Pattern Formation and Bistability in a Synthetic Intercellular Genetic Toggle

Differentiation within multicellular organisms is a complex process that helps to establish spatial patterning and tissue formation within the body. Often, the differentiation of cells is governed by morphogens and intercellular signaling molecules that guide the fate of each cell, frequently using toggle-like regulatory components. Synthetic biologists have long sought to recapitulate patterned differentiation with engineered cellular communities, and various methods for differentiating bacteria have been invented. Here, we couple a synthetic corepressive toggle switch with intercellular signaling pathways to create a "quorum-sensing toggle". We show that this circuit not only exhibits population-wide bistability in a well-mixed liquid environment but also generates patterns of differentiation in colonies grown on agar containing an externally supplied morphogen. If coupled to other metabolic processes, circuits such as the one described here would allow for the engineering of spatially patterned, differentiated bacteria for use in biomaterials and bioelectronics.

Harnessing synthetic biology to engineer organoids and tissues

The development of an organism depends on intrinsic genetic programs of progenitor cells and their spatiotemporally complex extrinsic environment. Ex vivo generation of organoids from progenitor cells provides a platform for recapitulating and exploring development. Current approaches rely largely on soluble morphogens or engineered biomaterials to manipulate the physical environment, but the emerging field of synthetic biology provides a powerful toolbox to genetically manipulate cell communication, adhesion, and even cell fate. Applying these modular tools to organoids should lead to a deeper understanding of developmental principles, improved organoid models, and an enhanced capability to design tissues for regenerative purposes.

Synthetic spatial patterning in bacteria: advances based on novel diffusible signals

Engineering multicellular patterning may help in the understanding of some fundamental laws of pattern formation and thus may contribute to the field of developmental biology. Furthermore, advanced spatial control over gene expression may revolutionize fields such as medicine, through organoid or tissue engineering. To date, foundational advances in spatial synthetic biology have often been made in prokaryotes, using artificial gene circuits. In this review, engineered patterns are classified into four levels of increasing complexity, ranging from spatial systems with no diffusible signals to systems with complex multi-diffusor interactions. This classification highlights how the field was held back by a lack of diffusible components. Consequently, we provide a summary of both previously characterized and some new potential candidate small-molecule signals that can regulate gene expression in Escherichia coli. These diffusive signals will help synthetic biologists to successfully engineer increasingly intricate, robust and tuneable spatial structures.

Synthetic Morphogenesis: introducing IEEE journal readers to programming living mammalian cells to make structures

Synthetic morphogenesis is a new engineering discipline, in which cells are genetically engineered to make designed shapes and structures. At least in this early phase of the field, devices tend to make use of natural shape-generating processes that operate in embryonic development, but invoke them artificially at times and in orders of a technologist's choosing. This requires construction of genetic control, sequencing and feedback systems that have close parallels to electronic design, which is one reason the field may be of interest to readers of IEEE journals. The other reason is that synthetic morphogenesis allows the construction of two-way interfaces, especially opto-genetic and opto-electronic, between the living and the electronic, allowing unprecedented information flow and control between the two types of 'machine'. This review introduces synthetic morphogenesis, illustrates what has been achieved, drawing parallels wherever possible between biology and electronics, and looks forward to likely next steps and challenges to be overcome.

Novel synthetic biology approaches for developmental systems

Recently, developmental systems are investigated with increasing technological power. Still, open questions remain, especially concerning self-organization capacity and its control. Here, we present three areas where synthetic biology tools are used in top-down and bottom-up approaches for studying and constructing developmental systems. First, we discuss how synthetic biology tools can improve stem cell-based organoid models. Second, we discuss recent studies employing user-defined perturbations to study embryonic patterning in model species. Third, we present "toy models" of patterning and morphogenesis using synthetic genetic circuits in non-developmental systems. Finally, we discuss how these tools and approaches can specifically benefit the field of embryo models.

Engineered Living Materials: Taxonomies and Emerging Trends

At the intersection of synthetic biology and materials science, the field of engineered living materials (ELMs) has evolved into a new, standalone discipline. The fusion of bioengineering's design-build-test-learn approaches with classical materials science has yielded breakthrough innovations in the synthesis of complex, biologically active materials for functional applications in therapeutics, electronics, construction, and beyond. However, the transdisciplinary nature of the ELM field - and its rapid growth - has made holistic comprehension of achievements related to the tools, techniques, and applications of ELMs difficult across disciplines. To this end, this review proposes an emergent taxonomy of ELM research and uses the categorization to discuss current trends and state-of-the-art advancements, significant opportunities, and imminent challenges for scientists and engineers in the field.

Engineering pattern formation and morphogenesis

The development of natural tissues, organs and bodies depends on mechanisms of patterning and of morphogenesis, typically (but not invariably) in that order, and often several times at different final scales. Using synthetic biology to engineer patterning and morphogenesis will both enhance our basic understanding of how development works, and provide important technologies for advanced tissue engineering. Focusing on mammalian systems built to date, this review describes patterning systems, both contact-mediated and reaction-diffusion, and morphogenetic effectors. It also describes early attempts to connect the two to create self-organizing physical form. The review goes on to consider how these self-organized systems might be modified to increase the complexity and scale of the order they produce, and outlines some possible directions for future research and development.

Cell-in-the-loop pattern formation with optogenetically emulated cell-to-cell signaling

Designing and implementing synthetic biological pattern formation remains challenging due to underlying theoretical complexity as well as the difficulty of engineering multicellular networks biochemically. Here, we introduce a cell-in-the-loop approach where living cells interact through in silico signaling, establishing a new testbed to interrogate theoretical principles when internal cell dynamics are incorporated rather than modeled. We present an easy-to-use theoretical test to predict the emergence of contrasting patterns in gene expression among laterally inhibiting cells. Guided by the theory, we experimentally demonstrate spontaneous checkerboard patterning in an optogenetic setup, where cell-to-cell signaling is emulated with light inputs calculated in silico from real-time gene expression measurements. The scheme successfully produces spontaneous, persistent checkerboard patterns for systems of sixteen patches, in quantitative agreement with theoretical predictions. Our research highlights how tools from dynamical systems theory may inform our understanding of patterning, and illustrates the potential of cell-in-the-loop for engineering synthetic multicellular systems.

Dual-controlled optogenetic system for the rapid down-regulation of protein levels in mammalian cells

Optogenetic switches are emerging molecular tools for studying cellular processes as they offer higher spatiotemporal and quantitative precision than classical, chemical-based switches. Light-controllable gene expression systems designed to upregulate protein expression levels meanwhile show performances superior to their chemical-based counterparts. However, systems to reduce protein levels with similar efficiency are lagging behind. Here, we present a novel two-component, blue light-responsive optogenetic OFF switch ('Blue-OFF'), which enables a rapid and quantitative down-regulation of a protein upon illumination. Blue-OFF combines the first light responsive repressor KRAB-EL222 with the protein degradation module B-LID (blue light-inducible degradation domain) to simultaneously control gene expression and protein stability with a single wavelength. Blue-OFF thus outperforms current optogenetic systems for controlling protein levels. The system is described by a mathematical model which aids in the choice of experimental conditions such as light intensity and illumination regime to obtain the desired outcome. This approach represents an advancement of dual-controlled optogenetic systems in which multiple photosensory modules operate synergistically. As exemplified here for the control of apoptosis in mammalian cell culture, the approach opens up novel perspectives in fundamental research and applications such as tissue engineering.