxyribonucleic acid (DNA) chips:

    The Fraunhofer Group for Life Sciences owns a pilot plant for manufacturing low-/ medium-density DNA chips suited for small and medium series of up to 10,000 arrays per day. The arrays can also be captured in microtiter plate (MTP) format or directly in MTPs.
  • Protein chips:

    Our specialists develop protein chips and provide both the antibody-based content and bioactive surfaces. Nano- and micro-chips are fabricated using different techniques, for example by coating surfaces with nanoparticles. Chemical methods and nanobiotechnological processes are used to adjust these chips to specific protein and peptide systems.
  • Cell chips:

    The techniques developed by the Fraunhofer Group for Life Sciences allow, for example, for non-contact and parallel manipulation of suspended cells, which can simultaneously be characterized using image analysis.
  • Lab-on-a-chip:

    For biochemical and molecular biological analytics, the Fraunhofer Group for Life Sciences has developed microfluid constituent systems for diagnostic biochips. Examples are an integrated silicon-based multiparameter biosensor chip and a hormone-based microarray chip for whole-blood diagnosis.
  • Automated in vitro cell culturing techniques:

    The technologies developed in the European Commission’s Integrated Project CellPROM for automated in vitro handling of individual cells under physiological conditions have made available a technology platform which allows cell culture automation for adherent cells to be implemented flexibly and according to user specifications.

 

Biohybrid systems

Biohybrid systems combine microtechnological components with biological systems in such a way that these can be used as novel bioanalytical or physiological sensors.

The characteristic feature of biohybrid systems is a miniaturization of technical functional units with integrated biological components. Biohybrid functional units are important components for novel concepts for the automation of analytical and diagnostic procedures.

Biohybrid systems are being increasingly used in medicine and in biomedical research: on the one hand for collecting analytical data in medical diagnostic processes, and on the other hand as components of test systems for screening drug candidates and for evaluating different therapeutic options. In the Fraunhofer Group for Life Sciences, an interdisciplinary team of molecular and cell biologists, pharmacists, biophysicists, and engineers are working together as research and development partners at this interface between biotechnology, microsystem technology, and sensor technology. They are tackling a variety of issues relating to the development of cell- and tissue-based biosensor systems, drug delivery systems, implants, transplants, and gene therapies. The focus of their work concerns cardiology/angiology, neurology, oncology, and osteology. Examples of their development work are in vitro testing platforms for cardiovascular research and neurotoxicology, each combining the relevant cell models, and systems for non-destructive characterization of therapeutically relevant cellular material.

In vivo diagnosis using imaging techniques

The Fraunhofer Group for Life Sciences develops specific contrast media for molecular imaging, binding disease-specific antibodies to nanoparticles. In conjunction with appropriate imaging techniques, this enables earlier and more targeted diagnosis of in particular oncological disorders. The Group also designs specific coils for magnetic resonance tomography, in particular for micro-imaging up to a resolution of 6 µm. In addition, we utilize ultrasound sensors in vivo as non-invasive sensors and, based on these, develop acoustic imaging systems.

Non-invasive diagnosis

Analysis of the exhaled breath of patients with respiratory diseases provides important information on the type and severity of the disease. This allows, for example, inflammation mediators to be detected and their regulation determined. The Fraunhofer Group for Life Sciences offers such analyses as a service to external clients; measurement systems are available for measuring gaseous mediators (e.g. nitrogen monoxide) as well as nonvolatile substances in the breath condensate.

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Research for the early phases of drug development

Target identification

Antibody-based technologies in combination with 2-D gel electrophoresis and mass spectrometry are used in the Fraunhofer Group for Life Sciences to detect and identify novel biomarkers of tumorous lesions. The scientists perform DNA sequence analyses and compare the gene expression profiles of healthy and diseased tissues, leading to the identification of disease-associated candidate genes and their tumor-specific proteins.

The “metabolome” is the complete set of metabolic products in an organism at a defined point in time. It enables a clear statement to be made about the organism’s physiological condition as a function of a variety of parameters. Comprehensive analysis of the metabolome – referred to as metabolomics – is therefore of great importance in the diagnosis and classification of diseases and in the development of a prognosis; furthermore, it allows the impact of a pharmacological intervention to be determined.

For the identification of new diagnostic and therapeutic target structures (target finding) and the development of novel therapeutic concepts, the Fraunhofer Group for Life Sciences possesses state-of-the-art methods of metabolomics, as well as molecular biological methods in the area of genomics and proteomics. Our aim is to provide and further develop leading-edge analytical methods.

New active substances (biopharmaceuticals)

The Fraunhofer Group for Life Sciences investigates and validates antibody-based active substances for use in oncological indications, allergies, and inflammatory and autoimmune diseases, as well as in infections (Candida albicans). Recombinant technologies are used for this, in particular to obtain antibody, enzyme, and cytokine fusions. For pre-clinical evaluation of these new drug candidates, the Group has access to all relevant in vitro methods, three-dimensional organoid test systems, and a variety of different animal models.

Highly promising approaches for the development of novel medications are also being pursued in the field of pharmaceutical entomology; the focus here is on the development of new antibiotics that will also be effective against pathogens which are resistant to today’s commonly used antibiotics. A new protein has been detected in the larvae of the greater wax moth which interferes with the metabolism of bacteria. This protein inhibits metalloproteases of pathogenic bacteria of the genera Clostridium, Pseudomonas, and Vibrio. The structure and function of this protein were previously unknown and now offer promise for the development of novel antibiotics.

The search for novel oncological agents is also being pursued in pharmaceutical entomology; in this context, the insect realm is a promising resource for the detection of new lead structures. Not only the insects themselves, but also the microorganisms associated with them represent valuable resources for novel substances and are included in the research undertaken in the Fraunhofer Group for Life Sciences.

Rational protein design

The Fraunhofer Group for Life Sciences has at its disposal the complete infrastructure for protein synthesis and structure analysis. Besides crystal growing, this also includes diffraction analysis and the computer hardware required for structure analysis. In the search for protein-based active substances, in silico screening methods are becoming more and more attractive. Structural data in combination with microcalorimetric results are used in this context for rational protein design.

Nano-/microparticle-based drug delivery systems

Another focus of research is nanoparticle/nanobead and microparticle systems and their biofunctionalization. The particles consist of organic polymers, sol-gel-generated hybrid materials, or inorganic materials. Molecular imprinting, chemical surface functionalization, and immobilization of biomolecules are the technologies the Fraunhofer scientists use to biomimetically modify the surfaces of nanoparticle systems. In addition, they develop biodegradable long-term depots.

3D test systems

Three-dimensional organoid test systems exhibit organ-specific functions and are thus particularly well suited for cellular and molecular biological analyses of pharmaceutical, cosmetic, and chemical ingredients. These systems, produced on the basis of human organ cells and certified according to DIN ISO 10993-5, can replace animal experiments. The Fraunhofer Group for Life Sciences further develops such test systems and establishes, for example, vascularized organoid structures which have both an intact capillary system and afferent artery and an efferent vein. This not only allows the development of defined tissue and organ structures; it also opens up for the first time the possibility of culturing human vascularized tumors ex vivo and subjecting them to treatment for a period of up to three weeks. The effects of the treatment can be demonstrated macroscopically, histologically, and molecularly at the cellular level. The results can be analyzed chronologically as well as in relation to the individual patient.

Pre-clinical test models

A high percentage of drug candidates fail even as late as in clinical phase-I and -IIa trials due to insufficient kinetics, lack of efficacy, or unexpected side effects. Models allowing for reliable predictions in these areas during pre-clinical research and development are, therefore, urgently required. The Fraunhofer Group for Life Sciences develops approaches for preclinical trials with human cells, tissues, and stem cells, placing the emphasis on system biology approaches.

Aerosol technology for administration by inhalation

The Fraunhofer Group for Life Sciences develops nebulizing systems for liquid and solid pharmaceuticals and creates prototypes. Positive results have been obtained also with substances such as proteins, peptides, and DNA/RNA vectors, which represent a great challenge as they are sensitive to mechanical forces and easily change their conformation during aerosolization. Furthermore, we characterize nebulizing systems using spray visualization by particle image velocimetry (PIV) or by means of particle size distribution analyses.

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The way into the clinic: clinical investigational drugs and registration trials

 

Active biopharmaceutical ingredients for pre-clinical and clinical trials

The Fraunhofer Group for Life Sciences develops manufacturing processes for biopharmaceutical candidate drugs and manufactures pilot batches for early-phase clinical trials in compliance with the Good Manufacturing Practice (GMP) guidelines. Heterologous expression systems based on microorganisms (E. coli), plants, and mammalian cells (CHO) are normally used for this. This allows antibodies, growth factors, ligands, and nucleic acids to be provided as raw materials for clinical investigational drug products. But also specialties such as bacteriophages, viruses, and virus-like particles can be manufactured on a gram scale for clinical trials.

A category of increasing importance is that of active ingredients based on antibodies and nucleic acids. They are duly considered by the Fraunhofer Group for Life Sciences in fundamental research to develop platform technologies comprising robust and standardized production cell lines, culturing techniques, and strategies for purification of the active ingredients. The aim is to use platform technologies for the manufacture of investigational drug products and to optimally exploit the synergy within the Fraunhofer Group for Life Sciences in order to significantly reduce the time span from the idea stage to clinical testing.

For the manufacture of active pharmaceutical ingredients for pre-clinical and clinical research, multi-purpose GMP facilities with bioreactors for cell culturing and appropriate process chromatography and filtration systems are available. These facilities comply with the requirements of both the European Medicines Agency EMA and the American Food and Drug Administration FDA. In addition, the Group operates a GMP clean-room unit for the aseptic filling and finishing of clinical investigational drug products.

Pre-clinical studies

For drug testing, animal experiments continue to be mandatory in many areas. The Fraunhofer Group for Life Sciences offers investigations and toxicity studies in rodents and non-rodents, performed in compliance with GLP regulations, in order to analyze, for instance, aspects of toxico- and pharmacokinetics. These studies allow subchronic and chronic toxicity to be recognized, and furthermore carcinogenic, teratogenic, and mutagenic effects can be identified. Different models are available for the study of respiratory diseases such as allergies, inflammations, infections, asthma, and chronic obstructive pulmonary disease (COPD).

In vitro methods are used whenever possible to replace animal experiments. Of special importance in this regard are studies in primary human cells as well as in whole pieces of tissue using the precision-cut slice technology.

Phase-0 trials

The institutes of the Fraunhofer Group for Life Sciences are capable of conducting both pre-clinical and clinical trials for respiratory diseases in-house. Important aims of the Group include the definition and introduction of a phase 0 in clinical testing, featuring administration of the drug candidate to humans at a very early stage and at very low doses. This low dosage, corresponding to one hundredth of the pharmacologically effective dose, requires sufficiently sensitive analytical methods: high-performance liquid chromatography combined with tandem mass spectrometry (HPLC-MS/MS). This guarantees seamless integration of pre-clinical investigations and clinical trials.

Clinical trials airways

The Fraunhofer Group for Life Sciences conducts phase-I and -II clinical trials for the registration of pharmaceuticals, the focus being on diseases of the respiratory tract with the indications asthma, COPD, and allergic rhinitis. Due to the challenge chambers for airborne allergens (grass pollen, house dust) which the Group has at its disposal, there is no necessity to perform field studies. Superior clinical research expertise exists in the field of segmental allergen challenge and segmental drug administration with a bronchoscope as well as in the collection of lung lavage fluid and biopsies for a wide range of endpoints including gene and protein expressions. The studies are performed in compliance with GCP requirements.

Translational research

In spite of enormous investment in research and development (R&D) on the part of the pharmaceutical industry, the relative return on that expenditure as determined by the number of registered novel medications is continually decreasing. Ninety percent of all drug candidates fail because of deficiencies in efficacy and/or safety after the first trials in man. This shows that there is a major problem transferring pre-clinical studies to the clinical situation. The aims of translational research are to assure better “translatability” of early development data to late clinical data and thus to increase the reliability of predictions. In close cooperation between research organizations and clinical institutions, new methods are jointly developed which directly implement the results of basic research in disease prevention, diagnosis, and therapy. Vice versa, observations made in patients can quickly be communicated to the scientists involved in basic research.

By means of a methodological, systematic translation process, the aim is to develop methods and processes that offer high predictive reliability and are therefore capable of supporting the critical step from the preclinical to the clinical stage. This includes the establishment of new validated biomarkers, phase-O clinical trials with micro-doses of the candidate drug, and also high-throughput methods of modern molecular biology to enable integration of comparisons between patients and healthy volunteers.

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Pharmaco-ecology – environmental risks and side effects

Pharmaceutically active substances may be introduced into the environment in a variety of different ways. The main source is humankind, excreting previously ingested medicines or disposing of remainders via the sewage system. Many pharmaceuticals are soluble in lipids (lipophilic) and thus likely to accumulate in the environment (bioaccumulation). Therapeutic preparations are designed to be stable and may therefore persist in the environment for a long time, in particular when they are deposited in sediments. Problems are caused above all by substance mixtures, which induce specific effects that are desired in the human patient but may lead to unwanted effects in the environment, even at low concentrations and over a long period of time.

Assessment of potential environmental risks of pharmaceuticals

Many studies have provided evidence of the presence of pharmaceutical agents in bodies of water and sediments. This is why the registration of new drugs requires an ever increasing amount of testing with regard to their environmental behavior. The Fraunhofer Group for Life Sciences has many years of experience in environmental chemistry and ecotoxicology and performs such testing on behalf of its clients. In the assessment of risks both to consumers and to the environment associated with pharmaceuticals and their residues, the Group pursues an integrative strategy. This strategy includes sensitive detection methods, ecotoxicity tests and bioaccumulation studies, models for exposure assessment, and biotechnological and procedural elimination processes.

Ecologically compatible product design

Fraunhofer scientists collaborate in ecotoxicology and toxicology committees and are thus involved in the elaboration of fundamentals that serve as a basis for draft submissions to authorities and for the definition of requirements to be met by future pharmaceuticals. For the pharmaceutical industry, we conduct studies and develop models for ecologically compatible product design. Expert reports created at an early stage in the drug development process put companies in a position to save unnecessary expenses.

Specific removal of pharmaceuticals from the water cycle

As the available methods for degradation and removal of pharmaceuticals from wastewater, such as ozonolysis or adsorption on activated carbon, are either very costly or the process itself may produce toxic degradation products, we are pursuing a completely new approach: we are removing the pollutants using specific adsorbers produced from nanostructured plastics. During the manufacturing process, the plastic beads are provided with a biofunctional surface – a process referred to as “molecular imprinting”. It creates selective molecular recognition sites in the polymers (NanoMIPs), which remain after the manufacturing process.

In a model, we were able to adsorb 500 micrograms of pentoxifylline, which is a widespread micropollutant, in one gram of the NanoMIPs. Pentoxifylline has been classified in the highest water pollution class – namely it is considered to be “severely hazardous to water”. The specific adsorber beads can be incorporated into a membrane. It is also possible to give the beads a magnetizable core to allow for adsorber particles – together with the adsorbed pharmaceuticals – to be trapped using a magnetic separator. In particular for organizations producing large amounts of micropollutants (such as hospitals) NanoMIPs may help minimize pollution or even prevent such pollutants from being introduced into the water cycle via contaminated wastewater.

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