Defined matrices for epithelial organoid culture and disease modelling

Advances in our understanding of the biology of stem cells and their niches have provided the necessary foundation to create in vitro complex self-organizing three-dimensional (3D) structures called organoids. While organoids represent a highly promising new class of biological model systems, the translational potential of these systems is currently limited by their dependence on animal-derived matrices, particularly Matrigel, an extracellular matrix (ECM) derived from mouse tumors. Apart from their immunogenicity and batch-to-batch variability, these matrices do not allow modulation of ECM composition and, accordingly, systematic adaptation of properties to specific cells and tissues. To address this issue, new biomaterial-based approaches have focused on the development of synthetic alternatives to Matrigel. This work focuses on the development of chemically defined matrices to elucidate the specific effects of ECM, with the goal of further increasing the translational relevance of epithelial organoids for regenerative medicine and disease modeling applications. Given the critical functionality of the intestine and the liver, and emergence of debilitating diseases due to damage to these organs, I have mainly focused on intestinal and liver organoids. First, I developed a new family of synthetic poly(ethylene glycol) (PEG)-based hydrogels, so-called low-defect thiol-Michael addition (LDTM) hydrogels, by modifying the conventional crosslinking strategy of existing PEG-co-peptide hydrogels formed by Michael addition of bis-cysteine peptides and vinyl sulfone-terminated PEG macromers. These mechanically tunable hydrogels are chemically defined and can be prepared with minimal batch-to-batch variability. They also allow the derivation of mouse and human intestinal and liver organoids, the latter without any animal components. Furthermore, I leveraged the modularity of synthetic matrices and derivation of liver ductal organoids in these matrices, to model some aspects of liver fibrosis, a global health problem affecting millions of people, and for which organ transplantation is the only medical solution. I demonstrated the role of tissue stiffness, a feature usually neglected in fibrosis models, on a regenerative mechanism associated with liver fibrosis called ductular reaction (DR). Human ductal liver organoids showed reduced proliferative capacity in LDTM gels with stiffness values similar to those of fibrotic liver tissue. In addition, transcriptomic analysis revealed impaired stemness potential, as well as concomitant induction of inflammatory responses. Overall, the newly developed hydrogels provide a reproducible, chemically defined environment that can be readily prepared with minimal batch-to-batch variability for multiple stem cell types and for organoid culture. Successful derivation of human intestinal and liver organoids in these matrices may open exciting prospects for clinical applications of organoids. In addition, the modularity of these matrices to mimic the ECM in pathological tissues, particularly the aberrant mechanical properties of fibrotic tissues, will enable the development of powerful disease models and predictive drug screening platforms and promote the development of new therapies.

New Tools for Hydrogel-Based 3D Bioprinting

Andrea Negro

The in vitro recapitulation of tissue and organ function represents one of the main objectives of tissue engineering. Developments in this field have numerous applications, from alleviating the shortage of donor organs to providingmore representative platforms for drug testing. As such, there is an increasingly significant body of literature devoted to the development of better strategies to reconstruct living matter outside of the body. The three-dimensional (3D) architecture of a tissue, its histoarchitecture, is a key aspect to consider when engineering a tissue. Indeed, tissue function not only arises from individual elements that compose the tissue, its different cell types and their extracellular matrices (ECM), but also fromtheir precise spatial arrangement and interactions. Bioprinting is considered as one of the most promising techniques to recapitulate the complexity of in vivo histoarchitectures. Early bioprinting examples have shown successful application of inkjet printing to geometrically arrange cells and biomolecules in 2D and, to a much lesser extent, in 3D. However, no group has shown yet a technological platformable to print a living tissue construct whose make-up could even closelymimic the histoarchitecture of a native tissue. In this thesis the most significant challenges in using inkjet printers for tissue engineering were tackled. Perhaps the most critical bottleneck of state-of-the-art bioprinting is the lack of suitable bioinks; precursor liquids with distinct physico-chemical properties that very rapidly transforminto solid hydrogels and also possess the necessary bioactive characteristics to guide cell development into a functional tissue. To this end, a novel double network hydrogel systemwas conceived which combines ultra-rapid cross-linking of alginate, a biologically inert polysaccharide network, with the slower enzymatic crosslinking of a synthetic but highly bioactive poly(ethylene glycol) (PEG) gel. The latter could be tailored virtually on demand tomimic a desired ECM in a tissue. Based on this bioink concept it was demonstrated that complex multicomponent 3D shapes could be printed. Importantly, using primary human fibroblasts as model system, the bioinks showed outstanding characteristics as cellular microenvironments, facilitating rapid 3D cell migration and self-organization into multicellular networks. To mimic the spatial complexity of living tissues, it is crucial to master the deposition of multiple, cell-containing bioinks into user-defined 3D structures. Each bioink could thus mimic a specific cell/ECMcomponent present in a native tissue. To be able to reproduce an appropriate histoarchitecture, bioinks have to be deposited precisely enough to approximate their natural 3D spatial arrangement down to a cellular scale. Technically, this implies that the dispensing units must be extremely well aligned and synchronized to one another in order to pattern according to a specified design. In order to address these challenges, several novel bioprinting concepts were developed, which allowed the patterning of multiple bioinks containing living cells into 3D tissue-like geometries. In the last part of this thesis, an important first step towards the engineering of macroscopic tissue models was taken. Accordingly, a fundamental requirement for the viability and maturation of a printed tissue construct is the supply of nutrients and growth factors through a microfluidic network, similar to the vascularization in a native tissue. To this end, a novel approach for the printing of 3D constructs with an interconnected channel network enabling rapid nutrient transport was devised. This was achieved by exploiting the multicomponent printing developed earlier. A channel network inside the construct was patterned using a degradable hydrogel that could be selectively removed to leave behind the perfusable microfluidic system. Moreover, it was possible to combine this sacrificial layer approach with cell-containing bioinks to generate a cellularized perfusable tissue model. Encouraging preliminary long-termculture experiments revealed that dynamic cell culture conditions could be maintained, leading to viable cell growth over more than one week under perfusion conditions. Taken together, this thesis presents several important steps toward an inkjet-based platform for in vitro tissue engineering. It is expected that the strategies developed here will provide a solid basis for future advances in the emerging bioprinting field.

EPFL2014

Photopatterning of Synthetic Hydrogels

Katarzyna Mosiewicz

In recent years sophisticated biomaterials have made a significant impact on our understanding of cellular behavior, particularly in the fields of stem cell research and tissue engineering. Nevertheless, the promising potential of stem cells for regenerative medicine has remained largely unmet. One reason for such limitations could be that there is still incomplete understanding of stem cell behavior due to a lack of advanced in vitro tools suitable to achieve adequate control over cellular processes. By mimicking the dynamic and complex biophysical and biochemical interactions between cells and their natural extracellular matrixes (ECMs), it is possible that we may bridge this gap between current limited in vitro models and complex in vivo organisms. In this thesis, an innovative class of biomaterials is presented that enables the flexible in vitro recapitulation of the dynamic biochemical and biophysical signaling involved in controlling cell fate. Such systems of increasing fidelity to real physiological processes could bring new insights into fundamental cell biology as well as bring us to closer towards cell-based therapeutics applications. In order to achieve a dynamic artificial ECM (aECM), we designed chemical schemes which would allow us to control the biochemical and biophysical properties of the hydrogel in space, time and intensity. The chosen concept is built on a synthetic hydrogel providing static physicochemical support, while spatiotemporal control over a single or multiple signals is achieved by spatiotemporal photoactivation reactions within this hydrogel. Indeed, by modulating the duration, location and intensity of illumination, desired heterogeneities in biochemical and biophysical signal can be introduced in the otherwise homogeneous and static hydrogel network. To implement the designed hydrogel photo-patterning tool, new chemical components were synthesized. Synthetic hydrogels based on poly (ethylene glycol) (PEG) were utilized due to their inert properties, cell biocompatibility and lack of unspecific protein binding. Biochemical signal tethering was rendered spatiotemporally controllable by adding photosensitivity to the existing enzyme-based crosslinking scheme. This was achieved by functionalizing one of enzymatic substrate with a photo-labile “caging” moiety, thereby preventing crosslinking to occur until light illumination. This caged substrate was incorporated into the hydrogel network and served as a light-controllable and specific ligand-binding site. Importantly, it was possible to photo-pattern proteins, which are much complex than peptide-based biomolecules, and their bioactivity was fully preserved with this site-specific immobilization scheme. It was also possible to pattern biophysical cues by making the Michael-type (MT) addition reaction for crosslinking PEG-based hydrogel photosensitive. In this case, the thiol moieties of one of the reactive PEG macromers undergoing crosslinking, were equipped with a caging group which prevented its susceptibility to the counter-reactive functionality, the vinyl sulfone group. Thus, the crosslinking density of the hydrogel backbone could be controlled by light, which was directly translated into differential patterns of hydrogel stiffness. Using this approach, user-defined biochemical and biophysical patterns and even gradients could be obtained in the spatiotemporal manner within the same hydrogel. The crosslinking reaction is the critical parameter in the success of hydrogel photo-patterning, and must rely on a well-controlled and highly selective chemical scheme. Therefore, we also developed a novel enzyme-based cross-linking scheme for synthetic PEG hydrogels. The reaction originates from the naturally occurring post-translational modification of proteins by phosphopantetheine (Ppant) group performed by a family of enzymes known as Ppant transferases (PPTases). By synthesizing biochemical components of this reaction, we implemented a PPTase-catalyzed reaction to form and bio-functionalize PEG hydrogel. The utility of the developed hydrogel platforms was determined in the context of 2D and 3D cell culture. Photo-directed patterns of a cell-adhesive fibronectin fragment triggered adhesion and spreading of muscle progenitor cells, a phenomenon which occurred only within the areas of patterned signaling protein. A photo-patterned elasticity gradient was used to direct mesenchymal stem cell spreading and migration. Finally, the PPTase-based hydrogel was proven to be suitable for 3D culture, as shown by encapsulation of primary human fibroblasts. In this thesis, we demonstrated that a combination of chemical schemes could be assembled to achieve a functional materials toolbox which would begin to reconstruct the complexity of the dynamic in vivo ECM. Such a tool is expected to contribute to the field of cell biology by allowing us to study questions which previously could not be addressed in vitro, and could ultimately contribute to cell-based regenerative medicine.

EPFL2012

Bioengineering stem cell niches in 2D and 3D

Nora Leonardi

Muscle degenerative disorders, such as Duchenne muscular dystrophy, have a profound impact on the quality of life and survival of patients. Transplantation of myoblasts to restore muscle function has been discouraging since these cells die and don't migrate but it has more recently been reported that muscle stem cells, known as satellite cells, have an extraordinary potential to contribute to muscle fiber regeneration, home to their niche and replenish the stem cell pool when injected freshly into damaged muscle. These cells however quickly lose their regenerative potential when cultured in vitro. Adult stem cells are known to be regulated by their microenvironment through a complex mixture of signals including soluble factors, matrix bound proteins, neural input and mechanical properties and the identification of extrinsic factors that can regulate muscle stem cell quiescence and self-renewal has been a focus of research in the Blau lab. Strikingly, recent studies in the Blau lab have shown that muscle stem cells cultured on compliant hydrogels coated with laminin were more viable than those cultured on tissue culture plastic and robustly contributed to muscle regeneration when transplanted into irradiated mouse leg muscles. The aim of this project was to follow up on these findings and to further elucidate the role biophysical and biochemical microenvironmental cues play in the regulation of muscle stem cell fate. Hydrogels have emerged as a popular material to recreate the stem cell niche in vitro due to their biocompatibility, high water content, tissue-like elasticity and diffusive properties and were employed here to fabricate substrates of varying rigidities. The physicochemical properties and tethered protein densities of a range of poyl(ethylene glycol) hydrogels were first characterized to define a suitable set of cell culture substrates. Gel stiffness could be linearly modulated from 2.5 to 45 kPa and the ligand density was found to be in the low femtomolar range. ELISA showed similar protein density on gels of different stiffnesses but immunofluorescence could not fully confirm this. Committed myoblasts were then seeded on these gels and shown to respond to substrate stiffness and ligand density in terms of morphology. Lastly, freshly isolated muscle stem cells were cultured on these gels and on rigid tissue culture plastic and shown to spread more, be more viable and grow more rapidly on stiffer gels as compared to soft ones. Myogenic progression was retrospectively analysed using immunohistochemistry but no differences between culture conditions were observed. Based on the influences of gel rigidity and ligand density observed in vitro, an in vivo assay, the ultimate test of stem cell function, is currently underway.

2009