A method to recapitulate early embryonic spatial patterning in human embryonic stem cells

Application of CRISPR-Based Epigenome Editing Tools for Engineering Programmable Embryo Models

Stem cell-based embryo models (SEMs) have the potential to transform our understanding of early human embryogenesis. A critical step in engineering SEMs is the generation of the major cell types that compose preimplantation embryos including two primary extraembryonic lineages: (i) trophoblast cells, which are crucial for implantation and the establishment of maternal-fetal exchange, and (ii) hypoblast cells, which contribute to yolk sac formation. In addition, both cell types provide key signaling cues necessary for embryonic development. CRISPR-based epigenome editors are programmable devices that allow for efficient and precise activation (CRISPRa) or repression (CRISPRi) of cell fate-determining factors by modulating endogenous regulatory elements. Here, we present a step-by-step method to implement CRISPRa for controlling cell fate in embryonic stem cells based on our work in generation of CRISPR-programmed mouse embryo models.

A high-throughput microfluidic platform for functional hiPSC-derived liver organoids with bile duct- and lobule-like structures

HiPSC-derived organoids have attracted significant attention in stem cell research and regenerative medicine. However, obtaining functional organoids in sufficient quantities, consistent sizes, and reproducible formats remains a significant challenge. Here, we present an innovative microfluidic platform for the high-throughput production of HAMA core-shell microspheres (HCSM) for the encapsulation and differentiation of hiPSCs. Fish gelatin and HAMA were employed as the core and shell materials, respectively. Using this platform, we successfully fabricated HCSM with uniform and controllable sizes in a high-throughput manner. Single-cell hiPSC suspensions self-organized into spheroids within HCSM, leading to the formation of EBs exhibiting cavitation. These EBs effectively differentiated into brain organoids, beating cardiac organoids, and liver organoids. Detailed structural and functional analyses of the liver organoids revealed a heterogeneous cellular composition including hepatocyte-, bile duct epithelial-, epithelial-, and stellate-like cells. Structurally, they exhibited bile duct- and hepatic lobule-like formations. Functionally, liver organoids displayed lipid and glycogen accumulation, ICG uptake and release, albumin and urea secretion, as well as metabolic responses to APAP and rifampin. Consequently, our study introduces a high-throughput manufacturing platform for hiPSC-derived organoids, with the potential to generate functional organoids for therapeutic applications and drug screening.

MIXL1 activation in endoderm differentiation of human induced pluripotent stem cells

Human induced pluripotent stem cells (hiPSCs) possess the ability to differentiate into a multitude of cell and tissue types but display heterogeneous propensity of differentiation into specific lineage. Characterization of the transcriptome of 11 hiPSC lines showed that activation of MIXL1 at the early stage of stem cell differentiation correlated with higher efficacy in generating definitive endoderm and advancing differentiation and maturation of endoderm derivatives. Enforced expression of MIXL1 in the endoderm-inefficient hiPSCs enhanced the propensity of endoderm differentiation, suggesting that modulation of key drivers of lineage differentiation can re-wire hiPSC to the desired lineage propensity to generate the requisite stem cell products.

Extended culture of 2D gastruloids to model human mesoderm development

Micropatterned human pluripotent stem cells treated with BMP4 (two-dimensional (2D) gastruloids) are among the most widely used stem cell models for human gastrulation. Due to its simplicity and reproducibility, this system is ideal for high-throughput quantitative studies of tissue patterning and has led to many insights into the mechanisms of mammalian gastrulation. However, 2D gastruloids have been studied only up to about 2 days owing to a loss of organization beyond this time with earlier protocols. Here we report an extended 2D gastruloid model to up to 10 days. We discovered a phase of highly reproducible morphogenesis between 2 and 4 days during which directed migration from the primitive streak-like region gives rise to a mesodermal layer beneath an epiblast-like layer. Multiple types of mesoderm arise with striking spatial organization including lateral plate mesoderm-like cells on the colony border and paraxial mesoderm-like cells further inside the colony. Single-cell transcriptomics showed strong similarity of these cells to mesoderm in human and nonhuman primate embryos. Our results illustrate that extended culture of 2D gastruloids provides a powerful model for human mesoderm differentiation and morphogenesis.

Glycolytic activity instructs germ layer proportions through regulation of Nodal and Wnt signaling

Metabolic pathways can influence cell fate decisions, yet their regulative role during embryonic development remains poorly understood. Here, we demonstrate an instructive role of glycolytic activity in regulating signaling pathways involved in mesoderm and endoderm specification. Using a mouse embryonic stem cell (mESC)-based in vitro model for gastrulation, we found that glycolysis inhibition increases ectodermal cell fates at the expense of mesodermal and endodermal lineages. We demonstrate that this relationship is dose dependent, enabling metabolic control of germ layer proportions through exogenous glucose levels. We further show that glycolysis acts as an upstream regulator of Nodal and Wnt signaling and that its influence on cell fate specification can be decoupled from its effects on growth. Finally, we confirm the generality of our findings using a human gastrulation model. Our work underscores the dependence of signaling pathways on metabolic conditions and provides mechanistic insight into the nutritional regulation of cell fate decision-making.

Towards an integrated view and understanding of embryonic signalling during murine gastrulation

At the onset of mammalian gastrulation, secreted signalling molecules belonging to the Bmp, Wnt, Nodal and Fgf signalling pathways induce and pattern the primitive streak, marking the start for the cellular rearrangements that generate the body plan. Our current understanding of how signalling specifies and organises the germ layers in three dimensions, was mainly derived from genetic experimentation using mouse embryos performed over many decades. However, the exact spatiotemporal sequence of events is still poorly understood, both because of a lack of tractable models that allow for real time visualisation of signalling and differentiation and because of the molecular and cellular complexity of these early developmental events. In recent years, a new wave of in vitro embryo models has begun to shed light on the dynamics of signalling during primitive streak formation. Here we discuss the similarities and differences between a widely adopted mouse embryo model, termed gastruloids, and real embryos from a signalling perspective. We focus on the gene regulatory networks that underlie signalling pathway interactions and outline some of the challenges ahead. Finally, we provide a perspective on how embryo models may be used to advance our understanding of signalling dynamics through computational modelling.

Moving toward totipotency: the molecular and cellular features of totipotent and naive pluripotent stem cells

BACKGROUND

Dissecting the key molecular mechanism of embryonic development provides novel insights into embryogenesis and potential intervention strategies for clinical practices. However, the ability to study the molecular mechanisms of early embryo development in humans, such as zygotic genome activation and lineage segregation, is meaningfully constrained by methodological limitations and ethical concerns. Totipotent stem cells have an extended developmental potential to differentiate into embryonic and extraembryonic tissues, providing a suitable model for studying early embryo development. Recently, a series of ground-breaking results on stem cells have identified totipotent-like cells or induced pluripotent stem cells into totipotent-like cells.

OBJECTIVE AND RATIONALE

This review followed the PRISMA guidelines, surveys the current works of literature on totipotent, naive, and formative pluripotent stem cells, introduces the molecular and biological characteristics of those stem cells, and gives advice for future research.

SEARCH METHODS

The search method employed the terms 'totipotent' OR 'naive pluripotent stem cell' OR 'formative pluripotent stem cell' for unfiltered search on PubMed, Web of Science, and Cochrane Library. Papers included were those with information on totipotent stem cells, naive pluripotent stem cells, or formative pluripotent stem cells until June 2024 and were published in the English language. Articles that have no relevance to stem cells, or totipotent, naive pluripotent, or formative pluripotent cells were excluded.

OUTCOMES

There were 152 records included in this review. These publications were divided into four groups according to the species of the cells included in the studies: 67 human stem cell studies, 70 mouse stem cell studies, 9 porcine stem cell studies, and 6 cynomolgus stem cell studies. Naive pluripotent stem cell models have been established in other species such as porcine and cynomolgus. Human and mouse totipotent stem cells, e.g. human 8-cell-like cells, human totipotent blastomere-like cells, and mouse 2-cell-like cells, have been successfully established and exhibit high developmental potency for both embryonic and extraembryonic contributions. However, the observed discrepancies between these cells and real embryos in terms of epigenetics and transcription suggest that further research is warranted. Our results systematically reviewed the established methods, molecular characteristics, and developmental potency of different naive, formative pluripotent, and totipotent stem cells. Furthermore, we provide a parallel comparison between animal and human models, and offer recommendations for future applications to advance early embryo research and assisted reproduction technologies.

WIDER IMPLICATIONS

Totipotent cell models provide a valuable resource to understand the underlying mechanisms of embryo development and forge new paths toward future treatment of infertility and regenerative medicine. However, current in vitro cell models exhibit epigenetic and transcriptional differences from in vivo embryos, and many cell models are unstable across passages, thus imperfectly recapitulating embryonic development. In this regard, standardizing and expanding current research on totipotent stem cell models are essential to enhance our capability to resemble and decipher embryogenesis.

The building blocks of embryo models: embryonic and extraembryonic stem cells

The process of a single-celled zygote developing into a complex multicellular organism is precisely regulated at spatial and temporal levels in vivo. However, understanding the mechanisms underlying development, particularly in humans, has been constrained by technical and ethical limitations associated with studying natural embryos. Harnessing the intrinsic ability of embryonic stem cells (ESCs) to self-organize when induced and assembled, researchers have established several embryo models as alternative approaches to studying early development in vitro. Recent studies have revealed the critical role of extraembryonic cells in early development; and many groups have created more sophisticated and precise ESC-derived embryo models by incorporating extraembryonic stem cell lines, such as trophoblast stem cells (TSCs), extraembryonic mesoderm cells (EXMCs), extraembryonic endoderm cells (XENs, in rodents), and hypoblast stem cells (in primates). Here, we summarize the characteristics of existing mouse and human embryonic and extraembryonic stem cells and review recent advancements in developing mouse and human embryo models.

Lineage-specific CDK activity dynamics characterize early mammalian development

Cyclin-dependent kinases (CDKs) regulate proliferation dynamics and cell fate in response to extracellular inputs. It remains largely unknown how CDK activity fluctuates and influences cell commitment during early mammalian development. Here, we generated a mouse model expressing a CDK translocation reporter that enabled quantification of CDK activity in live single cells. By examining pre- and post-implantation mouse embryos at different stages, we observed a progressive decrease in CDK activity in cells from the trophectoderm (TE) prior to implantation. This drop seems to correlate with the available levels of ICM-derived FGF4 as CDK activity downregulation is rescued by exogenous FGF4. Furthermore, we showed that cell fate decisions in the pre-implantation embryo are not determined by the establishment of oscillatory CDK activity or overall changes in CDK activity. Finally, we uncovered the existence of conserved regulatory mechanisms in mammals by revealing lineage-specific regulation of CDK activity in TE-like human cells.

Imaging 3D cell cultures with optical microscopy

Three-dimensional (3D) cell cultures have gained popularity in recent years due to their ability to represent complex tissues or organs more faithfully than conventional two-dimensional (2D) cell culture. This article reviews the application of both 2D and 3D microscopy approaches for monitoring and studying 3D cell cultures. We first summarize the most popular optical microscopy methods that have been used with 3D cell cultures. We then discuss the general advantages and disadvantages of various microscopy techniques for several broad categories of investigation involving 3D cell cultures. Finally, we provide perspectives on key areas of technical need in which there are clear opportunities for innovation. Our goal is to guide microscope engineers and biomedical end users toward optimal imaging methods for specific investigational scenarios and to identify use cases in which additional innovations in high-resolution imaging could be helpful.

Stem cell-based models of early human development

Stem cell-based embryo models (SCBEMs) are structures generated from three-dimensional (3D) culture of pluripotent stem cells and their derivatives, utilizing mechanical and/or chemical cues to facilitate lineage differentiation, self-organization and morphogenesis. These models partially mimic early embryos, which would otherwise be difficult to access. SCBEMs have been established in mice, livestock, nonhuman primates and humans. Here, we focus on recently developed human models, with an emphasis on the peri-implantation stage and the aspects of human development these SCBEMs recapitulate.

Exploring early extraembryonic cells of epiblast origin: Questions on human amniotic ectoderm and extraembryonic mesoderm

Extraembryonic tissues are essential for proper fetal development and exhibit great diversity across species. Despite its importance, human extraembryonic development has been relatively overlooked. Previously, we established an in vitro model to study human amniogenesis and extraembryonic mesoderm formation. In this article, I develop discussions on four topics inspired by this study: (1) Features of amniotic cell populations described to date. A recently reported early amniotic cell type is examined based on its signature genes to consider how this population should be incorporated into models of primate amniogenesis. (2) Molecular mechanisms underlying the effect of cell density in regulating non-neural ectoderm specification. Fate specification by positional cues in mouse is revisited and possible mechanisms are suggested by drawing insights from human epiblast models. (3) Potential applications of the three-dimensional culture we established. Primate amniotic ectoderm is postulated as a gastrulation-inducing signaling center, and our technique could be used to effectively model its interactions with epiblast. (4) Extraembryonic mesoderm development in human embryos. The obscure origin of primate extraembryonic mesoderm and implications from recent in vitro differentiation models using human pluripotent stem cells are explained. The key concepts explored here will stimulate further studies into both amnion and extraembryonic mesoderm during human and non-human primate development.

Exploring and validating the marmoset as a primate model for chromosomal instability in early development

Aneuploidy in embryos poses a major barrier to successful human reproduction, contributing to nearly 50% of early miscarriages. Despite its high prevalence in human embryos, the molecular mechanisms regulating aneuploid cell fate during development remain poorly understood. This knowledge gap persists due to ethical constraints in human embryo research and the limitations of existing animal models. In this study, we identified the New World primate marmoset (Callithrix jacchus) as a suitable model for investigating aneuploidy. By calling copy number variants from single-cell RNA-sequencing data of marmoset embryonic cells, we identified heterogeneous aneuploidy, indicating chromosomal instability (CIN) in marmoset preimplantation embryos. Furthermore, marmoset aneuploidy displayed lineage-specific behavior during gastruloid differentiation, similar to humans, suggesting a conserved regulatory mechanism in lineage specification. To develop a more pluripotent cell line to study early specification, we established an efficient approach for generating naïve-like marmoset pluripotent stem cells (cjPSCs). These cells resemble preimplantation epiblast-like cells and exhibit inherent CIN. Transcriptome analysis identified potential pathways contributing to aneuploidy during early embryogenesis, including the downregulation of cell cycle checkpoint signaling and the upregulation of autophagy pathways. Additionally, we found no significant effect of spontaneously occurring aneuploidy in cjPSCs on blastoid formation, suggesting that the consequences of aneuploidy become evident only after gastrulation, with preimplantation lineages exhibiting a higher tolerance for genomic instability. Unexpectedly, aneuploidy enhanced cavity formation during blastoid development, suggesting a potential role in facilitating efficient trophectoderm differentiation. Our findings validate the marmoset as a valuable model for studying CIN during early primate development and provide insight into the mechanisms underlying the prevalence of aneuploidy in primates. Naïve-like cjPSCs recapitulate key phenotypic traits of early embryonic cells, providing a robust system for studying post-implantation aneuploid cell fates in vivo and serving as a foundation for future research in this field.

Measuring and manipulating mechanical forces during development

Tissue deformations are a central feature of development, from early embryogenesis, growth and building the body plan to the establishment of functional organs. These deformations often result from active contractile forces generated by cells and cell collectives, and are mediated by changes in their mechanical properties. Mechanical forces drive the formation of functional organ architectures, but they also coordinate cell behaviour and fate transitions, ensuring robustness of development. Advances in microscopy, genetics and chemistry have enabled increasingly powerful tools for measuring, generating and perturbing mechanical forces. Here we discuss approaches to measure and manipulate mechanical forces with a focus on developmental processes, ranging from quantification of molecular interactions to mapping the mechanical properties of tissues. We focus on contemporary methods, and discuss the biological discoveries that these approaches have enabled. We conclude with an outlook to methodologies at the interface of physics, chemistry and biology to build an integrated understanding of tissue morphodynamics.

Pluripotent cell states and fates in human embryo models

Pluripotency, the capacity to generate all cells of the body, is a defining property of a transient population of epiblast cells found in pre-, peri- and post-implantation mammalian embryos. As development progresses, the epiblast cells undergo dynamic transitions in pluripotency states, concurrent with the specification of extra-embryonic and embryonic lineages. Recently, stem cell-based models of pre- and post-implantation human embryonic development have been developed using stem cells that capture key properties of the epiblast at different developmental stages. Here, we review early primate development, comparing pluripotency states of the epiblast in vivo with cultured pluripotent cells representative of these states. We consider how the pluripotency status of the starting cells influences the development of human embryo models and, in turn, what we can learn about the human pluripotent epiblast. Finally, we discuss the limitations of these models and questions arising from the pioneering studies in this emerging field.

Origin, fate and function of extraembryonic tissues during mammalian development

Extraembryonic tissues have pivotal roles in morphogenesis and patterning of the early mammalian embryo. Developmental programmes mediated through signalling pathways and gene regulatory networks determine the sequence in which fate determination and lineage commitment of extraembryonic tissues take place, and epigenetic processes allow the memory of cell identity and state to be sustained throughout and beyond embryo development, even extending across generations. In this Review, we discuss the molecular and cellular mechanisms necessary for the different extraembryonic tissues to develop and function, from their initial specification up until the end of gastrulation, when the body plan of the embryo and the anatomical organization of its supporting extraembryonic structures are established. We examine the interaction between extraembryonic and embryonic tissues during early patterning and morphogenesis, and outline how epigenetic memory supports extraembryonic tissue development.

Target-switchable nanoprobe based on BRD4 inhibition for induction and dynamic visualization of the mitochondrial apoptotic pathway

The exploration of the mitochondrial apoptotic pathway in living cells is of great significance for achieving tumor diagnosis and treatment. However, visualization of the mitochondrial apoptotic pathway induced by specific proteins has rarely been reported. In this paper, we designed and synthesized a fluorescent probe Cy-JQ1 based on the bromodomain-containing protein 4 (BRD4) inhibition. Cy-JQ1 can affect mitochondrial electron chain transfer and reduce the mitochondrial membrane potential, effectively activating the Bcl-2/Bax/caspase-3 signaling pathway at a concentration of 500 nM and then triggering cell apoptosis. Due to its high specificity and excellent fluorescence properties, the switching of Cy-JQ1 from mitochondria to endoplasmic reticulum could be observed. The difference in fluorescence intensity along the perinuclear aggregates could be well defined as ΔXOR and used as a sensitive indicator of apoptosis. Upon conjugating with polyethylene glycol (PEG) containing disulfide bonds, the performance of the formed nanoprobe (Cy-JQ1-S-S-M) is further enhanced by improving pharmacokinetics and tumor-specific accumulation. This study provides a new analytical method for the dynamic visualization of mitochondria-induced apoptosis pathways triggered by specific proteins, as well as for the development of apoptosis-related target drugs.

The emergence of human primordial germ cell-like cells in stem cell-derived gastruloids

Most advances in early human postimplantation development depend on animal studies and stem cell-based embryo models. Here, we present self-organized three-dimensional human gastruloids (hGs) derived from embryonic stem cells. The transcriptome profile of day 3 hGs aligned with Carnegie stage 7 human gastrula, with cell types and differentiation trajectories consistent with human gastrulation. Notably, we observed the emergence of nascent primordial germ cell-like cells (PGCLCs), but without exogenous bone morphogenetic protein (BMP) signaling, which is essential for the PGCLC fate. A mutation in the ISL1 gene affects amnion-like cells and leads to a loss of PGCLCs; the addition of exogenous BMP2 rescues the PGCLC fate, indicating that the amnion may provide endogenous BMP signaling. Our model of early human embryogenesis will enable further exploration of the germ line and other early human lineages.

Protocol for efficient generation of human artery and vein endothelial cells from pluripotent stem cells

Blood vessels permeate all organs and execute myriad roles in health and disease. Here, we present a protocol to efficiently generate human artery and vein endothelial cells (ECs) from pluripotent stem cells within 3-4 days of differentiation. We delineate how to seed human pluripotent stem cells and sequentially differentiate them into primitive streak, lateral mesoderm, and either artery or vein ECs. We differentiate stem cells in defined, serum-free culture media in monolayers, without feeder cells or genetic manipulations. For complete details on the use and execution of this protocol, please refer to Ang et al. 1.

Protocol for the generation of HLF+ HOXA+ human hematopoietic progenitor cells from pluripotent stem cells

Hematopoietic stem cells (HSCs) generate blood and immune cells. Here, we present a protocol to differentiate human pluripotent stem cells (hPSCs) into hematopoietic progenitors that express the signature HSC transcription factors HLF, HOXA5, HOXA7, HOXA9, and HOXA10. hPSCs are dissociated, seeded, and then sequentially differentiated into posterior primitive streak, lateral mesoderm, artery endothelium, hemogenic endothelium, and hematopoietic progenitors through the sequential addition of defined, serum-free media. This 10-day protocol enables the manufacturing of blood and immune cells in monolayer cultures. For complete details on the use and execution of this protocol, please refer to Fowler and Zheng et al.1.

Self-organization of mouse embryonic stem cells into reproducible pre-gastrulation embryo models via CRISPRa programming

Embryonic stem cells (ESCs) can self-organize into structures with spatial and molecular similarities to natural embryos. During development, embryonic and extraembryonic cells differentiate through activation of endogenous regulatory elements while co-developing via cell-cell interactions. However, engineering regulatory elements to self-organize ESCs into embryo models remains underexplored. Here, we demonstrate that CRISPR activation (CRISPRa) of two regulatory elements near Gata6 and Cdx2 generates embryonic patterns resembling pre-gastrulation mouse embryos. Live single-cell imaging revealed that self-patterning occurs through orchestrated collective movement driven by cell-intrinsic fate induction. In 3D, CRISPRa-programmed embryo models (CPEMs) exhibit morphological and transcriptomic similarity to pre-gastrulation mouse embryos. CPEMs allow versatile perturbations, including dual Cdx2-Elf5 activation to enhance trophoblast differentiation and lineage-specific activation of laminin and matrix metalloproteinases, uncovering their roles in basement membrane remodeling and embryo model morphology. Our findings demonstrate that minimal intrinsic epigenome editing can self-organize ESCs into programmable pre-gastrulation embryo models with robust lineage-specific perturbation capabilities.

Lineage contribution of the mesendoderm progenitors in the gastrulating mouse embryo

A population of putative mesendoderm progenitors that can contribute cellular descendants to both mesoderm and endoderm lineages is identified in the gastrulating mouse embryo. These progenitor cells are localized to the posterior epiblast, primitive streak, and nascent mesoderm of mid-streak- (E7.0) to late-streak-stage (E7.5) embryos. Lineage tracing in vivo identified that putative mesendoderm progenitors contribute descendants to the definitive endoderm and the axial mesendoderm of E7.75 embryos and to the endoderm of the foregut and hindgut of the E8.5-8.75 embryos. Differentiation of mouse epiblast stem cells identified that the choice between endoderm and mesoderm cell fates depends on the timing of Mixl1 activation upon exit from pluripotency. The knowledge gained on the spatiotemporal distribution of mesendoderm progenitors and the molecular drivers underpinning the divergence of cell lineages in these progenitors enriches our mechanistic understanding of the allocation of the tissue progenitors to germ layer derivatives in early development.

Unlocking the potential of stem-cell-derived 'synthetic' embryo models

Stem-cell-derived 'synthetic' embryo models represent a revolutionary avenue in developmental biology, offering unprecedented insights into embryogenesis and tissue formation. However, the majority of current research on embryo models resides predominantly in the engineering construction phase, with limited substantive applications. This review explores the utilization of these embryo models and their applications in deciphering fundamental developmental processes. We delve into the methodologies employed in generating these models, emphasizing their potential to advance our understanding of embryonic development and disease. By evaluating current advancements and challenges, this review provides a comprehensive overview of the opportunities and implications of employing stem-cell-derived embryo models.

ETVs dictate hPSC differentiation by tuning biophysical properties

Stem cells maintain a dynamic dialog with their niche, integrating biochemical and biophysical cues to modulate cellular behavior. Yet, the transcriptional networks that regulate cellular biophysical properties remain poorly defined. Here, we leverage human pluripotent stem cells (hPSCs) and two morphogenesis models - gastruloids and pancreatic differentiation - to establish ETV transcription factors as critical regulators of biophysical parameters and lineage commitment. Genetic ablation of ETV1 or ETV1/ETV4/ETV5 in hPSCs enhances cell-cell and cell-ECM adhesion, leading to aberrant multilineage differentiation including disrupted germ-layer organization, ectoderm loss, and extraembryonic cell overgrowth in gastruloids. Furthermore, ETV1 loss abolishes pancreatic progenitor formation. Single-cell RNA sequencing and follow-up assays reveal dysregulated mechanotransduction via the PI3K/AKT signaling. Our findings highlight the importance of transcriptional control over cell biophysical properties and suggest that manipulating these properties may improve in vitro cell and tissue engineering strategies.

Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling

Developing tissues interpret dynamic changes in morphogen activity to generate cell type diversity. To quantitatively study bone morphogenetic protein (BMP) signaling dynamics in the mouse neural tube, we developed an embryonic stem cell differentiation system tailored for growing tissues. Differentiating cells form striking self-organized patterns of dorsal neural tube cell types driven by sequential phases of BMP signaling that are observed both in vitro and in vivo. Data-driven biophysical modeling showed that these dynamics result from coupling fast negative feedback with slow positive regulation of signaling by the specification of an endogenous BMP source. Thus, in contrast to relays that propagate morphogen signaling in space, we identify a BMP signaling relay that operates in time. This mechanism allows for a rapid initial concentration-sensitive response that is robustly terminated, thereby regulating balanced sequential cell type generation. Our study provides an experimental and theoretical framework to understand how signaling dynamics are exploited in developing tissues.

Advancing cellular transfer printing: achieving bioadhesion-free deposition via vibration microstreaming

Cell transfer printing plays an essential role in biomedical research and clinical diagnostics. Traditional bioadhesion-based methods often necessitate complex surface modifications and offer limited control over the quantity of transferred cells. There is a critical need for a modification-free, non-labeling, and high-throughput cell transfer printing technique. In this study, an adhesion-free cellular transfer printing method based on vibration-induced microstreaming is introduced. By adjusting the volume of the microcavity, the number of cells transferred per microtiter well can be realized to the level of a single cell. Additionally, it allows for precise control of large-scale cellular spatial distribution, leading to the formation of biomimetic patterns. Moreover, the demonstrated biocompatibility and high throughput of this cell transfer printing method highlight its potential utility. The correspondence of the transferred cell amount to the vibration and frequencies allows the system to exhibit excellent tunability of the transferred cell amount and pattern. This bioadhesion-free cell transfer printing method holds promise for advancing cell manipulation in biomedical research and analysis.

Twinning and Individuation: An Appraisal of the Current Model and Ethical Implications

Discourses on human embryo experimentation often refer to monozygotic twinning and individuation. A criterion to establish regulations that guide human embryo research proposes that individuation is achieved once the embryo ceases to have the potential for dividing into two or more viable entities at about 15 days of gestational age. This standard is based on an updated version of a developmental model initially proposed by George Corner. A fundamental problem with this approach is the model's lack of sufficient evidence to explain adequately human embryo twinning and, consequently, to serve as a basis to establish appropriate ethical guidelines for embryo experimentation. In addition, subsequent formulations of Corner's model added an extension of blastomere totipotency to different moments of gestation, without a proper scientific basis. The model is also challenged by monozygotic twinnings that result in placental and amniotic arrangements incompatible with Corner's framework. Investigations into the physiology of fertilisation and of the zygote suggest that individuation may occur at a very early stage. An alternative description of monozygotic twinning may explain better sesquizygotic twinning events and serve to re-evaluate the individuation criterion. The study aims to investigate deficiencies in the embryology of this model and assess their ethical implications.

Assembly of a stem cell-derived human postimplantation embryo model

The embryonic and extraembryonic tissue interactions underlying human embryogenesis at implantation stages are not currently understood. We have generated a pluripotent stem cell-derived model that mimics aspects of peri-implantation development, allowing tractable experimentation otherwise impossible in the human embryo. Activation of the extraembryonic lineage-specific transcription factors GATA6 and SOX17 (hypoblast factors) or GATA3 and TFAP2C (encoding AP2γ; trophoblast factors) in human embryonic stem (ES) cells drive conversion to extraembryonic-like cells. When combined with wild-type ES cells, self-organized embryo-like structures form in the absence of exogenous factors, termed human inducible embryoids (hiEmbryoids). The epiblast-like domain of hiEmbryoids polarizes and differentiates in response to extraembryonic-secreted extracellular matrix and morphogen cues. Extraembryonic mesenchyme, amnion and primordial germ cells are specified in hiEmbryoids in a stepwise fashion. After establishing stable inducible ES lines and converting ES cells to RSeT culture media, the protocol takes 7-10 d to generate hiEmbryoids. Generation of hiEmbryoids can be performed by researchers with basic expertise in stem cell culture.

Timely TGFβ signalling inhibition induces notochord

The formation of the vertebrate body involves the coordinated production of trunk tissues from progenitors located in the posterior of the embryo. Although in vitro models using pluripotent stem cells replicate aspects of this process1-10, they lack crucial components, most notably the notochord-a defining feature of chordates that patterns surrounding tissues11. Consequently, cell types dependent on notochord signals are absent from current models of human trunk formation. Here we performed single-cell transcriptomic analysis of chick embryos to map molecularly distinct progenitor populations and their spatial organization. Guided by this map, we investigated how differentiating human pluripotent stem cells develop a stereotypical spatial organization of trunk cell types. We found that YAP inactivation in conjunction with FGF-mediated MAPK signalling facilitated WNT pathway activation and induced expression of TBXT (also known as BRA). In addition, timely inhibition of WNT-induced NODAL and BMP signalling regulated the proportions of different tissue types, including notochordal cells. This enabled us to create a three-dimensional model of human trunk development that undergoes morphogenetic movements, producing elongated structures with a notochord and ventral neural and mesodermal tissues. Our findings provide insights into the mechanisms underlying vertebrate notochord formation and establish a more comprehensive in vitro model of human trunk development. This paves the way for future studies of tissue patterning in a physiologically relevant environment.

Protocol for fabricating elastomeric stencils for patterned stem cell differentiation

Geometrically controlled stem cell differentiation promotes reproducible pattern formation. Here, we present a protocol to fabricate elastomeric stencils for patterned stem cell differentiation. We describe procedures for using photolithography to produce molds, followed by molding polydimethylsiloxane (PDMS) to obtain stencils with through holes. We then provide instructions for culturing cells on stencils and, finally, removing stencils to allow colony growth and cell migration. This approach yields reproducible two-dimensional organoids tailored for quantitative studies of growth and pattern formation. For complete details on the use and execution of this protocol, please refer to Lehr et al.1.

In vitro modelling of anterior primitive streak patterning with human pluripotent stem cells identifies the path to notochord progenitors

Notochord progenitors (NotoPs) represent a scarce yet crucial embryonic cell population, playing important roles in embryo patterning and eventually giving rise to the cells that form and maintain intervertebral discs. The mechanisms regulating NotoPs emergence are unclear. This knowledge gap persists due to the inherent complexity of cell fate patterning during gastrulation, particularly within the anterior primitive streak (APS), where NotoPs first arise alongside neuro-mesoderm and endoderm. To gain insights into this process, we use micropatterning together with FGF and the WNT pathway activator CHIR9901 to guide the development of human embryonic stem cells into reproducible patterns of APS cell fates. We show that CHIR9901 dosage dictates the downstream dynamics of endogenous TGFβ signalling, which in turn controls cell fate decisions. While sustained NODAL signalling defines endoderm and NODAL inhibition is imperative for neuro-mesoderm emergence, timely inhibition of NODAL signalling with spatial confinement potentiates WNT activity and enables us to generate NotoPs efficiently. Our work elucidates the signalling regimes underpinning NotoP emergence and provides insights into the regulatory mechanisms controlling the balance of APS cell fates during gastrulation.

Spatially-Resolved Organoid Transfection by Porous Silicon-Mediated Optoporation

Engineering the spatial organisation of organotypic cultures is pivotal for refining tissue models that are useful for gaining deeper insights into complex, non-cell autonomous processes. These advanced models are key to improving the understanding of fundamental biological mechanisms and therapeutic strategies. Controlling gene regulation through spatially-resolved delivery of nucleic acids provides an attractive approach to produce such tissue models. An emerging strategy for spatially-resolved transfection uses photosensitizing nanoparticles coupled with laser pulses to optoporate cells in culture and locally mediate gene delivery. However, localized optoporation in 3D systems remains challenging. Here we propose a solution to this longstanding hurdle, demonstrating that porous silicon nanoparticles are a safe and bioresorbable photosensitising nanomaterial capable of spatially-resolved transfection of mRNA in MCF-7 organoids by near-infrared two-photon optoporation. Functionalization with an azobenzene-lysine photo-switchable moiety enhances the transfection efficiency of the nanoparticles up to 84% in a 2D cell system. Moreover, the nanoparticles enable spatially selective mRNA transfection to MCF-7 spheroids, demonstrating targeted  gene delivery in complex 3D cellular environments. The approach for spatially-resolved 3D optoporation offers a way forward for the design of tailored spheroids and organoids by spatially selective nucleic acids delivery.

Polarization of organoids by bioengineered symmetry breaking

Symmetry breaking leading to axis formation and spatial patterning is crucial for achieving more accurate recapitulation of human development in organoids. While these processes can occur spontaneously by self-organizing capabilities of pluripotent stem cells, they can often result in variation in structure and composition of cell types within organoids. To address this limitation, bioengineering techniques that utilize geometric, topological and stiffness factors are increasingly employed to enhance control and consistency. Here, we review how spontaneous manners and engineering tools such as micropattern, microfluidics, biomaterials, etc. can facilitate the process of symmetry breaking leading to germ layer patterning and the formation of anteroposterior and dorsoventral axes in blastoids, gastruloids, neuruloids and neural organoids. Furthermore, brain assembloids, which are composed of multiple brain regions through fusion processes are discussed. The overview of organoid polarization in terms of patterning tools can offer valuable insights for enhancing the physiological relevance of organoid system.

Three-dimensional stem cell models of mammalian gastrulation

Gastrulation is a key milestone in the development of an organism. It is a period of cell proliferation and coordinated cellular rearrangement, that creates an outline of the body plan. Our current understanding of mammalian gastrulation has been improved by embryo culture, but there are still many open questions that are difficult to address because of the intrauterine development of the embryos and the low number of specimens. In the case of humans, there are additional difficulties associated with technical and ethical challenges. Over the last few years, pluripotent stem cell models are being developed that have the potential to become useful tools to understand the mammalian gastrulation. Here we review these models with a special emphasis on gastruloids and provide a survey of the methods to produce them robustly, their uses, relationship to embryos, and their prospects as well as their limitations.

Current Status of Synthetic Mammalian Embryo Models

Advances in three-dimensional culture technologies have facilitated the development of synthetic embryo models, such as blastoids, through the co-culturing of diverse stem cell types. These in vitro models enable precise investigation of developmental processes, including gastrulation, neurulation, and lineage specification, thereby advancing our understanding of early embryogenesis. By providing controllable, ethically viable platforms, they help circumvent the limitations of in vivo mammalian embryo studies and contribute to developing regenerative medicine strategies. Nonetheless, ethical challenges, particularly regarding human applications, persist. Comparative studies across various species-such as mice, humans, non-human primates, and ungulates, like pigs and cattle-offer crucial insights into both species-specific and conserved developmental mechanisms. In this review, we outline the species-specific differences in embryonic development and discuss recent advancements in stem cell and synthetic embryo models. Specifically, we focus on the latest stem cell research involving ungulates, such as pigs and cattle, and provide a comprehensive overview of the improvements in synthetic embryo technology. These insights contribute to our understanding of species-specific developmental biology, help improve model efficiency, and guide the development of new models.

Automated live-cell single-molecule tracking in enteroid monolayers reveals transcription factor dynamics probing lineage-determining function

Lineage transcription factors (TFs) provide one regulatory level of differentiation crucial for the generation and maintenance of healthy tissues. To probe TF function by measuring their dynamics during adult intestinal homeostasis, we established HILO-illumination-based live-cell single-molecule tracking (SMT) in mouse small intestinal enteroid monolayers recapitulating tissue differentiation hierarchies in vitro. To increase the throughput, capture cellular features, and correlate morphological characteristics with diffusion parameters, we developed an automated imaging and analysis pipeline, broadly applicable to two-dimensional culture systems. Studying two absorptive lineage-determining TFs, we found an expression level-independent contrasting diffusive behavior: while Hes1, key determinant of absorptive lineage commitment, displays a large cell-to-cell variability and an average fraction of DNA-bound molecules of ∼32%, Hnf4g, conferring enterocyte identity, exhibits more uniform dynamics and a bound fraction of ∼56%. Our results suggest that TF diffusive behavior could indicate the progression of differentiation and modulate early versus late differentiation within a lineage.

Early autonomous patterning of the anteroposterior axis in gastruloids

Minimal in vitro systems composed of embryonic stem cells (ESCs) have been shown to recapitulate the establishment of the anteroposterior (AP) axis. In contrast to the native embryo, ESC aggregates - such as gastruloids - can break symmetry, which is demarcated by polarization of the mesodermal marker T, autonomously without any localized external cues. However, associated earliest patterning events, such as the spatial restriction of cell fates and concomitant transcriptional changes, remain poorly understood. Here, we dissect the dynamics of AP axis establishment in mouse gastruloids, particularly before external Wnt stimulation. Through single-cell RNA sequencing, we identify key cell state transitions and the molecular signatures of T+ and T- populations underpinning AP polarization. We also show that this process is robust to modifications of aggregate size. Finally, transcriptomic comparison with the mouse embryo indicates that gastruloids develop similar mesendodermal cell types, despite initial differences in their primed pluripotent populations, which adopt a more mesenchymal state in lieu of an epiblast-like transcriptome. Hence, our findings suggest the possibility of alternate ESC states in vivo and in vitro that can converge onto similar cell fates.

Advanced bioengineering strategies broaden the therapeutic landscape for corneal failure

The cornea acts as the eye foremost protective layer and is essential for its focusing power. Corneal blindness may arise from physical trauma or conditions like dystrophies, keratitis, keratoconus, or ulceration. While conventional treatments involve medical therapies and donor allografts-sometimes supplemented with keratoprostheses-these options are not suitable for all corneal defects. Consequently, the development of bioartificial corneal tissue has emerged as a critical research area, aiming to address the global shortage of human cornea donors. Bioengineered corneas hold considerable promise as substitutes, with the potential to replace either specific layers or the entire thickness of damaged corneas. This review first delves into the structural anatomy of the human cornea, identifying key attributes necessary for successful corneal tissue bioengineering. It then examines various corneal pathologies, current treatments, and their limitations. Finally, the review outlines the primary approaches in corneal tissue engineering, exploring cell-free, cell-based, and scaffold-based options as three emerging strategies to address corneal failure.

Construction methods and latest applications of kidney cancer organoids

Renal cell carcinoma (RCC) is one of the deadliest malignant tumors. Despite significant advances in RCC treatment over the past decade, complete remission is rarely achieved. Consequently, there is an urgent need to explore and develop new therapies to improve the survival rates and quality of life for patients. In recent years, the development of tumor organoid technology has attracted widespread attention as it can more accurately simulate the spatial structure and physiological characteristics of tumors within the human body. In this review, we summarize the main methods currently used to construct kidney cancer organoids, as well as their various biological and clinical applications. Furthermore, combining organoids with other technologies, such as co-culture techniques and microfluidic technologies, can further develop organoids and address their limitations, creating more practical models. This approach summarizes the interactions between different tissues or organs during tumor progression. Finally, we also provide an outlook on the construction and application of kidney cancer organoids. These rapidly evolving kidney cancer organoids may soon become a focal point in the development of in vitro clinical models and therapeutic research for kidney cancer.

Morphogen-driven differentiation is precluded by physical confinement in human iPSCs spheroids

Introduction

Cell lineage specification is tightly associated with profound morphological changes in the developing human embryo, particularly during gastrulation. The interplay between mechanical forces and biochemical signals is poorly understood.

Methods

Here, we dissect the effects of biochemical cues and physical confinement on a 3D in vitro model based on spheroids formed from human induced pluripotent stem cells (hiPSCs).

Results

First, we compare self-renewing versus differentiating media conditions in free-floating cultures and observe the emergence of tri-germ layers. In these unconfined conditions, BMP4 exposure induces polarised expression of SOX17 in conjunction with spheroid elongation. We then physically confine spheroids using PEG-peptide hydrogels and observe dramatically reduced SOX17 expression, albeit rescued if gels that soften over time are used instead.

Discussion

Our study combines high-content imaging, synthetic hydrogels, and hiPSCs-derived models of early development to define the drivers that cause changes in the shape and the emergence of germ layers.

Oviductal extracellular matrix hydrogels enhance in vitro culture of rabbit embryos and reduce deficiencies during assisted reproductive technologies

In vitro embryo culture often falls short of mimicking the physiological dynamism occurring in the reproductive tract, prompting developmental plasticity in mammalian embryos with consequential genotypic and phenotypic deviations. Recent research highlights the potential of biological derivatives in in vitro culture to mitigate these effects, being the extracellular matrix (ECM) one of the most important components in retaining structural and biological signals derived from the native source tissue. Current bioengineering techniques could provide ECM-based biomaterials mimicking the native environment and offering optimal embryonic development. Rabbit oviducts (n = 24) were decellularized and solubilized to create tissue-specific ECM (OviECM) hydrogels. Following physicochemical characterization, these hydrogels were applied as coatings for the in vitro culture of two-cell embryos over 48 h, along with embryos cultured under In vitro control conditions (n = 218/group), which were subsequently transferred to recipient females. A subset of embryos was recovered on day 6 for transcriptomic analysis (n = 75-80/group), while the remaining embryos were used to assess implantation and birth rates. Rabbit weights were monitored over 20 weeks post-delivery, with blood tests conducted at weeks 8 and 20. Bayesian inference methods were used for statistical analysis. Differences were considered relevant if P ≥ 0.8 (80%). No differences in embryo development and morphology were detected between the OviECM coating and In vitro control conditions. However, embryos cultured on these coatings exhibited upregulation of pathways involved in antigen presentation and immune system activation, as well as, increased cellular response to external stimulus and intracellular protein transport. The implantation and live birth rates were significantly higher in the coating group than in the In vitro control group (30.8% vs. 26.1% and 21.2% vs. 18.1%, respectively). During the first 20 weeks of life, the animals from the coating group showed higher weights than the In vitro control group P0 > 0.8. The animals of both experimental groups showed normal blood parameters. Implementation of OviECM coatings allows for improving in vitro conditions and decreases postnatal phenotypic deviations after assisted reproductive technology (ART). This study could initiate a new embryo culture techniques era to guarantee that ART is utilized in the most efficient and safest possible practice.

Rapid Whole-Plate Cell and Tissue Micropatterning Using a Budget 3D Resin Printer

The ability to precisely pattern cells and proteins is crucial in various scientific disciplines, including cell biology, bioengineering, and materials chemistry. Current techniques, such as microcontact stamping, 3D bioprinting, and direct photopatterning, have limitations in terms of cost, versatility, and throughput. In this Article, we present an accessible approach that combines the throughput of photomask systems with the versatility of programmable light patterning using a low-cost consumer LCD resin printer. The method involves utilizing a bioinert hydrogel, poly(ethylene glycol) diacrylate (PEGDA), and a 405 nm sensitive photoinitiator (LAP) that are selectively cross-linked to form a hydrogel upon light exposure, creating specific regions that are protein and cell-repellent. Our result highlights that a low-cost LCD resin printer can project virtual photomasks onto the hydrogel, allowing for reasonable resolution and large-area printing at a fraction of the cost of traditional systems. The study demonstrates the calibration of exposure times for optimal resolution and accuracy and shape corrections to overcome the inherent challenges of wide-field resin printing. The potential of this approach is validated through widely studied 2D and 3D stem cell applications, showcasing its biocompatibility and ability to replicate complex tissue engineering patterns. We also validate the method with a cell-adhesive polymer (gelatin methacrylate; GelMA). The combination of low cost, high throughput, and accessibility makes this method broadly applicable across fields for enabling rapid and precise fabrication of cells and tissues in standard laboratory culture vessels.

Intercellular fluid dynamics in tissue morphogenesis

During embryonic development, cells shape our body, which is mostly made up of water. It is often forgotten that some of this water is found in intercellular fluid, which, for example, immerses the cells of developing embryos. Intercellular fluid contributes to the properties of tissues and influences cell behaviour, thereby participating in tissue morphogenesis. While our understanding of the role of cells in shaping tissues advances, the exploration of the contribution of intercellular fluid dynamics is just beginning. In this review, we delve into the intricate mechanisms employed by cells to control fluid movements both across and within sealed tissue compartments. These mechanisms encompass sealing by tight junctions and controlled leakage, osmotic pumping, hydraulic fracturing of cell adhesion, cell and tissue contractions, as well as beating cilia. We illustrate key concepts by drawing extensively from the early mouse embryo, which successively forms multiple lumens that play essential roles in its development. Finally, we detail experimental approaches and emerging techniques that allow for the quantitative characterization and the manipulation of intercellular fluids in vivo, as well as theoretical frameworks that are crucial for comprehending their dynamics.

Templated Pluripotent Stem Cell Differentiation via Substratum-Guided Artificial Signaling

The emerging field of synthetic morphogenesis implements synthetic biology tools to investigate the minimal cellular processes sufficient for orchestrating key developmental events. As the field continues to grow, there is a need for new tools that enable scientists to uncover nuances in the molecular mechanisms driving cell fate patterning that emerge during morphogenesis. Here, we present a platform that combines cell engineering with biomaterial design to potentiate artificial signaling in pluripotent stem cells (PSCs). This platform, referred to as PSC-MATRIX, extends the use of programmable biomaterials to PSCs competent to activate morphogen production through orthogonal signaling, giving rise to the opportunity to probe developmental events by initiating morphogenetic programs in a spatially constrained manner through non-native signaling channels. We show that the PSC-MATRIX platform enables temporal and spatial control of transgene expression in response to bulk, soluble inputs in synthetic Notch (synNotch)-engineered human PSCs for an extended culture of up to 11 days. Furthermore, we used PSC-MATRIX to regulate multiple differentiation events via material-mediated artificial signaling in engineered PSCs using the orthogonal ligand green fluorescent protein, highlighting the potential of this platform for probing and guiding fate acquisition. Overall, this platform offers a synthetic approach to interrogate the molecular mechanisms driving PSC differentiation that could be applied to a variety of differentiation protocols.

Early human development and stem cell-based human embryo models

The use of stem cells to model the early human embryo promises to transform our understanding of developmental biology and human reproduction. In this review, we present our current knowledge of the first 2 weeks of human embryo development. We first focus on the distinct cell lineages of the embryo and the derivation of stem cell lines. We then discuss the intercellular crosstalk that guides early embryo development and how this crosstalk is recapitulated in vitro to generate stem cell-based embryo models. We highlight advances in this fast-developing field, discuss current limitations, and provide a vision for the future.

Embryonic Stem Cell Differentiation to Definitive Endoderm As a Model of Heterogeneity Onset During Germ Layer Specification

Embryonic stem cells (ESCs) hold great promise for regenerative medicine thanks to their ability to self-renew and differentiate into somatic cells and the germline. ESCs correspond to pluripotent epiblast - the tissue from which the following three germ layers originate during embryonic gastrulation: the ectoderm, mesoderm, and endoderm. Importantly, ESCs can be induced to differentiate toward various cell types by varying culture conditions, which can be exploited for in vitro modeling of developmental processes such as gastrulation. The classical model of gastrulation postulates that mesoderm and endoderm specification is made possible through the FGF-, BMP-, Wnt-, and Nodal-signaling gradients. Hence, it can be expected that one of these signals should direct ESC differentiation towards specific germ layers. However, ESC specification appears to be more complicated, and the same signal can be interpreted differently depending on the readout. In this research, using chemically defined culture conditions, homogeneous naïve ESCs as a starting cell population, and the Foxa2 gene-driven EGFP reporter tool, we established a robust model of definitive endoderm (DE) specification. This in vitro model features formative pluripotency as an intermediate state acquired by the epiblast in vivo shortly after implantation. Despite the initially homogeneous state of the cells in the model and high Activin concentration during endodermal specification, there remains a cell subpopulation that does not reach the endodermal state. This simple model developed by us can be used to study the origins of cellular heterogeneity during germ layer specification.

Deep learning for quantifying spatial patterning and formation process of early differentiated human-induced pluripotent stem cells with micropattern images

Micropatterning is reliable method for quantifying pluripotency of human-induced pluripotent stem cells (hiPSCs) that differentiate to form a spatial pattern of sorted, ordered and nonoverlapped three germ layers on the micropattern. In this study, we propose a deep learning method to quantify spatial patterning of the germ layers in the early differentiation stage of hiPSCs using micropattern images. We propose decoding and encoding U-net structures learning labelled Hoechst (DNA-stained) hiPSC regions with corresponding Hoechst and bright-field micropattern images to segment hiPSCs on Hoechst or bright-field images. We also propose a U-net structure to extract extraembryonic regions on a micropattern, and an algorithm to compares intensities of the fluorescence images staining respective germ-layer cells and extract their regions. The proposed method thus can quantify the pluripotency of a hiPSC line with spatial patterning including cell numbers, areas and distributions of germ-layer and extraembryonic cells on a micropattern, and reveal the formation process of hiPSCs and germ layers in the early differentiation stage by segmenting live-cell bright-field images. In our assay, the cell-number accuracy achieved 86% and 85%, and the cell region accuracy 89% and 81% for segmenting Hoechst and bright-field micropattern images, respectively. Applications to micropattern images of multiple hiPSC lines, micropattern sizes, groups of markers, living and fixed cells show the proposed method can be expected to be a useful protocol and tool to quantify pluripotency of a new hiPSC line before providing it to the scientific community.

Bioprinting of Cells, Organoids and Organs-on-a-Chip Together with Hydrogels Improves Structural and Mechanical Cues

The 3D bioprinting technique has made enormous progress in tissue engineering, regenerative medicine and research into diseases such as cancer. Apart from individual cells, a collection of cells, such as organoids, can be printed in combination with various hydrogels. It can be hypothesized that 3D bioprinting will even become a promising tool for mechanobiological analyses of cells, organoids and their matrix environments in highly defined and precisely structured 3D environments, in which the mechanical properties of the cell environment can be individually adjusted. Mechanical obstacles or bead markers can be integrated into bioprinted samples to analyze mechanical deformations and forces within these bioprinted constructs, such as 3D organoids, and to perform biophysical analysis in complex 3D systems, which are still not standard techniques. The review highlights the advances of 3D and 4D printing technologies in integrating mechanobiological cues so that the next step will be a detailed analysis of key future biophysical research directions in organoid generation for the development of disease model systems, tissue regeneration and drug testing from a biophysical perspective. Finally, the review highlights the combination of bioprinted hydrogels, such as pure natural or synthetic hydrogels and mixtures, with organoids, organoid-cell co-cultures, organ-on-a-chip systems and organoid-organ-on-a chip combinations and introduces the use of assembloids to determine the mutual interactions of different cell types and cell-matrix interferences in specific biological and mechanical environments.

An explainable map of human gastruloid morphospace reveals gastrulation failure modes and predicts teratogens

Human gastrulation is a critical stage of development where many pregnancies fail due to poorly understood mechanisms. Using the 2D gastruloid, a stem cell model of human gastrulation, we combined high-throughput drug perturbations and mathematical modelling to create an explainable map of gastruloid morphospace. This map outlines patterning outcomes in response to diverse perturbations and identifies variations in canonical patterning and failure modes. We modeled morphogen dynamics to embed simulated gastruloids into experimentally-determined morphospace to explain how developmental parameters drive patterning. Our model predicted and validated the two greatest sources of patterning variance: cell density-based modulations in Wnt signaling and SOX2 stability. Assigning these parameters as axes of morphospace imparted interpretability. To demonstrate its utility, we predicted novel teratogens that we validated in zebrafish. Overall, we show how stem cell models of development can be used to build a comprehensive and interpretable understanding of the set of developmental outcomes.