Development-on-chip: in vitro neural tube patterning with a microfluidic device

Patterning of brain organoids derived from human pluripotent stem cells

The emerging technology of brain organoids deriving from human pluripotent stem cells provides unprecedented opportunities to study human brain development and associated disorders. Various brain organoid protocols have been developed that can recapitulate some key features of cell type diversity, cytoarchitectural organization, developmental processes, functions, and pathologies of the developing human brain. In this review, we focus on patterning of human stem cell-derived brain organoids. We start with an overview of general procedures to generate brain organoids. We then highlight some recently developed brain organoid protocols and chemical cues involved in modeling development of specific human brain regions, subregions, and multiple regions together. We also discuss limitations and potential future improvements of human brain organoid technology.

Engineering multiscale structural orders for high-fidelity embryoids and organoids

Embryoids and organoids hold great promise for human biology and medicine. Herein, we discuss conceptual and technological frameworks useful for developing high-fidelity embryoids and organoids that display tissue- and organ-level phenotypes and functions, which are critically needed for decoding developmental programs and improving translational applications. Through dissecting the layers of inputs controlling mammalian embryogenesis, we review recent progress in reconstructing multiscale structural orders in embryoids and organoids. Bioengineering tools useful for multiscale, multimodal structural engineering of tissue- and organ-level cellular organization and microenvironment are also discussed to present integrative, bioengineering-directed approaches to achieve next-generation, high-fidelity embryoids and organoids.

Synthetic developmental biology: Engineering approaches to guide multicellular organization

Multicellular organisms of various complexities self-organize in nature. Organoids are in vitro 3D structures that display important aspects of the anatomy and physiology of their in vivo counterparts and that develop from pluripotent or tissue-specific stem cells through a self-organization process. In this review, we describe the multidisciplinary concept of “synthetic developmental biology” where engineering approaches are employed to guide multicellular organization in an experimental setting. We introduce a novel classification of engineering approaches based on the extent of microenvironmental manipulation applied to organoids. In the final section, we discuss how engineering tools might help overcome current limitations in organoid construction.

Single-cell transcriptomics captures features of human midbrain development and dopamine neuron diversity in brain organoids

Three-dimensional brain organoids have emerged as a valuable model system for studies of human brain development and pathology. Here we establish a midbrain organoid culture system to study the developmental trajectory from pluripotent stem cells to mature dopamine neurons. Using single cell RNA sequencing, we identify the presence of three molecularly distinct subtypes of human dopamine neurons with high similarity to those in developing and adult human midbrain. However, despite significant advancements in the field, the use of brain organoids can be limited by issues of reproducibility and incomplete maturation which was also observed in this study. We therefore designed bioengineered ventral midbrain organoids supported by recombinant spider-silk microfibers functionalized with full-length human laminin. We show that silk organoids reproduce key molecular aspects of dopamine neurogenesis and reduce inter-organoid variability in terms of cell type composition and dopamine neuron formation.

From Spheroids to Organoids: The Next Generation of Model Systems of Human Cardiac Regeneration in a Dish

Organoids are tiny, self-organized, three-dimensional tissue cultures that are derived from the differentiation of stem cells. The growing interest in the use of organoids arises from their ability to mimic the biology and physiology of specific tissue structures in vitro. Organoids indeed represent promising systems for the in vitro modeling of tissue morphogenesis and organogenesis, regenerative medicine and tissue engineering, drug therapy testing, toxicology screening, and disease modeling. Although 2D cell cultures have been used for more than 50 years, even for their simplicity and low-cost maintenance, recent years have witnessed a steep rise in the availability of organoid model systems. Exploiting the ability of cells to re-aggregate and reconstruct the original architecture of an organ makes it possible to overcome many limitations of 2D cell culture systems. In vitro replication of the cellular micro-environment of a specific tissue leads to reproducing the molecular, biochemical, and biomechanical mechanisms that directly influence cell behavior and fate within that specific tissue. Lineage-specific self-organizing organoids have now been generated for many organs. Currently, growing cardiac organoid (cardioids) from pluripotent stem cells and cardiac stem/progenitor cells remains an open challenge due to the complexity of the spreading, differentiation, and migration of cardiac muscle and vascular layers. Here, we summarize the evolution of biological model systems from the generation of 2D spheroids to 3D organoids by focusing on the generation of cardioids based on the currently available laboratory technologies and outline their high potential for cardiovascular research.

Tumor organoids: synergistic applications, current challenges, and future prospects in cancer therapy

Patient-derived cancer cells (PDCs) and patient-derived xenografts (PDXs) are often used as tumor models, but have many shortcomings. PDCs not only lack diversity in terms of cell type, spatial organization, and microenvironment but also have adverse effects in stem cell cultures, whereas PDX are expensive with a low transplantation success rate and require a long culture time. In recent years, advances in three-dimensional (3D) organoid culture technology have led to the development of novel physiological systems that model the tissues of origin more precisely than traditional culture methods. Patient-derived cancer organoids bridge the conventional gaps in PDC and PDX models and closely reflect the pathophysiological features of natural tumorigenesis and metastasis, and have led to new patient-specific drug screening techniques, development of individualized treatment regimens, and discovery of prognostic biomarkers and mechanisms of resistance. Synergistic combinations of cancer organoids with other technologies, for example, organ-on-a-chip, 3D bio-printing, and CRISPR-Cas9-mediated homology-independent organoid transgenesis, and with treatments, such as immunotherapy, have been useful in overcoming their limitations and led to the development of more suitable model systems that recapitulate the complex stroma of cancer, inter-organ and intra-organ communications, and potentially multiorgan metastasis. In this review, we discuss various methods for the creation of organ-specific cancer organoids and summarize organ-specific advances and applications, synergistic technologies, and treatments as well as current limitations and future prospects for cancer organoids. Further advances will bring this novel 3D organoid culture technique closer to clinical practice in the future.

Engineered neural circuits for modeling brain physiology and neuropathology

The neural circuits of the central nervous system are the regulatory pathways for feeling, motion control, learning, and memory, and their dysfunction is closely related to various neurodegenerative diseases. Despite the growing demand for the unraveling of the physiology and functional connectivity of the neural circuits, their fundamental investigation is hampered because of the inability to access the components of neural circuits and the complex microenvironment. As an alternative approach, in vitro human neural circuits show principles of in vivo human neuronal circuit function. They allow access to the cellular compartment and permit real-time monitoring of neural circuits. In this review, we summarize recent advances in reconstituted in vitro neural circuits using engineering techniques. To this end, we provide an overview of the fabrication techniques and methods for stimulation and measurement of in vitro neural circuits. Subsequently, representative examples of in vitro neural circuits are reviewed with a particular focus on the recapitulation of structures and functions observed in vivo, and we summarize their application in the study of various brain diseases. We believe that the in vitro neural circuits can help neuroscience and the neuropharmacology. STATEMENT OF SIGNIFICANCE: Despite the growing demand to unravel the physiology and functional connectivity of the neural circuits, the studies on the in vivo neural circuits are frequently limited due to the poor accessibility. Furthermore, single neuron-based analysis has an inherent limitation in that it does not reflect the full spectrum of the neural circuit physiology. As an alternative approach, in vitro engineered neural circuit models have arisen because they can recapitulate the structural and functional characteristics of in vivo neural circuits. These in vitro neural circuits allow the mimicking of dysregulation of the neural circuits, including neurodegenerative diseases and traumatic brain injury. Emerging in vitro engineered neural circuits will provide a better understanding of the (patho-)physiology of neural circuits.

Biomaterial-guided stem cell organoid engineering for modeling development and diseases

Organoids are miniature models of organs to recapitulate spatiotemporal cellular organization and tissue functionality. The production of organoids has revolutionized the field of developmental biology, providing the possibility to study and guide human development and diseases in a dish. More recently, novel biomaterial-based culture systems demonstrated the feasibility and versatility to engineer and produce the organoids in a consistent and reproducible manner. By engineering proper tissue microenvironment, functional organoids have been able to exhibit spatial-distinct tissue patterning and morphogenesis. This review focuses on enabling technologies in the field of organoid engineering, including the control of biochemical and biophysical cues via hydrogels, as well as size and geometry control via microwell and microfabrication techniques. In addition, this review discusses the enhancement of organoid systems for therapeutic applications using biofabrication and organoid-on-chip platforms, which facilitate the assembly of complex organoid systems for in vitro modeling of development and diseases. STATEMENT OF SIGNIFICANCE: Stem cell organoids have revolutionized the fields of developmental biology and tissue engineering, providing the opportunity to study human organ development and disease progression in vitro. Various works have demonstrated that organoids can be generated using a wide variety of engineering tools, materials, and systems. Specific culture microenvironment is tailored to support the formation, function, and physiology of the organ of interest. This review highlights the importance of cellular microenvironment in organoid culture, the versatility of organoid engineering techniques, and future perspectives to build better organoid systems.

A microfluidic approach to rescue ALS motor neuron degeneration using rapamycin

TAR DNA-binding protein-43 (TDP-43) is known to accumulate in ubiquitinated inclusions of amyotrophic lateral sclerosis affected motor neurons, resulting in motor neuron degeneration, loss of motor functions, and eventually death. Rapamycin, an mTOR inhibitor and a commonly used immunosuppressive drug, has been shown to increase the survivability of Amyotrophic Lateral Sclerosis (ALS) affected motor neurons. Here we present a transgenic, TDP-43-A315T, mouse model expressing an ALS phenotype and demonstrate the presence of ubiquitinated cytoplasmic TDP-43 aggregates with > 80% cell death by 28 days post differentiation in vitro. Embryonic stem cells from this mouse model were used to study the onset, progression, and therapeutic remediation of TDP-43 aggregates using a novel microfluidic rapamycin concentration gradient generator. Results using a microfluidic device show that ALS affected motor neuron survival can be increased by 40.44% in a rapamycin dosage range between 0.4-1.0 µM.

Deciphering and reconstitution of positional information in the human brain development

Organoid has become a novel in vitro model to research human development and relevant disorders in recent years. With many improvements on the culture protocols, current brain organoids could self-organize into a complicated three-dimensional organization that mimics most of the features of the real human brain at the molecular, cellular, and further physiological level. However, lacking positional information, an important characteristic conveyed by gradients of signaling molecules called morphogens, leads to the deficiency of spatiotemporally regulated cell arrangements and cell–cell interactions in the brain organoid development. In this review, we will overview the role of morphogen both in the vertebrate neural development in vivo as well as the brain organoid culture in vitro, the strategies to apply morphogen concentration gradients in the organoid system and future perspectives of the brain organoid technology.

Building bridges between fields: bringing together development and homeostasis

Despite striking parallels between the fields of developmental biology and adult tissue homeostasis, these are disconnected in contemporary research. Although development describes tissue generation and homeostasis describes tissue maintenance, it is the balance between stem cell proliferation and differentiation that coordinates both processes. Upstream signalling regulates this balance to achieve the required outcome at the population level. Both development and homeostasis require tight regulation of stem cells at the single-cell level and establishment of patterns at the tissue-wide level. Here, we emphasize that the general principles of embryonic development and tissue homeostasis are similar, and argue that interactions between these disciplines will be beneficial for both research fields.

Dopamine Neuron Diversity: Recent Advances and Current Challenges in Human Stem Cell Models and Single Cell Sequencing

Human midbrain dopamine (DA) neurons are a heterogeneous group of cells that share a common neurotransmitter phenotype and are in close anatomical proximity but display different functions, sensitivity to degeneration, and axonal innervation targets. The A9 DA neuron subtype controls motor function and is primarily degenerated in Parkinson’s disease (PD), whereas A10 neurons are largely unaffected by the condition, and their dysfunction is associated with neuropsychiatric disorders. Currently, DA neurons can only be reliably classified on the basis of topographical features, including anatomical location in the midbrain and projection targets in the forebrain. No systematic molecular classification at the genome-wide level has been proposed to date. Although many years of scientific efforts in embryonic and adult mouse brain have positioned us to better understand the complexity of DA neuron biology, many biological phenomena specific to humans are not amenable to being reproduced in animal models. The establishment of human cell-based systems combined with advanced computational single-cell transcriptomics holds great promise for decoding the mechanisms underlying maturation and diversification of human DA neurons, and linking their molecular heterogeneity to functions in the midbrain. Human pluripotent stem cells have emerged as a useful tool to recapitulate key molecular features of mature DA neuron subtypes. Here, we review some of the most recent advances and discuss the current challenges in using stem cells, to model human DA biology. We also describe how single cell RNA sequencing may provide key insights into the molecular programs driving DA progenitor specification into mature DA neuron subtypes. Exploiting the state-of-the-art approaches will lead to a better understanding of stem cell-derived DA neurons and their use in disease modeling and regenerative medicine.

Actuation enhances patterning in human neural tube organoids

Tissues achieve their complex spatial organization through an interplay between gene regulatory networks, cell-cell communication, and physical interactions mediated by mechanical forces. Current strategies to generate in-vitro tissues have largely failed to implement such active, dynamically coordinated mechanical manipulations, relying instead on extracellular matrices which respond to, rather than impose mechanical forces. Here, we develop devices that enable the actuation of organoids. We show that active mechanical forces increase growth and lead to enhanced patterning in an organoid model of the neural tube derived from single human pluripotent stem cells (hPSC). Using a combination of single-cell transcriptomics and immunohistochemistry, we demonstrate that organoid mechanoregulation due to actuation operates in a temporally restricted competence window, and that organoid response to stretch is mediated extracellularly by matrix stiffness and intracellularly by cytoskeleton contractility and planar cell polarity. Exerting active mechanical forces on organoids using the approaches developed here is widely applicable and should enable the generation of more reproducible, programmable organoid shape, identity and patterns, opening avenues for the use of these tools in regenerative medicine and disease modelling applications.

Mechanical forces, along with gene regulatory networks and cell-cell signalling, play an important role in the complex organization of tissues. Here the authors describe devices that actively apply mechanical force to developing neural tube, demonstrating that mechanical forces increase growth and enhance patterning.

Microphysiological models of the central nervous system with fluid flow

There are over 1,000 described neurological and neurodegenerative disorders affecting nearly 100 million Americans - roughly one third of the U.S. population. Collectively, treatment of neurological conditions is estimated to cost $800 billion every year. Lowering this societal burden will require developing better model systems in which to study these diverse disorders. Microphysiological systems are promising tools for modeling healthy and diseased neural tissues to study mechanisms and treatment of neuropathology. One major benefit of microphysiological systems is the ability to incorporate biophysical forces, namely the forces derived from biological fluid flow. Fluid flow in the central nervous system (CNS) is a complex but important element of physiology, and pathologies as diverse as traumatic or ischemic injury, cancer, neurodegenerative disease, and natural aging have all been found to alter flow pathways. In this review, we summarize recent advances in three-dimensional microphysiological systems for studying the biology and therapy of CNS disorders and highlight the ability and growing need to incorporate biological fluid flow in these miniaturized model systems.

Biomaterials-based approaches to model embryogenesis

Understanding, reproducing, and regulating the cellular and molecular processes underlying human embryogenesis is critical to improve our ability to recapitulate tissues with proper architecture and function, and to address the dysregulation of embryonic programs that underlies birth defects and cancer. The rapid emergence of stem cell technologies is enabling enormous progress in understanding embryogenesis using simple, powerful, and accessible in vitro models. Biomaterials are playing a central role in providing the spatiotemporal organisation of biophysical and biochemical signalling necessary to mimic, regulate and dissect the evolving embryonic niche in vitro. This contribution is rapidly improving our understanding of the mechanisms underlying embryonic patterning, in turn enabling the development of more effective clinical interventions for regenerative medicine and oncology. Here we highlight how key biomaterial approaches contribute to organise signalling in human embryogenesis models, and we summarise the biological insights gained from these contributions. Importantly, we highlight how nanotechnology approaches have remained largely untapped in this space, and we identify their key potential contributions.

Gene Environment Interactions in the Etiology of Neural Tube Defects

Human structural congenital malformations are the leading cause of infant mortality in the United States. Estimates from the United States Center for Disease Control and Prevention (CDC) determine that close to 3% of all United States newborns present with birth defects; the worldwide estimate approaches 6% of infants presenting with congenital anomalies. The scientific community has recognized for decades that the majority of birth defects have undetermined etiologies, although we propose that environmental agents interacting with inherited susceptibility genes are the major contributing factors. Neural tube defects (NTDs) are among the most prevalent human birth defects and as such, these malformations will be the primary focus of this review. NTDs result from failures in embryonic central nervous system development and are classified by their anatomical locations. Defects in the posterior portion of the neural tube are referred to as meningomyeloceles (spina bifida), while the more anterior defects are differentiated as anencephaly, encephalocele, or iniencephaly. Craniorachischisis involves a failure of the neural folds to elevate and thus disrupt the entire length of the neural tube. Worldwide NTDs have a prevalence of approximately 18.6 per 10,000 live births. It is widely believed that genetic factors are responsible for some 70% of NTDs, while the intrauterine environment tips the balance toward neurulation failure in at risk individuals. Despite aggressive educational campaigns to inform the public about folic acid supplementation and the benefits of providing mandatory folic acid food fortification in the United States, NTDs still affect up to 2,300 United States births annually and some 166,000 spina bifida patients currently live in the United States, more than half of whom are now adults. Within the context of this review, we will consider the role of maternal nutritional status (deficiency states involving B vitamins and one carbon analytes) and the potential modifiers of NTD risk beyond folic acid. There are several well-established human teratogens that contribute to the population burden of NTDs, including: industrial waste and pollutants [e.g., arsenic, pesticides, and polycyclic aromatic hydrocarbons (PAHs)], pharmaceuticals (e.g., anti-epileptic medications), and maternal hyperthermia during the first trimester. Animal models for these teratogens are described with attention focused on valproic acid (VPA; Depakote). Genetic interrogation of model systems involving VPA will be used as a model approach to discerning susceptibility factors that define the gene-environment interactions contributing to the etiology of NTDs.

Pierre S, Hong K, Pavon N, Pak C, Sun Y. Patterning Neuroepithelial Cell Sheet via a Sustained Chemical Gradient Generated by Localized Passive Diffusion Devices

Recent advances in human pluripotent stem cells (hPSCs)-derived in vitro models open a new avenue for studying early stage human development. While current approaches leverage the self-organizing capability of hPSCs, it remains unclear whether extrinsic morphogen gradients are sufficient to pattern neuroectoderm tissues in vitro. While microfluidics or hydrogel-based approaches to generate chemical gradients are well-established, these systems either require continuous pumping or encapsulating cells in gels, making it difficult for adaptation in standard biology laboratories and downstream analysis. In this work, we report a new device design that leverages localized passive diffusion, or LPaD for short, to generate a stable chemical gradient in an open environment. As LPaD is operated simply by media changing, common issues for microfluidic systems such as leakage, bubble formation, and contamination can be avoided. The device contains a slit carved in a film filled with solid gelatin and connected to a static aqueous morphogen reservoir. Concentration gradients generated by the device were visualized via DAPI fluorescent intensity and were found to be stable for up to 168 h. Using this device, we successfully induced cellular response of Madin-Darby canine kidney (MDCK) cells to the concentration gradient of a small-molecule drug, cytochalasin D. Furthermore, we efficiently patterned the dorsal-ventral axis of hPSC-derived forebrain neuroepithelial cells with the sonic hedgehog (Shh) signal gradient generated by the LPaD devices. Together, LPaD devices are powerful tools to control the local chemical microenvironment for engineering organotypic structures in vitro.

Organoids as a new model system to study neural tube defects

The neural tube is the first critically important structure that develops in the embryo. It serves as the primordium of the central nervous system; therefore, the proper formation of the neural tube is essential to the developing organism. Neural tube defects (NTDs) are severe congenital defects caused by failed neural tube closure during early embryogenesis. The pathogenesis of NTDs is complicated and still not fully understood even after decades of research. While it is an ethically impossible proposition to investigate the in vivo formation process of the neural tube in human embryos, a newly developed technology involving the creation of neural tube organoids serves as an excellent model system with which to study human neural tube formation and the occurrence of NTDs. Herein we reviewed the recent literature on the process of neural tube formation, the progress of NTDs investigations, and particularly the exciting potential to use neural tube organoids to model the cellular and molecular mechanisms underlying the etiology of NTDs.

Advances in Central Nervous System Organoids: A Focus on Organoid-Based Models for Motor Neuron Disease

Despite their large societal burden, the development of therapeutic treatments for neurodegenerative diseases (NDDs) has been relatively unsuccessful. This is, in part, due to a lack of representative experimental models that reveal fundamental aspects of human brain pathology. Recently, assays for in vitro modeling of the human central nervous system (CNS) have significantly improved with the development of brain and spinal cord organoids. Coupled with induced-pluripotent stem cell and genome editing technologies, CNS organoids are a promising tool for studying neurodegeneration in a patient-specific manner. An extensive array of protocols for the generation of organoids for different brain regions has been developed and used for studying neurodegenerative and other brain diseases. However, their application in the field of motor neuron disease (MND) has been limited due to a lack of adequate organoid models. The development of protocols to derive spinal cord and trunk organoids and progress in the field of assembloids are providing new opportunities for modeling MND. In this study here we review recent advances in the development of CNS organoid models, their application in NDDs, and technical limitations. Finally, we discuss future perspectives for the development of organoid-based systems for MND and provide a framework for their development. Impact statement Animal models and two-dimensional cultures are currently the main platforms for studying neurodegenerative diseases (NDDs). However, central nervous system (CNS) organoid technology offers novel possibilities for studying these diseases. Organoid modeling in combination with emerging organ-on-a-chip approaches, induced-pluripotent stem cell technology, and genome editing render in vitro modeling of NDDs more robust and physiologically relevant. In this study, we review the principles underlying CNS organoid generation, their use in NDD research, and future perspectives in organoid technology. Finally, we discuss how advances in different fields could be combined to generate a multisystem organoid-on-a-chip model to investigate a specific class of NDDs, motor neuron diseases.

Current Challenges Associated with the Use of Human Induced Pluripotent Stem Cell-Derived Organoids in Regenerative Medicine

Innovative advances in stem cell research have resulted in the development of organoids, which are widely used as in vitro models of human organ development and for disease. The long-term goals of scientists include the generation of high-quality organoids with properties like those of native organs, and to expand their use to a variety of applications such as drug discovery and organoid-based cell therapy. In particular, the combination of human induced pluripotent stem cell (iPSC)-derived organoids with the recently developed genome engineering, biotechnology serve as an attractive platform in precision medicine. This review briefly summarizes the generation of organoids derived mostly from iPSCs without ethical issues, and describes the applications and technological advances of organoids under their differentiation and culture conditions. We also discuss the approaches to improve the organoid models, and how organoids can recapitulate mature organ systems of the human body for regenerative medicine. Finally, the future perspectives and remaining challenges in the field have been discussed to provide a better understanding of the potential applications of organoids.

Human iPSC-Based Modeling of Central Nerve System Disorders for Drug Discovery

A high-throughput drug screen identifies potentially promising therapeutics for clinical trials. However, limitations that persist in current disease modeling with limited physiological relevancy of human patients skew drug responses, hamper translation of clinical efficacy, and contribute to high clinical attritions. The emergence of induced pluripotent stem cell (iPSC) technology revolutionizes the paradigm of drug discovery. In particular, iPSC-based three-dimensional (3D) tissue engineering that appears as a promising vehicle of in vitro disease modeling provides more sophisticated tissue architectures and micro-environmental cues than a traditional two-dimensional (2D) culture. Here we discuss 3D based organoids/spheroids that construct the advanced modeling with evolved structural complexity, which propels drug discovery by exhibiting more human specific and diverse pathologies that are not perceived in 2D or animal models. We will then focus on various central nerve system (CNS) disease modeling using human iPSCs, leading to uncovering disease pathogenesis that guides the development of therapeutic strategies. Finally, we will address new opportunities of iPSC-assisted drug discovery with multi-disciplinary approaches from bioengineering to Omics technology. Despite technological challenges, iPSC-derived cytoarchitectures through interactions of diverse cell types mimic patients' CNS and serve as a platform for therapeutic development and personalized precision medicine.

Electrophysiology Read-Out Tools for Brain-on-Chip Biotechnology

Brain-on-Chip (BoC) biotechnology is emerging as a promising tool for biomedical and pharmaceutical research applied to the neurosciences. At the convergence between lab-on-chip and cell biology, BoC couples in vitro three-dimensional brain-like systems to an engineered microfluidics platform designed to provide an in vivo-like extrinsic microenvironment with the aim of replicating tissue- or organ-level physiological functions. BoC therefore offers the advantage of an in vitro reproduction of brain structures that is more faithful to the native correlate than what is obtained with conventional cell culture techniques. As brain function ultimately results in the generation of electrical signals, electrophysiology techniques are paramount for studying brain activity in health and disease. However, as BoC is still in its infancy, the availability of combined BoC-electrophysiology platforms is still limited. Here, we summarize the available biological substrates for BoC, starting with a historical perspective. We then describe the available tools enabling BoC electrophysiology studies, detailing their fabrication process and technical features, along with their advantages and limitations. We discuss the current and future applications of BoC electrophysiology, also expanding to complementary approaches. We conclude with an evaluation of the potential translational applications and prospective technology developments.

Electrophysiological Analysis of Brain Organoids: Current Approaches and Advancements

Brain organoids, or cerebral organoids, have become widely used to study the human brain in vitro. As pluripotent stem cell-derived structures capable of self-organization and recapitulation of physiological cell types and architecture, brain organoids bridge the gap between relatively simple two-dimensional human cell cultures and non-human animal models. This allows for high complexity and physiological relevance in a controlled in vitro setting, opening the door for a variety of applications including development and disease modeling and high-throughput screening. While technologies such as single cell sequencing have led to significant advances in brain organoid characterization and understanding, improved functional analysis (especially electrophysiology) is needed to realize the full potential of brain organoids. In this review, we highlight key technologies for brain organoid development and characterization, then discuss current electrophysiological methods for brain organoid analysis. While electrophysiological approaches have improved rapidly for two-dimensional cultures, only in the past several years have advances been made to overcome limitations posed by the three-dimensionality of brain organoids. Here, we review major advances in electrophysiological technologies and analytical methods with a focus on advances with applicability for brain organoid analysis.

Engineering organoids

Organoids are in vitro miniaturized and simplified model systems of organs that have gained enormous interest for modelling tissue development and disease, and for personalized medicine, drug screening and cell therapy. Despite considerable success in culturing physiologically relevant organoids, challenges remain to achieve real-life applications. In particular, the high variability of self-organizing growth and restricted experimental and analytical access hamper the translatability of organoid systems. In this Review, we argue that many limitations of traditional organoid culture can be addressed by engineering approaches at all levels of organoid systems. We investigate cell surface and genetic engineering approaches, and discuss stem cell niche engineering based on the design of matrices that allow spatiotemporal control of organoid growth and shape-guided morphogenesis. We examine how microfluidic approaches and lessons learnt from organs-on-a-chip enable the integration of mechano-physiological parameters and increase accessibility of organoids to improve functional readouts. Applying engineering principles to organoids increases reproducibility and provides experimental control, which will, ultimately, be required to enable clinical translation.

Toward Spatial Identities in Human Brain Organoids-on-Chip Induced by Morphogen-Soaked Beads

Recent advances in stem-cell technologies include the differentiation of human embryonic stem cells (hESCs) into organ-like structures (organoids). These organoids exhibit remarkable self-organization that resembles key aspects of in vivo organ development. However, organoids have an unpredictable anatomy, and poorly reflect the topography of the dorsoventral, mediolateral, and anteroposterior axes. In vivo the temporal and the spatial patterning of the developing tissue is orchestrated by signaling molecules called morphogens. Here, we used morphogen-soaked beads to influence the spatial identities within hESC-derived brain organoids. The morphogen- and synthetic molecules-soaked beads were interpreted as local organizers, and key transcription factor expression levels within the organoids were affected as a function of the distance from the bead. We used an on-chip imaging device that we have developed, that allows live imaging of the developing hESC-derived organoids. This platform enabled studying the effect of changes in WNT/BMP gradients on the expression of key landmark genes in the on-chip human brain organoids. Titration of CHIR99201 (WNT agonist) and BMP4 directed the expression of telencephalon and medial pallium genes; dorsal and ventral midbrain markers; and isthmus-related genes. Overall, our protocol provides an opportunity to study phenotypes of altered regional specification and defected connectivity, which are found in neurodevelopmental diseases.

Recent progress in translational engineered in vitro models of the central nervous system

The complexity of the human brain poses a substantial challenge for the development of models of the CNS. Current animal models lack many essential human characteristics (in addition to raising operational challenges and ethical concerns), and conventional in vitro models, in turn, are limited in their capacity to provide information regarding many functional and systemic responses. Indeed, these challenges may underlie the notoriously low success rates of CNS drug development efforts. During the past 5 years, there has been a leap in the complexity and functionality of in vitro systems of the CNS, which have the potential to overcome many of the limitations of traditional model systems. The availability of human-derived induced pluripotent stem cell technology has further increased the translational potential of these systems. Yet, the adoption of state-of-the-art in vitro platforms within the CNS research community is limited. This may be attributable to the high costs or the immaturity of the systems. Nevertheless, the costs of fabrication have decreased, and there are tremendous ongoing efforts to improve the quality of cell differentiation. Herein, we aim to raise awareness of the capabilities and accessibility of advanced in vitro CNS technologies. We provide an overview of some of the main recent developments (since 2015) in in vitro CNS models. In particular, we focus on engineered in vitro models based on cell culture systems combined with microfluidic platforms (e.g. 'organ-on-a-chip' systems). We delve into the fundamental principles underlying these systems and review several applications of these platforms for the study of the CNS in health and disease. Our discussion further addresses the challenges that hinder the implementation of advanced in vitro platforms in personalized medicine or in large-scale industrial settings, and outlines the existing differentiation protocols and industrial cell sources. We conclude by providing practical guidelines for laboratories that are considering adopting organ-on-a-chip technologies.

Modeling neural tube development by differentiation of human embryonic stem cells in a microfluidic WNT gradient

The study of brain development in humans is limited by the lack of tissue samples and suitable in vitro models. Here, we model early human neural tube development using human embryonic stem cells cultured in a microfluidic device. The approach, named microfluidic-controlled stem cell regionalization (MiSTR), exposes pluripotent stem cells to signaling gradients that mimic developmental patterning. Using a WNT-activating gradient, we generated a neural tissue exhibiting progressive caudalization from forebrain to midbrain to hindbrain, including formation of isthmic organizer characteristics. Single-cell transcriptomics revealed that rostro-caudal organization was already established at 24 h of differentiation, and that the first markers of a neural-specific transcription program emerged in the rostral cells at 48 h. The transcriptomic hallmarks of rostro-caudal organization recapitulated gene expression patterns of the early rostro-caudal neural plate in mouse embryos. Thus, MiSTR will facilitate research on the factors and processes underlying rostro-caudal neural tube patterning.

Development of a microfluidic approach for the real-time analysis of extrinsic TGF-β signalling

Autocrine and paracrine signalling are traditionally difficult to study due to the sub-micromolar concentrations involved. This has proven to be especially limiting in the study of embryonic stem cells that rely on such signalling for viability, self-renewal, and proliferation. Microfluidics allows to achieve local concentrations of ligands representative of the in vivo stem cell niche, gaining more precise control over the cell microenvironment, as well as to manipulate ligands availability with high temporal resolution and minimal amount of reagents. Here we developed a microfluidics-based system for monitoring the dynamics of TGF-β pathway activity by means of a SMAD2/3-dependent luciferase reporter. We first validated our system by showing dose-dependent transcriptional activation. We then tested the effects of pulsatile stimulation and delayed inhibition of TGF-β activity on signalling dynamics. Finally, we show that our microfluidic system, unlike conventional culture systems, can detect TGF-β ligands secreted in the conditioned medium from hESCs.

Wnt/β-catenin Signaling in Tissue Self-Organization

Across metazoans, animal body structures and tissues exist in robust patterns that arise seemingly out of stochasticity of a few early cells in the embryo. These patterns ensure proper tissue form and function during early embryogenesis, development, homeostasis, and regeneration. Fundamental questions are how these patterns are generated and maintained during tissue homeostasis and regeneration. Though fascinating scientists for generations, these ideas remain poorly understood. Today, it is apparent that the Wnt/β-catenin pathway plays a central role in tissue patterning. Wnt proteins are small diffusible morphogens which are essential for cell type specification and patterning of tissues. In this review, we highlight several mechanisms described where the spatial properties of Wnt/β-catenin signaling are controlled, allowing them to work in combination with other diffusible molecules to control tissue patterning. We discuss examples of this self-patterning behavior during development and adult tissues' maintenance. The combination of new physiological culture systems, mathematical approaches, and synthetic biology will continue to fuel discoveries about how tissues are patterned. These insights are critical for understanding the intricate interplay of core patterning signals and how they become disrupted in disease.

Engineering Stem Cell Self-organization to Build Better Organoids

Organoids form through self-organization processes in which initially homogeneous populations of stem cells spontaneously break symmetry and undergo in-vivo-like pattern formation and morphogenesis, though the processes controlling this are poorly characterized. While these in vitro self-organized tissues far exceed the microscopic and functional complexity obtained by current tissue engineering technologies, they are non-physiological in shape and size and have limited function and lifespan. Here, we discuss how engineering efforts for guiding stem-cell-based development at multiple stages can form the basis for the assembly of highly complex and rationally designed self-organizing multicellular systems with increased robustness and physiological relevance.

Exploiting CRISPR Cas9 in Three-Dimensional Stem Cell Cultures to Model Disease

Three-dimensional (3D) cell culture methods have been widely used on a range of cell types, including stem cells to modulate precisely the cellular biophysical and biochemical microenvironment and control various cell signaling cues. As a result, more in vivo-like microenvironments are recapitulated, particularly through the formation of multicellular spheroids and organoids, which may yield more valid mechanisms of disease. Recently, genome-engineering tools such as CRISPR Cas9 have expanded the repertoire of techniques to control gene expression, which complements external signaling cues with intracellular control elements. As a result, the combination of CRISPR Cas9 and 3D cell culture methods enhance our understanding of the molecular mechanisms underpinning several disease phenotypes and may lead to developing new therapeutics that may advance more quickly and effectively into clinical candidates. In addition, using CRISPR Cas9 tools to rescue genes brings us one step closer to its use as a gene therapy tool for various degenerative diseases. Herein, we provide an overview of bridging of CRISPR Cas9 genome editing with 3D spheroid and organoid cell culture to better understand disease progression in both patient and non-patient derived cells, and we address potential remaining gaps that must be overcome to gain widespread use.

Microfluidics as a Novel Tool for Biological and Toxicological Assays in Drug Discovery Processes: Focus on Microchip Electrophoresis

The last decades of biological, toxicological, and pharmacological research have deeply changed the way researchers select the most appropriate 'pre-clinical model'. The absence of relevant animal models for many human diseases, as well as the inaccurate prognosis coming from 'conventional' pre-clinical models, are among the major reasons of the failures observed in clinical trials. This evidence has pushed several research groups to move more often from a classic cellular or animal modeling approach to an alternative and broader vision that includes the involvement of microfluidic-based technologies. The use of microfluidic devices offers several benefits including fast analysis times, high sensitivity and reproducibility, the ability to quantitate multiple chemical species, and the simulation of cellular response mimicking the closest human in vivo milieu. Therefore, they represent a useful way to study drug-organ interactions and related safety and toxicity, and to model organ development and various pathologies 'in a dish'. The present review will address the applicability of microfluidic-based technologies in different systems (2D and 3D). We will focus our attention on applications of microchip electrophoresis (ME) to biological and toxicological studies as well as in drug discovery and development processes. These include high-throughput single-cell gene expression profiling, simultaneous determination of antioxidants and reactive oxygen and nitrogen species, DNA analysis, and sensitive determination of neurotransmitters in biological fluids. We will discuss new data obtained by ME coupled to laser-induced fluorescence (ME-LIF) and electrochemical detection (ME-EC) regarding the production and degradation of nitric oxide, a fundamental signaling molecule regulating virtually every critical cellular function. Finally, the integration of microfluidics with recent innovative technologies-such as organoids, organ-on-chip, and 3D printing-for the design of new in vitro experimental devices will be presented with a specific attention to drug development applications. This 'composite' review highlights the potential impact of 2D and 3D microfluidic systems as a fast, inexpensive, and highly sensitive tool for high-throughput drug screening and preclinical toxicological studies.

Spatially controlled stem cell differentiation via morphogen gradients: A comparison of static and dynamic microfluidic platforms

The ability to harness the processes by which complex tissues arise during embryonic development would improve the ability to engineer complex tissuelike constructs in vitro-a longstanding goal of tissue engineering and regenerative medicine. In embryos, uniform populations of stem cells are exposed to spatial gradients of diffusible extracellular signaling proteins, known as morphogens. Varying levels of these signaling proteins induce stem cells to differentiate into distinct cell types at different positions along the gradient, thus creating spatially patterned tissues. Here, the authors describe two straightforward and easy-to-adopt microfluidic strategies to expose human pluripotent stem cells in vitro to spatial gradients of desired differentiation-inducing extracellular signals. Both approaches afford a high degree of control over the distribution of extracellular signals, while preserving the viability of the cultured stem cells. The first microfluidic platform is commercially available and entails static culture, whereas the second microfluidic platform requires fabrication and dynamic fluid exchange. In each platform, the authors first computationally modeled the spatial distribution of differentiation-inducing extracellular signals. Then, the authors used each platform to expose human pluripotent stem cells to a gradient of these signals (in this case, inducing a cell type known as the primitive streak), resulting in a regionalized culture with differentiated primitive streak cells predominately localized on one side and undifferentiated stem cells at the other side of the device. By combining this approach with a fluorescent reporter for differentiated cells and live-cell fluorescence imaging, the authors characterized the spatial and temporal dynamics of primitive streak differentiation within the induced signaling gradients. Microfluidic approaches to create precisely controlled morphogen gradients will add to the stem cell and developmental biology toolkit, and may eventually pave the way to create increasingly spatially patterned tissuelike constructs in vitro.

Spatially controlled stem cell differentiation via morphogen gradients: A comparison of static and dynamic microfluidic platforms

The ability to harness the processes by which complex tissues arise during embryonic development would improve the ability to engineer complex tissuelike constructs in vitro-a longstanding goal of tissue engineering and regenerative medicine. In embryos, uniform populations of stem cells are exposed to spatial gradients of diffusible extracellular signaling proteins, known as morphogens. Varying levels of these signaling proteins induce stem cells to differentiate into distinct cell types at different positions along the gradient, thus creating spatially patterned tissues. Here, the authors describe two straightforward and easy-to-adopt microfluidic strategies to expose human pluripotent stem cells in vitro to spatial gradients of desired differentiation-inducing extracellular signals. Both approaches afford a high degree of control over the distribution of extracellular signals, while preserving the viability of the cultured stem cells. The first microfluidic platform is commercially available and entails static culture, whereas the second microfluidic platform requires fabrication and dynamic fluid exchange. In each platform, the authors first computationally modeled the spatial distribution of differentiation-inducing extracellular signals. Then, the authors used each platform to expose human pluripotent stem cells to a gradient of these signals (in this case, inducing a cell type known as the primitive streak), resulting in a regionalized culture with differentiated primitive streak cells predominately localized on one side and undifferentiated stem cells at the other side of the device. By combining this approach with a fluorescent reporter for differentiated cells and live-cell fluorescence imaging, the authors characterized the spatial and temporal dynamics of primitive streak differentiation within the induced signaling gradients. Microfluidic approaches to create precisely controlled morphogen gradients will add to the stem cell and developmental biology toolkit, and may eventually pave the way to create increasingly spatially patterned tissuelike constructs in vitro.

Recent Advancements in Engineering Strategies for Manipulating Neural Stem Cell Behavior

Purpose of Review

Stem cells are exquisitely sensitive to biophysical and biochemical cues within the native microenvironment. This review focuses on emerging strategies to manipulate neural cell behavior using these influences in three-dimensional (3D) culture systems.

Recent Findings

Traditional systems for neural cell differentiation typically produce heterogeneous populations with limited diversity rather than the complex, organized tissue structures observed in vivo. Advancements in developing engineering tools to direct neural cell fates can enable new applications in basic research, disease modeling, and regenerative medicine.

Summary

This review article highlights engineering strategies that facilitate controlled presentation of biophysical and biochemical cues to guide differentiation and impart desired phenotypes on neural cell populations. Specific highlighted examples include engineered biomaterials and microfluidic platforms for spatiotemporal control over the presentation of morphogen gradients.

One-Stop Microfluidic Assembly of Human Brain Organoids To Model Prenatal Cannabis Exposure

Prenatal cannabis exposure (PCE) influences human brain development, but it is challenging to model PCE using animals and current cell culture techniques. Here, we developed a one-stop microfluidic platform to assemble and culture human cerebral organoids from human embryonic stem cells (hESC) to investigate the effect of PCE on early human brain development. By incorporating perfusable culture chambers, air-liquid interface, and one-stop protocol, this microfluidic platform can simplify the fabrication procedure and produce a large number of organoids (169 organoids per 3.5 cm × 3.5 cm device area) without fusion, as compared with conventional fabrication methods. These one-stop microfluidic assembled cerebral organoids not only recapitulate early human brain structure, biology, and electrophysiology but also have minimal size variation and hypoxia. Under on-chip exposure to the psychoactive cannabinoid, Δ-9-tetrahydrocannabinol (THC), cerebral organoids exhibited reduced neuronal maturation, downregulation of cannabinoid receptor type 1 (CB1) receptors, and impaired neurite outgrowth. Moreover, transient on-chip THC treatment also decreased spontaneous firing in these organoids. This one-stop microfluidic technique enables a simple, scalable, and repeatable organoid culture method that can be used not only for human brain organoids but also for many other human organoids including liver, kidney, retina, and tumor organoids. This technology could be widely used in modeling brain and other organ development, developmental disorders, developmental pharmacology and toxicology, and drug screening.

Bioengineered microenvironment to culture early embryos

The abnormalities of early post-implantation embryos can lead to early pregnancy loss and many other syndromes. However, it is hard to study embryos after implantation due to the limited accessibility. The success of embryo culture in vitro can avoid the challenges of embryonic development in vivo and provide a powerful research platform for research in developmental biology. The biophysical and chemical cues of the microenvironments impart significant spatiotemporal effects on embryonic development. Here, we summarize the main strategies which enable researchers to grow embryos outside of the body while overcoming the implantation barrier, highlight the roles of engineered microenvironments in regulating early embryonic development, and finally discuss the future challenges and new insights of early embryo culture.

Engineering approaches to control and design the in vitro environment towards the reconstruction of organs

In vitro experimental models pertaining to human cells are considered essential for most biological experiments, such as drug development and analysis of disease mechanisms, because of their genetic consistency and ease for detailed and long-term analysis. Recent development of organoid cultures, such as intestine, liver, and kidney cultures, greatly promotes the potential of in vitro experiments. However, conventional culture methods that use manual pipetting have limitations in regenerating complex biosystems. Our body autonomously organizes cells to form a specific tissue shape, and the self-organization process occurs in an extremely systematic manner. In order to emulate this sophisticated process in vitro; first, methodologies for cell culture and organization of in vitro systems need to be updated; second, understanding the self-organizing system is a crucial issue. In this review, recent advancements in engineering technologies to control the microenvironment during cell culture are introduced. Both static and dynamic control have been developed for decades in engineering fields, and the means by which such technologies can help to elucidate and design a biosystem is discussed.

Spatiotemporal Control of Morphogen Delivery to Pattern Stem Cell Differentiation in Three-Dimensional Hydrogels

Morphogens are biological molecules that alter cellular identity and behavior across both space and time. During embryonic development, morphogen spatial localization can be confined to small volumes in a single tissue or permeate throughout an entire organism, and the temporal effects of morphogens can range from fractions of a second to several days. In most cases, morphogens are presented as a gradient to adjacent cells within tissues to pattern cell fate. As such, to appropriately model development and build representative multicellular architectures in vitro, it is vital to recapitulate these gradients during stem cell differentiation. However, the ability to control morphogen presentation within in vitro systems remains challenging. Here, we describe an innovative platform using channels patterned within thick, three-dimensional hydrogels that deliver multiple morphogens to embedded cells, thereby demonstrating exquisite control over both spatial and temporal variations in morphogen presentation. This generalizable approach should have broad utility for researchers interested in patterning in vitro tissue structures. © 2019 by John Wiley & Sons, Inc.

Automated Design of Pluripotent Stem Cell Self-Organization

Human pluripotent stem cells (hPSCs) have the intrinsic ability to self-organize into complex multicellular organoids that recapitulate many aspects of tissue development. However, robustly directing morphogenesis of hPSC-derived organoids requires novel approaches to accurately control self-directed pattern formation. Here, we combined genetic engineering with computational modeling, machine learning, and mathematical pattern optimization to create a data-driven approach to control hPSC self-organization by knock down of genes previously shown to affect stem cell colony organization, CDH1 and ROCK1. Computational replication of the in vitro system in silico using an extended cellular Potts model enabled machine learning-driven optimization of parameters that yielded emergence of desired patterns. Furthermore, in vitro the predicted experimental parameters quantitatively recapitulated the in silico patterns. These results demonstrate that morphogenic dynamics can be accurately predicted through model-driven exploration of hPSC behaviors via machine learning, thereby enabling spatial control of multicellular patterning to engineer human organoids and tissues. A record of this paper's Transparent Peer Review process is included in the Supplemental Information.

Toward the formation of neural circuits in human brain organoids

Because of the ability to recapitulate normal developmental processes, brain organoids derived from pluripotent stem cells are an important experimental resource to investigate the development and pathogenesis of human brains. Although brain organoids are used in research on diseases such as microcephaly, it has traditionally been difficult to analyze diseases that affect neuronal networks between distant brain regions, as effective brain organoids containing multiple brain regions with defined connectivity have yet to be established. In this review, we discuss strategies to construct such organoids and provide a review on recent progress on brain organoids.

Microfluidics as an Emerging Precision Tool in Developmental Biology

Microfluidics has become a precision tool in modern biology. It enables omics data to be obtained from individual cells, as compared to averaged signals from cell populations, and it allows manipulation of biological specimens in entirely new ways. Cells and organisms can be perturbed at extraordinary spatiotemporal resolution, revealing mechanistic insights that would otherwise remain hidden. In this perspective article, we discuss the current and future impact of microfluidic technology in the field of developmental biology. In addition, we provide detailed information on how to start using this technology even without prior experience.

In Vitro Modelling of Nerve-Muscle Connectivity in a Compartmentalised Tissue Culture Device

Motor neurons project axons from the hindbrain and spinal cord to muscle, where they induce myofibre contractions through neurotransmitter release at neuromuscular junctions. Studies of neuromuscular junction formation and homeostasis have been largely confined to in vivo models. In this study we have merged three powerful tools - pluripotent stem cells, optogenetics and microfabrication - and designed an open microdevice in which motor axons grow from a neural compartment containing embryonic stem cell-derived motor neurons and astrocytes through microchannels to form functional neuromuscular junctions with contractile myofibers in a separate compartment. Optogenetic entrainment of motor neurons in this reductionist neuromuscular circuit enhanced neuromuscular junction formation more than two-fold, mirroring the activity-dependence of synapse development in vivo. We incorporated an established motor neuron disease model into our system and found that coculture of motor neurons with SOD1G93A astrocytes resulted in denervation of the central compartment and diminished myofiber contractions, a phenotype which was rescued by the Receptor Interacting Serine/Threonine Kinase 1 (RIPK1) inhibitor Necrostatin. This coculture system replicates key aspects of nerve-muscle connectivity in vivo and represents a rapid and scalable alternative to animal models of neuromuscular function and disease.

Organoids-on-a-chip

Recent studies have demonstrated an array of stem cell-derived, self-organizing miniature organs, termed organoids, that replicate the key structural and functional characteristics of their in vivo counterparts. As organoid technology opens up new frontiers of research in biomedicine, there is an emerging need for innovative engineering approaches for the production, control, and analysis of organoids and their microenvironment. In this Review, we explore organ-on-a-chip technology as a platform to fulfill this need and examine how this technology may be leveraged to address major technical challenges in organoid research. We also discuss emerging opportunities and future obstacles for the development and application of organoid-on-a-chip technology.