Optogenetic control of apical constriction induces synthetic morphogenesis in mammalian tissues

The evolution of developmental biology through conceptual and technological revolutions

Developmental biology-the study of the processes by which cells, tissues, and organisms develop and change over time-has entered a new golden age. After the molecular genetics revolution in the 80s and 90s and the diversification of the field in the early 21st century, we have entered a phase when powerful technologies provide new approaches and open unexplored avenues. Progress in the field has been accelerated by advances in genomics, imaging, engineering, and computational biology and by emerging model systems ranging from tardigrades to organoids. We summarize how revolutionary technologies have led to remarkable progress in understanding animal development. We describe how classic questions in gene regulation, pattern formation, morphogenesis, organogenesis, and stem cell biology are being revisited. We discuss the connections of development with evolution, self-organization, metabolism, time, and ecology. We speculate how developmental biology might evolve in an era of synthetic biology, artificial intelligence, and human engineering.

The Role of Biophysical Factors in Organ Development: Insights from Current Organoid Models

Biophysical factors play a fundamental role in human embryonic development. Traditional in vitro models of organogenesis focused on the biochemical environment and did not consider the effects of mechanical forces on developing tissue. While most human tissue has a Young's modulus in the low kilopascal range, the standard cell culture substrate, plasma-treated polystyrene, has a Young's modulus of 3 gigapascals, making it 10,000-100,000 times stiffer than native tissues. Modern in vitro approaches attempt to recapitulate the biophysical niche of native organs and have yielded more clinically relevant models of human tissues. Since Clevers' conception of intestinal organoids in 2009, the field has expanded rapidly, generating stem-cell derived structures, which are transcriptionally similar to fetal tissues, for nearly every organ system in the human body. For this reason, we conjecture that organoids will make their first clinical impact in fetal regenerative medicine as the structures generated ex vivo will better match native fetal tissues. Moreover, autologously sourced transplanted tissues would be able to grow with the developing embryo in a dynamic, fetal environment. As organoid technologies evolve, the resultant tissues will approach the structure and function of adult human organs and may help bridge the gap between preclinical drug candidates and clinically approved therapeutics. In this review, we discuss roles of tissue stiffness, viscoelasticity, and shear forces in organ formation and disease development, suggesting that these physical parameters should be further integrated into organoid models to improve their physiological relevance and therapeutic applicability. It also points to the mechanotransductive Hippo-YAP/TAZ signaling pathway as a key player in the interplay between extracellular matrix stiffness, cellular mechanics, and biochemical pathways. We conclude by highlighting how frontiers in physics can be applied to biology, for example, how quantum entanglement may be applied to better predict spontaneous DNA mutations. In the future, contemporary physical theories may be leveraged to better understand seemingly stochastic events during organogenesis.

Engineering Cell Instructive Microenvironments for In Vitro Replication of Functional Barrier Organs

Multicellular organisms exhibit synergistic effects among their components, giving rise to emergent properties crucial for their genesis and overall functionality and survival. Morphogenesis involves and relies upon intricate and biunivocal interactions among cells and their environment, that is, the extracellular matrix (ECM). Cells secrete their own ECM, which in turn, regulates their morphogenetic program by controlling time and space presentation of matricellular signals. The ECM, once considered passive, is now recognized as an informative space where both biochemical and biophysical signals are tightly orchestrated. Replicating this sophisticated and highly interconnected informative media in a synthetic scaffold for tissue engineering is unattainable with current technology and this limits the capability to engineer functional human organs in vitro and in vivo. This review explores current limitations to in vitro organ morphogenesis, emphasizing the interplay of gene regulatory networks, mechanical factors, and tissue microenvironment cues. In vitro efforts to replicate biological processes for barrier organs such as the lung and intestine, are examined. The importance of maintaining cells within their native microenvironmental context is highlighted to accurately replicate organ-specific properties. The review underscores the necessity for microphysiological systems that faithfully reproduce cell-native interactions, for advancing the understanding of developmental disorders and disease progression.

Advanced 3D imaging and organoid bioprinting for biomedical research and therapeutic applications

Organoid cultures offer a valuable platform for studying organ-level biology, allowing for a closer mimicry of human physiology compared to traditional two-dimensional cell culture systems or non-primate animal models. While many organoid cultures use cell aggregates or decellularized extracellular matrices as scaffolds, they often lack precise biochemical and biophysical microenvironments. In contrast, three-dimensional (3D) bioprinting allows precise placement of organoids or spheroids, providing enhanced spatial control and facilitating the direct fusion for the formation of large-scale functional tissues in vitro. In addition, 3D bioprinting enables fine tuning of biochemical and biophysical cues to support organoid development and maturation. With advances in the organoid technology and its potential applications across diverse research fields such as cell biology, developmental biology, disease pathology, precision medicine, drug toxicology, and tissue engineering, organoid imaging has become a crucial aspect of physiological and pathological studies. This review highlights the recent advancements in imaging technologies that have significantly contributed to organoid research. Additionally, we discuss various bioprinting techniques, emphasizing their applications in organoid bioprinting. Integrating 3D imaging tools into a bioprinting platform allows real-time visualization while facilitating quality control, optimization, and comprehensive bioprinting assessment. Similarly, combining imaging technologies with organoid bioprinting can provide valuable insights into tissue formation, maturation, functions, and therapeutic responses. This approach not only improves the reproducibility of physiologically relevant tissues but also enhances understanding of complex biological processes. Thus, careful selection of bioprinting modalities, coupled with appropriate imaging techniques, holds the potential to create a versatile platform capable of addressing existing challenges and harnessing opportunities in these rapidly evolving fields.

Photoactivation of LOV domains with chemiluminescence

Optogenetics has opened new possibilities in the remote control of diverse cellular functions with high spatiotemporal precision using light. However, delivering light to optically non-transparent systems remains a challenge. Here, we describe the photoactivation of light-oxygen-voltage-sensing domains (LOV domains) with in situ generated light from a chemiluminescence reaction between luminol and H2O2. This activation is possible due to the spectral overlap between the blue chemiluminescence emission and the absorption bands of the flavin chromophore in LOV domains. All four LOV domain proteins with diverse backgrounds and structures (iLID, BcLOV4, nMagHigh/pMagHigh, and VVDHigh) were photoactivated by chemiluminescence as demonstrated using a bead aggregation assay. The photoactivation with chemiluminescence required a critical light-output below which the LOV domains reversed back to their dark state with protein characteristic kinetics. Furthermore, spatially confined chemiluminescence produced inside giant unilamellar vesicles (GUVs) was able to photoactivate proteins both on the membrane and in solution, leading to the recruitment of the corresponding proteins to the GUV membrane. Finally, we showed that reactive oxygen species produced by neutrophil like cells can be converted into sufficient chemiluminescence to recruit the photoswitchable protein BcLOV4-mCherry from solution to the cell membrane. The findings highlight the utility of chemiluminescence as an endogenous light source for optogenetic applications, offering new possibilities for studying cellular processes in optically non-transparent systems.

Mapping morphogenesis and mechanics in embryo models

Recent methodological advances in measurements of geometry and forces in the early embryo and its models are enabling a deeper understanding of the complex interplay of genetics, mechanics and geometry during development.

Light-Induced Nanoscale Deformation in Azobenzene Thin Film Triggers Rapid Intracellular Ca2+ Increase via Mechanosensitive Cation Channels

Epithelial cells are in continuous dynamic biochemical and physical interaction with their extracellular environment. Ultimately, this interplay guides fundamental physiological processes. In these interactions, cells generate fast local and global transients of Ca2+ ions, which act as key intracellular messengers. However, the mechanical triggers initiating these responses have remained unclear. Light-responsive materials offer intriguing possibilities to dynamically modify the physical niche of the cells. Here, a light-sensitive azobenzene-based glassy material that can be micropatterned with visible light to undergo spatiotemporally controlled deformations is used. Real-time monitoring of consequential rapid intracellular Ca2+ signals reveals that the mechanosensitive cation channel Piezo1 has a major role in generating the Ca2+ transients after nanoscale mechanical deformation of the cell culture substrate. Furthermore, the studies indicate that Piezo1 preferably responds to shear deformation at the cell-material interphase rather than to absolute topographical change of the substrate. Finally, the experimentally verified computational model suggests that Na+ entering alongside Ca2+ through the mechanosensitive cation channels modulates the duration of Ca2+ transients, influencing differently the directly stimulated cells and their neighbors. This highlights the complexity of mechanical signaling in multicellular systems. These results give mechanistic understanding on how cells respond to rapid nanoscale material dynamics and deformations.

'Chip'-ing away at morphogenesis - application of organ-on-chip technologies to study tissue morphogenesis

Emergent cell behaviors that drive tissue morphogenesis are the integrated product of instructions from gene regulatory networks, mechanics and signals from the local tissue microenvironment. How these discrete inputs intersect to coordinate diverse morphogenic events is a critical area of interest. Organ-on-chip technology has revolutionized the ability to construct and manipulate miniaturized human tissues with organotypic three-dimensional architectures in vitro. Applications of organ-on-chip platforms have increasingly transitioned from proof-of-concept tissue engineering to discovery biology, furthering our understanding of molecular and mechanical mechanisms that operate across biological scales to orchestrate tissue morphogenesis. Here, we provide the biological framework to harness organ-on-chip systems to study tissue morphogenesis, and we highlight recent examples where organ-on-chips and associated microphysiological systems have enabled new mechanistic insight in diverse morphogenic settings. We further highlight the use of organ-on-chip platforms as emerging test beds for cell and developmental biology.

The reversibility of cellular mechano-activation

The cellular microenvironment is highly heterogeneous and dynamic. Therefore, cells must be equipped with molecular tools to adapt and respond to constantly fluctuating inputs. One such input is mechanical force, which activates signalling and regulates cell behaviour in the process of mechanotransduction. Whereas the mechanisms activating mechanotransduction are well studied, the reversibility of this process, whereby cells disassemble and reverse force-activated signalling pathways upon cessation of mechanical stimulation is far less understood. In this review we will outline some of the key experimental techniques to investigate the reversibility of mechanical signalling, and key discoveries arising from them.

Quantitative insights in tissue growth and morphogenesis with optogenetics

Cells communicate with each other to jointly regulate cellular processes during cellular differentiation and tissue morphogenesis. This multiscale coordination arises through the spatiotemporal activity of morphogens to pattern cell signaling and transcriptional factor activity. This coded information controls cell mechanics, proliferation, and differentiation to shape the growth and morphogenesis of organs. While many of the molecular components and physical interactions have been identified in key model developmental systems, there are still many unresolved questions related to the dynamics involved due to challenges in precisely perturbing and quantitatively measuring signaling dynamics. Recently, a broad range of synthetic optogenetic tools have been developed and employed to quantitatively define relationships between signal transduction and downstream cellular responses. These optogenetic tools can control intracellular activities at the single cell or whole tissue scale to direct subsequent biological processes. In this brief review, we highlight a selected set of studies that develop and implement optogenetic tools to unravel quantitative biophysical mechanisms for tissue growth and morphogenesis across a broad range of biological systems through the manipulation of morphogens, signal transduction cascades, and cell mechanics. More generally, we discuss how optogenetic tools have emerged as a powerful platform for probing and controlling multicellular development.

Mapping mechanical stress in curved epithelia of designed size and shape

The function of organs such as lungs, kidneys and mammary glands relies on the three-dimensional geometry of their epithelium. To adopt shapes such as spheres, tubes and ellipsoids, epithelia generate mechanical stresses that are generally unknown. Here we engineer curved epithelial monolayers of controlled size and shape and map their state of stress. We design pressurized epithelia with circular, rectangular and ellipsoidal footprints. We develop a computational method, called curved monolayer stress microscopy, to map the stress tensor in these epithelia. This method establishes a correspondence between epithelial shape and mechanical stress without assumptions of material properties. In epithelia with spherical geometry we show that stress weakly increases with areal strain in a size-independent manner. In epithelia with rectangular and ellipsoidal cross-section we find pronounced stress anisotropies that impact cell alignment. Our approach enables a systematic study of how geometry and stress influence epithelial fate and function in three-dimensions.

Engineering tools for quantifying and manipulating forces in epithelia

The integrity of epithelia is maintained within dynamic mechanical environments during tissue development and homeostasis. Understanding how epithelial cells mechanosignal and respond collectively or individually is critical to providing insight into developmental and (patho)physiological processes. Yet, inferring or mimicking mechanical forces and downstream mechanical signaling as they occur in epithelia presents unique challenges. A variety of in vitro approaches have been used to dissect the role of mechanics in regulating epithelia organization. Here, we review approaches and results from research into how epithelial cells communicate through mechanical cues to maintain tissue organization and integrity. We summarize the unique advantages and disadvantages of various reduced-order model systems to guide researchers in choosing appropriate experimental systems. These model systems include 3D, 2D, and 1D micromanipulation methods, single cell studies, and noninvasive force inference and measurement techniques. We also highlight a number of in silico biophysical models that are informed by in vitro and in vivo observations. Together, a combination of theoretical and experimental models will aid future experiment designs and provide predictive insight into mechanically driven behaviors of epithelial dynamics.

Wrinkling Instability in Unsupported Epithelial Sheets

We investigate the elasticity of an unsupported epithelial monolayer and we discover that unlike a thin solid plate, which wrinkles if geometrically incompatible with the underlying substrate, the epithelium may do so even in the absence of the substrate. From a cell-based model, we derive an exact elasticity theory and discover wrinkling driven by the differential apico-basal surface tension. Our theory is mapped onto that for supported plates by introducing a phantom substrate whose stiffness is finite beyond a critical differential tension. This suggests a new mechanism for an autonomous control of tissues over the length scale of their surface patterns.

A disordered tether to iLID improves photoswitchable protein patterning on model membranes

Reversible protein patterning on model membranes is important to reproduce spatiotemporal protein dynamics in vitro. An engineered version of iLID, disiLID, with a disordered domain as a membrane tether improves the recruitment of Nano under blue light and the reversibility in the dark, which enables protein patterning on membranes with higher spatiotemporal precision.

Middle-out methods for spatiotemporal tissue engineering of organoids

Organoids recapitulate many aspects of the complex three-dimensional (3D) organization found within native tissues and even display tissue and organ-level functionality. Traditional approaches to organoid culture have largely employed a top-down tissue engineering strategy, whereby cells are encapsulated in a 3D matrix, such as Matrigel, alongside well-defined biochemical cues that direct morphogenesis. However, the lack of spatiotemporal control over niche properties renders cellular processes largely stochastic. Therefore, bottom-up tissue engineering approaches have evolved to address some of these limitations and focus on strategies to assemble tissue building blocks with defined multi-scale spatial organization. However, bottom-up design reduces the capacity for self-organization that underpins organoid morphogenesis. Here, we introduce an emerging framework, which we term middle-out strategies, that relies on existing design principles and combines top-down design of defined synthetic matrices that support proliferation and self-organization with bottom-up modular engineered intervention to limit the degrees of freedom in the dynamic process of organoid morphogenesis. We posit that this strategy will provide key advances to guide the growth of organoids with precise geometries, structures and function, thereby facilitating an unprecedented level of biomimicry to accelerate the utility of organoids to more translationally relevant applications.

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.

Scaling up complexity in synthetic developmental biology

The application of synthetic biology approaches to study development opens the possibility to build and manipulate developmental processes to understand them better. Researchers have reconstituted fundamental developmental processes, such as cell patterning and sorting, by engineering gene circuits in vitro. Moreover, new tools have been created that allow for the control of developmental processes in more complex organoids and embryos. Synthetic approaches allow testing of which components are sufficient to reproduce a developmental process and under which conditions as well as what effect perturbations have on other processes. We envision that the future of synthetic developmental biology requires an increase in the diversity of available tools and further efforts to combine multiple developmental processes into one system.