ERC FUNDED PROJECTS

Large protein complexes carry out some of the most complex functions in biology. Such structures are often assembled spontaneously from individual components through the process of self-assembly. If self-assembled protein complexes could be engineered from first principle it would enable a wide range of applications in biomedicine, nanotechnology and materials science. Recently, approaches to rationally design proteins to self-assembly into predefined structures have emerged. The highlight of this work is the design of protein cages that may be engineered into protein containers. However, current approaches for self-assembly design does not result in the assemblies with the required structural complexity to encode many of the sophisticated functions found in nature. To move forward, we have to learn how to engineer protein subunits with more than one designed interface that can assemble into tightly interacting complexes. In this proposal we propose a new protein design paradigm, shape directed protein design, in order to address shortcomings of the current methodology. The proposed method combines geometric shape matching and computational protein design. Using this approach we will de novo design assemblies with a wide variety of structural states, including protein complexes with cyclic and dihedral symmetry as well as icosahedral protein capsids built from novel protein building blocks. To enable these two design challenges we also develop a high-throughput assay to measure assembly stability in vivo that builds on a three-color fluorescent assay. This method will not only facilitate the screening of orders of magnitude more design constructs, but also enable the application of directed evolution to experimentally improve stable and assembly properties of designed containers as well as other designed assemblies.

2 325 292 €

Start date: 2018-06-01, End date: 2023-05-31

Developing new therapeutic strategies for heart regeneration is a major goal for cardiac biology and medicine. While cardiomyocytes can be generated from human pluripotent stem (hPSC) cells in vitro, it has proven difficult to use these cells to generate a large scale, mature human heart ventricular muscle graft on the injured heart in vivo. The central objective of this proposal is to optimize the generation of a large-scale pure, fully functional human ventricular muscle patch in vivo through the self-assembly of purified human ventricular progenitors and the localized expression of defined paracrine factors that drive their expansion, differentiation, vascularization, matrix formation, and maturation. Recently, we have found that purified hPSC-derived ventricular progenitors (HVPs) can self-assemble in vivo on the epicardial surface into a 3D vascularized, and functional ventricular patch with its own extracellular matrix via a cell autonomous pathway. A two-step protocol and FACS purification of HVP receptors can generate billions of pure HVPs- The current proposal will lead to the identification of defined paracrine pathways to enhance the survival, grafting/implantation, expansion, differentiation, matrix formation, vascularization and maturation of the graft in vivo. We will captalize on our unique HVP system and our novel modRNA technology to deliver therapeutic strategies by using the in vivo human ventricular muscle to model in vivo arrhythmogenic cardiomyopathy, and optimize the ability of the graft to compensate for the massive loss of functional muscle during ischemic cardiomyopathy and post-myocardial infarction. The studies will lead to new in vivo chimeric models of human cardiac disease and an experimental paradigm to optimize organ-on-organ cardiac tissue engineers of an in vivo, functional mature ventricular patch for cardiomyopathy

2 149 228 €

Start date: 2017-12-01, End date: 2022-11-30

Spider silk is Nature’s high performance material that has the potential to revolutionize the materials industry. However, production and spinning of artificial spider silk fibers are challenging, and current methods to produce silk fibers include denaturing conditions which prevent the silk proteins from assembling into fibers in the same complex way as native silk proteins do. In order to fulfill the potential of spider silk we need to increase our understanding of the silk formation process and decipher how protein folding and interactions relate to mechanical properties of the resulting silk fiber. Recent insights into the physiology and molecular mechanisms of the spinning process has made it possible to develop a biomimetic artificial spider silk spinning device (see our publications Andersson et al. Nat Chem Biol. 2017; Otikovs et al. Angew Chemie Int Engl Ed. 2017). We are, for the first time, able to spin artificial silk fibers in which the proteins adopt correct secondary, tertiary and quaternary structures. The overall objective of ARTSILK is to build on these recent technical leaps and use state-of-the-art technologies to generate artificial silk fibers that are equal or superior to native spider silk in terms of toughness and tensile strength. To reach the overall objective we will use the recently mapped spider genome, protein engineering and single cell RNA (ScRNA) sequencing to design novel silk proteins for fiber production. We will also study the relationship between protein secondary structure formation and fiber mechanical properties in order to decipher the ques that determine mechanical properties of the fiber. This knowledge will be important also for the basic understanding of how soluble proteins covert into b-sheet rich fibrils in, e.g., Alzheimer’s disease. Finally, we will use microfluidic chips to engineer the next generation spinning device and 3D-printing techniques to make reproducible three-dimensional structures of spider silk.

2 000 000 €

Start date: 2019-05-01, End date: 2024-04-30

Cardiovascular disease (CVD), type 2 diabetes (T2D) and obesity, collectively referred to as cardiometabolic disease, together with cancer are the major morbidities and causes of death. With few exceptions, research on cardiometabolic disease and cancer is funded, studied and clinically applied separately without fully taking advantage of knowledge on common pathways and treatment targets through interdisciplinary synergies. The purpose of this proposal is to reveal causal factors connecting and disconnecting cardiometabolic diseases and cancer, and to understand interactions between gut microbiota, host diet and genetic susceptibility in a comprehensive prospective cohort study design to subsequently allow design of intervention strategies to guide more personalized disease prevention. 1. We investigate causality between genetic risk factors for cardiometabolic disease associated traits and future incidence of T2D, CVD, cancer (total/breast/colon/prostate) and mortality (total, CVD- and cancer mortality), searching for causal factors in a prospective cohort with >15 y follow-up (N>30,000, incident cases N=3550, 4713, 5975, 6115 for T2D, CVD, cancer, mortality) 2. For the first time in a large population (N=6000), we investigate how gut and oral microbiome are regulated by dietary factors, gut satiety peptides and host genetics, and how such connections relate to cardiometabolic disease associated traits and cancer 3. We investigate the role of diet and gene-diet interactions of importance for cardiometabolic disease and cancer 4. We perform genotype, biomarker and gut microbiota based diet intervention studies. This inter-disciplinary project contributes to biological understanding of basic disease mechanisms and takes steps towards better possibilities to prevent and treat individuals at high risk for cardiometabolic disease, cancer and death.

2 000 000 €

Start date: 2015-09-01, End date: 2020-08-31