Projekte

We engineer synthetic cellular memory platforms that enable the reconstruction of cellular histories and can be applied as living diagnostics.

A fundamental challenge in biology is to understand how cells function and integrate complex molecular information to perform different behaviors. For example, the differentiation of a stem cell into two daughter cells with distinct identities or the transformation of a normal cell into a cancer cell. This challenge has motivated the creation of numerous technologies facilitating detailed intracellular observations at the level of DNA, RNA, protein, and metabolites. Despite the power of these approaches, they generally require destructive methods and therefore observations are limited to a few snapshots in time or select asynchronous cellular processes. One provocative solution to this is to introduce DNA writing and molecular recording platforms within cells that enable the encoding, storage, and retrieval of molecular information.

Towards the goal of continuously recording molecular events within cells, my laboratory is developing and applying Record-seq, a ‘transcriptional recording’ platform that employs CRISPR spacer acquisition from RNA to capture and convert intracellular RNAs into DNA, permanently storing transcriptional information in the DNA of living cells. The newly acquired sequences serve as transcriptional records, which are retrievable via deep sequencing and can be leverage to reconstruct cellular histories. This technology provides an entirely new mode of interrogating dynamic biological and physiological processes and opens up numerous avenues for future work in engineering cellular systems.

Clinical and immunohistochemical studies indicate that the tumor microenvironment, including stromal and immunocompetent components, plays key roles in the control of tumor progression and response to treatment. Moreover, increased recognition is given to the importance of using human cell- based models to predict the outcome of therapeutic strategies.

The goal of the project is to engineer a 3D human organotypic model of colorectal cancer including associated tumor microenvironment components, as test system for new immune-oncology agents. The further inclusion of hepatocytes in the model in a second phase of the project will enable to investigate, along with the antitumor efficacy, also the possible liver toxicity of the therapeutic agents.

Dimethylfumarate is an emergent pharmaceutical compound with annual sales of 4412 Mio $ in 2016. Currently, the main clinical applications are in treating psoriasis and multiple sclerosis. In addition, dimethylfumarate might be therapeutic against asthma, cancer, inflammatory bowl disease, intracerebral hemorrhage, osteoarthritis, chronic pancreatitis, retinal ischemia, and ischemic stroke.

The goal of this project is to engineer a cell-like device for targeted delivery of the electrophilic drug dimethylfumarate. In the first phase of the project we plan to identify a vesicle based enzyme reaction that is triggered by external stimuli to produce and release dimethylfumarate.

An ideal cell-based diabetes therapy in humans should consist of an autonomous core system enabling closed-loop control of D-glucose sensing and insulin release, coupled to a user-defined control interface that allows the metabolically inert L-glucose to monitor the temporal activity of the therapeutic core. In this context, L-glucose functions as a patient-centred adjuvant molecule that is not only free of hepatic side- effects, but also represents an optimal nutritional sugar for diabetic patients.

The focus of this project is the design and construction of an L-glucose-dependent control interface for future cell-based diabetes therapies and the validation of L-glucose polymersome-dependent control of therapeutic transgene activities in mice.

The chemical and physical processes enabling the transformation of matter in living systems is regulated by complex feedback loops. Such tightly cross-regulated processes enable highly complex reaction cascades as well as transport and exchange mechanisms that have not yet been achieved in synthetic systems. The project „Nanopores as Solid-State Approach to Interlinked Reaction Compartments" strives to simulate isolated feedback mechanisms to investigate the underlying regulation mechanisms in detail and to identify the parameters governing the system.

To fabricate such interlinked reaction compartments, we aim at fabricating nanopore devices based on a solid-state approach using top-down fabrication techniques. Self-assembled monolayers (SAMs) of functional molecular building blocks are physically separated but remain addressable by electrical, optical or electrochemical means. The SAMs are highly oriented which enables correlations between chemical structure and electronic as well as ionic transport properties in single-molecular junctions to be studied. 

Preliminary studies will allow us to mimic a biological response and to investigate isolated feedback mechanisms in detail. Additionally, from a materials point of view, the resulting oligomers may be interesting. Their physical properties are length-dependent and, thanks to a feedback mechanism, their length-distribution may become tunable by specific parameters dictated by the system, leading to a new size-control approach with wide potential applications in material science. Modular systems can easily be expanded with additional functionalities. For example redox-­dependent chromophores that will facilitate the investigation of the systems dynamics as it can be investigated by optical microscopy.

The project is not only geared towards investigating feedback mechanisms across vesicle membranes but also towards integrating vesicles as molecular factories. With such vesicles, molecular devices enabling photo-induced charge separation across the vesicle membrane will be studied. In a later stage of the project, we envisage electrochemical interconnecting of different functionalized vesicles to build up gradients of chemical potentials. 

Molecular systems derive their functional breadth from the interplay of multiple elements. The successful cooperation of these elements is often limited to narrow windows of operation, which are often difficult to identify.

We are optimizing complex in vitro systems so they can successfully operate in these windows. For this, we develop cell free systems that allow the synthesis of multiple catalysts and other protein-based elements, and compartmentalize the synthesis in nanoliter or picoliter-sized droplets. This helps us to investigate thousands of system compositions per minute. We use this to develop design rules for multi-membered systems and prepare such droplets for analysis in a classical way (i.e., by fluorescence) and by label-free methods, such as mass-spectrometry. This way we can optimize system function for a variety of objectives, ranging from enzyme evolution to the engineering of smart systems for metabolic diseases.

This project shows true interdisciplinary, transversal research: Clinical tests are conducted with light sensitive, molecular systems in partnership with the Friedrich-Miescher Institute of our industry-partner, Novartis. Should the tests be successful, this project could enable blind people to see in black and white again and, eventually, regain their full color vision.

Retinitis pigmentosa (RP) refers to a diverse group of progressive, hereditary diseases of the retina that lead to incurable blindness and affects 2 million people worldwide. Artificial photoreceptors constructed by gene delivery of light-activated channels or pumps (functional molecular modules) to surviving cell types in the remaining retinal circuit have shown to restore photosensitivity in animal models of RP at the level of the retina and cortex as well as behaviourally.

Simply said, in a degenerated macula the first step is missing: there are no more rods and cones that can detect light and subsequently convert light into neural signal. The visual nerves however are intact. In tests with apes and dogs the genetically delivered molecular factories dock successfully with the visual nerve of the eye and are activated by light, producing certain impulses that enables blind animals to see again.

One major objective in synthetic biology is the bottom-up assembly of functional nanocells. These structures consist of lipid or polymer membranes, which serve as architectural scaffolds for functional modules such as membrane and soluble proteins. The former is embedded in the membrane, while the latter is encapsulated inside the container. The correct orientation of membrane proteins in the membrane is essential in order to avoid functional short circuits and obtain fully functional nanocells.

In this project, we propose the use of fusion proteins combined with clipping proteins to functionalize nanocells with more than one type of membrane protein.

This project uses state-of-the-art molecular and genomic editing platforms to engineer immune cells for applications in biotechnology and cellular immunotherapy.

Our ongoing projects are focused on applying molecular and genome editing tools to engineer various types of immune cells. The precise genomic exchange of highly similar immunogenomic genes has not been demonstrated before using genome-editing tools, thus a series of aims and milestones to advance this goal have been established. For example, in one of aims we are engineering mammalian cellular factories for protein production. In another aim we are using precise genome editing to improve cellular therapeutics for transplantation and cancer. We will combine our efforts with the network of NCCR researchers to push the boundaries of immunological systems engineering. 

Scientific Highlights

• Plug-and-(dis)play mammalian cells. We have used precise genome editing to develop a platform for rapid generation of stable cell lines capable of surface expression and secretion of recombinant proteins. The simplicity of our plug-and-(dis)play platform is highlighted by the fact that it only requires a single transfection and screening step to generate stable cells. We envision these cell lines can be applied for generating recombinant protein reagents and therapeutics. 
• Reprogramming MHC-specificity immune cells. We have established a proof-of-concept for MHC-allelic replacement, which could be used in the future for improving the donor-host matching, which is a major challenge in allogeneic cellular transplantations in cancer. We used genome editing methods to precisely exchange the MHC region of immune cells, which were then subsequently verified for functions immune activity. Our methods can be applied for the engineering of other immunogenomic regions, which would have value in cellular immunotherapy.