Generation and functional characterization of murine mammary organoids.

3D cultures of mammary epithelial cells purified from murine models provide a unique resource to study genetically defined breast cancer and response to targeted therapies. Here, we describe step-by-step experimental procedures for the successful establishment of murine mammary organoid lines isolated from mammary glands or mammary tumors driven by mutations in components of the PI3K pathway. These detailed protocols also include procedures to perform assays that can be adopted to screen response to drug treatments and to inform better therapies. For details on potential applications and use of this protocol, please refer to Yip et al. (2020).

Microfluidic device with brain extracellular matrix promotes structural and functional maturation of human brain organoids.

Brain organoids derived from human pluripotent stem cells provide a highly valuable in vitro model to recapitulate human brain development and neurological diseases. However, the current systems for brain organoid culture require further improvement for the reliable production of high-quality organoids. Here, we demonstrate two engineering elements to improve human brain organoid culture, (1) a human brain extracellular matrix to provide brain-specific cues and (2) a microfluidic device with periodic flow to improve the survival and reduce the variability of organoids. A three-dimensional culture modified with brain extracellular matrix significantly enhanced neurogenesis in developing brain organoids from human induced pluripotent stem cells. Cortical layer development, volumetric augmentation, and electrophysiological function of human brain organoids were further improved in a reproducible manner by dynamic culture in microfluidic chamber devices. Our engineering concept of reconstituting brain-mimetic microenvironments facilitates the development of a reliable culture platform for brain organoids, enabling effective modeling and drug development for human brain diseases.

The Last Half Century of Fish Explant and Organ Culture.

Explants are three-dimensional tissue fragments maintained outside the organism. The goals of this article are to review the history of fish explant culture and discuss applications of this technique that may assist the modern zebrafish laboratory. Because most zebrafish workers do not have a background in tissue culture, the key variables of this method are deliberately explained in a general way. This is followed by a review of fish-specific explantation approaches, including presurgical husbandry, aseptic dissection technique, choice of media and additives, incubation conditions, viability assays, and imaging studies. Relevant articles since 1970 are organized in a table grouped by organ system. From these, I highlight several recent studies using explant culture to study physiological and embryological processes in teleosts, including circadian rhythms, hormonal regulation, and cardiac development.

Multielectrode Arrays.

Multielectrode arrays (MEAs) are grids of substrate-integrated microelectrodes that allow for electrophysiological interrogation of dissociated cell cultures or tissue slices. Here we discuss the use of nonimplantable electrodes for studies. The methods described attempt to provide a starting point for researchers new to the field who wish to begin to utilize this powerful, but daunting technology and quickly apply the basic principles to their own research interests.

Ex vivo model of herpes simplex virus type I dendritic and geographic keratitis using a corneal active storage machine.

BACKGROUND: Herpetic keratitis (HK) models using whole human corneas are essential for studying virus-host relationships, because of high species specificity and the role of interactions between corneal cell populations that cell culture cannot reproduce. Nevertheless, the two current corneal storage methods (hypothermia and organ culture (OC)) do not preserve corneas in good physiological condition, as they are characterized by epithelial abrasion, stromal oedema, and excessive endothelial mortality. METHODS: To rehabilitate human corneas intended for scientific use, we used an active storage machine (ASM) that restores two physiological parameters that are essential for corneal homeostasis: intraocular pressure and storage medium renewal (21mmHg and 2.6 µL/min, respectively). ASM storage regenerates a normal multilayer epithelium in 2 weeks. We infected six pairs of corneas unsuitable for graft by inoculating the epithelium with herpes simplex virus type 1 (HSV-1), and compared each ASM-stored cornea with the other cornea stored in the same medium using the conventional OC method. RESULTS: Only corneas in the ASM developed a dendritic (n = 3) or geographic (n = 2) epithelial ulcer reproducing typical HSV-1-induced clinical lesions. Corneas in OC showed only extensive desquamations. None of the uninfected controls showed epithelial damage. Histology, immunohistochemistry, transmission electron microscopy and polymerase chain reaction on corneal tissue confirmed infection in all cases (excluding negative controls). CONCLUSIONS: The ASM provides an innovative ex vivo model of HK in whole human cornea that reproduces typical epithelial lesions.

Human Organs-on-Chips for Virology.

While conventional in vitro culture systems and animal models have been used to study the pathogenesis of viral infections and to facilitate development of vaccines and therapeutics for viral diseases, models that can accurately recapitulate human responses to infection are still lacking. Human organ-on-a-chip (Organ Chip) microfluidic culture devices that recapitulate tissue-tissue interfaces, fluid flows, mechanical cues, and organ-level physiology have been developed to narrow the gap between in vitro experimental models and human pathophysiology. Here, we describe how recent developments in Organ Chips have enabled re-creation of complex pathophysiological features of human viral infections in vitro.

Preparation of Organotypic Hippocampal Slice Cultures for the Study of CNS Disease and Damage.

Organotypic hippocampal slice cultures (OHSCs) retain in vivo-like neuronal architecture, synaptic connections, and resident cell populations but gain in vitro advantages of accessibility to experimental manipulation and observation. This chapter describes how to prepare OHSCs from neonatal mice to study mechanisms of neuronal damage, including synapse loss and quantifying Aß-containing axonal swellings from Alzheimer's disease transgenic mice.

Organotypic Culture Assay for Neuromuscular Synaptic Degeneration and Function.

We describe here an organotypic culture system we have used to investigate mechanisms that maintain structure and function of axon terminals at the neuromuscular junction (NMJ). We developed this by taking advantage of the slow Wallerian degeneration phenotype in mutant Wlds mice, using these to compare preservation of NMJs with degeneration in nerve-muscle preparations from wild-type mice. We take hind limb tibial nerve/flexor digitorum brevis and lumbrical muscles and incubate them in mammalian physiological saline at 32 °C for 24-48 h. Integrity of NMJs can then be compared using a combination of electrophysiological and morphological techniques. We illustrate our method with data showing synaptic preservation ex vivo in nerve-muscle explants from Sarm-1 null-mutant mice. The ex vivo assays of NMJ integrity we describe here may therefore be useful for detailed investigation of synaptic maintenance and degeneration.

Axon Degeneration Assays in Superior Cervical Ganglion Explant Cultures.

The ability of peripheral nervous system neurons to extend long, axon-like neurites in vitro makes them ideally suited for studies on mechanisms of axon survival and degeneration. In this chapter, we describe how to prepare explant cultures of sympathetic neurons of the superior cervical ganglion (SCG). We also describe how to induce and assess axon degeneration with an injury or a chemical insult.

Biomaterials and biosensors in intestinal organoid culture, a progress review.

As an emerging technology, intestinal organoids are promising new tools for basic and translational research in gastroenterology. Currently, culture of intestinal organoids relies mostly on a type of tumor-derived scaffolds, namely Matrigel, which may pose tumorigenic risks to organoid implantation. Apart from the traditional detection methods, such as tissue slicing and fluorescence staining, the monitoring of intestinal organoids requires real-time biosensors that can adapt to their three-dimensional dynamic growth patterns. In this review, we summarized the recent advances in developing definite hydrogel scaffolds for intestinal organoid culture and identified key parameters for scaffold design. In addition, classified by different substrate compositions like pH, electrolytes, and functional proteins, we concluded the existing live-imaging biosensors and elucidated their underlying mechanisms. We hope this review enhances the understanding of intestinal organoid culture and provides more practical approaches to investigate them.

Microfluidics in male reproduction: is ex vivo culture of primate testis tissue a future strategy for ART or toxicology research?

The significant rise in male infertility disorders over the years has led to extensive research efforts to recapitulate the process of male gametogenesis in vitro and to identify essential mechanisms involved in spermatogenesis, notably for clinical applications. A promising technology to bridge this research gap is organ-on-chip (OoC) technology, which has gradually transformed the research landscape in ART and offers new opportunities to develop advanced in vitro culture systems. With exquisite control on a cell or tissue microenvironment, customized organ-specific structures can be fabricated in in vitro OoC platforms, which can also simulate the effect of in vivo vascularization. Dynamic cultures using microfluidic devices enable us to create stimulatory effect and non-stimulatory culture conditions. Noteworthy is that recent studies demonstrated the potential of continuous perfusion in OoC systems using ex vivo mouse testis tissues. Here we review the existing literature and potential applications of such OoC systems for male reproduction in combination with novel bio-engineering and analytical tools. We first introduce OoC technology and highlight the opportunities offered in reproductive biology in general. In the subsequent section, we discuss the complex structural and functional organization of the testis and the role of the vasculature-associated testicular niche and fluid dynamics in modulating testis function. Next, we review significant technological breakthroughs in achieving in vitro spermatogenesis in various species and discuss the evidence from microfluidics-based testes culture studies in mouse. Lastly, we discuss a roadmap for the potential applications of the proposed testis-on-chip culture system in the field of primate male infertility, ART and reproductive toxicology.

A one-stop microfluidic-based lung cancer organoid culture platform for testing drug sensitivity.

Microfluidic devices as translational research tools provide a potential alternative to animal experiments due to their ability to mimic physiological parameters. Several approaches that can be used to predict the efficacy or toxicity of anticancer drugs are available. In general, standard cell culture systems have the advantages of being relatively cost-effective, having high-throughput capability, and providing convenience. However, these models are inadequate to accurately recapitulate the complex organ-level physiological and pharmacological responses. Here, we present a one-stop microfluidic device enabling both 3-dimensional (3D) lung cancer organoid culturing and drug sensitivity tests directly on a microphysiological system (MPS). Our platform reproducibly yields 3D lung cancer organoids in a size-controllable manner and demonstrates for the first time the production of lung cancer organoids from patients with small-cell lung cancer. Lung cancer organoids derived from primary small-cell lung cancer tumors can rapidly proliferate and exhibit disease-specific characteristics in our MPS. Cisplatin and etoposide, the standard regimen for lung cancer, showed increased apoptosis induction in a concentration-dependent manner, but the organoids contained chemo-resistant cells in the core. We envision that this system may provide important information to guide therapeutic approaches at the preclinical level.

Vascular Myography to Examine Functional Responses of Isolated Blood Vessels.

Vascular myography is an in vitro technique used to examine functional responses of isolated blood vessels. This classical pharmacological technique has been in use for over a century. The assay technique studies changes in isometric tone of large and small vessels, arteries and veins, and tissues from genetic or disease models. This chapter describes the apparatus required, tissue collection methods, and the mounting of the tissues in the chambers of both large organ baths and the small vessel myograph. Considerations of the experimental conditions and design are discussed as well as the analysis of the collected data.

Human organotypic lymphatic vessel model elucidates microenvironment-dependent signaling and barrier function.

The lymphatic system is an active player in the pathogenesis of several human diseases, including lymphedema and cancer. Relevant models are needed to advance our understanding of lymphatic biology in disease progression to improve therapy and patient outcomes. Currently, there are few 3D in vitro lymphatic models that can recapitulate the physiological structure, function, and interactions of lymphatic vessels in normal and diseased microenvironments. Here, we developed a 3D microscale lymphatic vessel (µLYMPH) system for generating human lymphatic vessels with physiological tubular structure and function. Consistent with characteristics of lymphatic vessels in vivo, the endothelium of cultured vessels was leaky with an average permeability of 1.38 × 10-5 ± 0.29 × 10-5 cm/s as compared to 0.68 × 10-5 ± 0.13 × 10-5 cm/s for blood vessels. This leakiness also resulted in higher uptake of solute by the lymphatic vessels under interstitial flow, demonstrating recapitulation of their natural draining function. The vessels secreted appropriate growth factors and inflammatory mediators. Our system identified the follistatin/activin axis as a novel pathway in lymphatic vessel maintenance and inflammation. Moreover, the µLYMPH system provided a platform for examining crosstalk between lymphatic vessels and tumor microenvironmental components, such as breast cancer-associated fibroblasts (CAFs). In co-culture with CAFs, vessel barrier function was significantly impaired by CAF-secreted IL-6, a possible pro-metastatic mechanism of lymphatic metastasis. Targeted blocking of the IL-6/IL-6R signaling pathway with an IL-6 neutralizing antibody fully rescued the vessels, demonstrating the potential of our system for screening therapeutic targets. These results collectively demonstrate the µLYMPH system as a powerful model for advancing lymphatic biology in health and disease.

Application of microscale culture technologies for studying lymphatic vessel biology.

Immense progress in microscale engineering technologies has significantly expanded the capabilities of in vitro cell culture systems for reconstituting physiological microenvironments that are mediated by biomolecular gradients, fluid transport, and mechanical forces. Here, we examine the innovative approaches based on microfabricated vessels for studying lymphatic biology. To help understand the necessary design requirements for microfluidic models, we first summarize lymphatic vessel structure and function. Next, we provide an overview of the molecular and biomechanical mediators of lymphatic vessel function. Then we discuss the past achievements and new opportunities for microfluidic culture models to a broad range of applications pertaining to lymphatic vessel physiology. We emphasize the unique attributes of microfluidic systems that enable the recapitulation of multiple physicochemical cues in vitro for studying lymphatic pathophysiology. Current challenges and future outlooks of microscale technology for studying lymphatics are also discussed. Collectively, we make the assertion that further progress in the development of microscale models will continue to enrich our mechanistic understanding of lymphatic biology and physiology to help realize the promise of the lymphatic vasculature as a therapeutic target for a broad spectrum of diseases.

Using Cell and Organ Culture Models to Analyze Responses of Bone Cells to Mechanical Stimulation.

The techniques that are useful for applying mechanical strain to bone and bone cells are now more diverse than described in the second Edition. Their output has also increased substantially and, perhaps most importantly, their significance is now broadly accepted. This growth in the use of methods for applying mechanical strain to bone and its constituent cells and increased awareness of the importance of the mechanical environment in controlling normal bone cell behavior has indeed heralded new therapeutic approaches. We have expanded the text to include additions and modifications made to the straining apparatus and updated the research cited to support this growing role of cell cultures, including co-culture systems and primary cells, tissue engineering, and organ culture models to analyze responses of bone cells to mechanical stimulation. We understand that there are approaches not covered here and appreciate that alternative strategies have their own value and utility.

The Ex Vivo Organ Culture of Bone.

The ex vivo organ culture of bone provides many of the advantages of both the whole organism and isolated cell strategies and can deliver valuable insight into the network of processes and activities that are fundamental to bone and cartilage biology. Through maintaining the bone and/or cartilage cells in their native environment, this model system provides the investigator with a powerful experimental protocol to address specific facets of skeletal growth and development. In this chapter, we outline the basic protocols and possible readouts of organ culture models to replicate; (a) linear bone growth (murine metatarsal culture model), (b) bone and cartilage metabolism (murine femoral head culture model), (c) bone response to mechanical stimulation (bovine trabecular core culture model), and (d) bone resorption and formation (murine calvaria culture model).

Ex-Vivo Model Systems of Cancer-Bone Cell Interactions.

This chapter elaborates on the state-of-the-art experimental procedures utilized in ex-vivo model systems of cancer-bone cell interactions under "static and dynamic" culture conditions and their potential use to understand cellular and molecular mechanisms as well as drug testing and discovery. An additional focus of this chapter is to provide details of how to incorporate varying oxygen tension, viz., hypoxic, normoxic, and hyperoxic, in such studies and regulate the bone biology toward dissociation of the bone remodeling stages to achieve only "bone resorption" or "bone formation" individually.

Live Cell Imaging of Bone Cell and Organ Cultures.

Over the past two decades there have been unprecedented advances in the capabilities for live cell imaging using light and confocal microscopy. Together with the discovery of green fluorescent protein and its derivatives and the development of a vast array of fluorescent imaging probes and conjugates, it is now possible to image virtually any intracellular or extracellular protein or structure. Traditional static imaging of fixed bone cells and tissues takes a snapshot view of events at a specific time point, but can often miss the dynamic aspects of the events being investigated. This chapter provides an overview of the application of live cell imaging approaches for the study of bone cells and bone organ cultures. Rather than emphasizing technical aspects of the imaging equipment, which may vary in different laboratories, we focus on what we consider to be the important principles that are of most practical use for an investigator setting up these techniques in their own laboratory. We also provide detailed protocols that our laboratory has used for live imaging of bone cell and organ cultures.

3D culture models for studying branching morphogenesis in the mammary gland and mammalian lung.

The intricate architecture of branched tissues and organs has fascinated scientists and engineers for centuries. Yet-despite their ubiquity-the biophysical and biochemical mechanisms by which tissues and organs undergo branching morphogenesis remain unclear. With the advent of three-dimensional (3D) culture models, an increasingly powerful and diverse set of tools are available for investigating the development and remodeling of branched tissues and organs. In this review, we discuss the application of 3D culture models for studying branching morphogenesis of the mammary gland and the mammalian lung in the context of normal development and disease. While current 3D culture models lack the cellular and molecular complexity observed in vivo, we emphasize how these models can be used to answer targeted questions about branching morphogenesis. We highlight the specific advantages and limitations of using 3D culture models to study the dynamics and mechanisms of branching in the mammary gland and mammalian lung. Finally, we discuss potential directions for future research and propose strategies for engineering the next generation of 3D culture models for studying tissue morphogenesis.