Pluripotent Stem Cell-derived Organoids Research Articles

Stretchable mesh microelectronics for the biointegration and stimulation of human neural organoids

Advances in tridimensional (3D) culture approaches have led to the generation of organoids that recapitulate cellular and physiological features of domains of the human nervous system. Although microelectrodes have been developed for long-term electrophysiological interfaces with neural tissue, studies of long-term interfaces between microelectrodes and free-floating organoids remain limited. In this study, we report a stretchable, soft mesh electrode system that establishes an intimate in vitro electrical interface with human neurons in 3D organoids. Our mesh is constructed with poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) based electrically conductive hydrogel electrode arrays and elastomeric poly(styrene-ethylene-butylene-styrene) (SEBS) as the substrate and encapsulation materials. This mesh electrode can maintain a stable electrochemical impedance in buffer solution under 50% compressive and 50% tensile strain. We have successfully cultured pluripotent stem cell-derived human cortical organoids (hCO) on this polymeric mesh for more than 3 months and demonstrated that organoids readily integrate with the mesh. Using simultaneous stimulation and calcium imaging, we show that electrical stimulation through the mesh can elicit intensity-dependent calcium signals comparable to stimulation from a bipolar stereotrode. This platform may serve as a tool for monitoring and modulating the electrical activity of in vitro models of neuropsychiatric diseases.

Generation of human-induced pluripotent stem cell-derived adherent 3-dimensional skin hair-follicle organoids

Regenerating hair follicles (HFs) is a critical medical need for patients who suffer from serious hair loss. To generate equivalent hair-bearing skin systems that could mimic the complexity of native tissues with pluripotent stem cells, floating culture has been employed as a standard method; however, it is still necessary to improve limitations such as the heterogeneity of organoids and the difficulty of handling them, which increases during long-term culture. Here, we devise a floating-adherent combinatory culture system to establish skin HF organoids from human-induced pluripotent stem cells (hiPSCs). Specifically, embryoid bodies were generated in a free-floating environment, followed by the induction process, which occurred in adherent conditions. With our approach, hair germ-like buds were shown to protrude and extend faster. After 100 days of culture, mature cystic skin organoids stratified to form the epidermis, dermis, and outer root sheath, as evident from quantitative polymerase chain reaction and immunohistochemistry analysis. Dermal condensate cells (Sox2+, PDGFRα+, P75+), which are the precursors of HFs, were detected together with HF stem cells (NFATC1+, LGR5+), putative bulge stem cells (LHX2+, KRT15+) and melanocytes (PMEL+). Notably, our constructed HFs could recapitulate the sensory function of native tissues, as illustrated by the formation of a network of sensory neurons and Schwann cells connecting towards HF cells and epidermal progenitors. In summary, our results demonstrate a new protocol for the simplified and efficient induction of skin HFs from hiPSCs, thereby contributing to research on optimizing HF growth and investigating novel therapeutic strategies to treat alopecia.

Limosilactobacillus reuteri DS0384 promotes intestinal epithelial maturation via the postbiotic effect in human intestinal organoids and infant mice

ABSTRACT Little is known about the modulatory capacity of the microbiota in early intestinal development. We examined various intestinal models that respond to gut microbial metabolites based on human pluripotent stem cell-derived human intestinal organoids (hIOs): physiologically relevant in vitro fetal-like intestine, intestinal stem cell, and intestinal disease models. We found that a newly isolated Limosilactobacillus reuteri strain DS0384 accelerated maturation of the fetal intestine using 3D hIO with immature fetal characteristics. Comparative metabolomic profiling analysis revealed that the secreted metabolite N-carbamyl glutamic acid (NCG) is involved in the beneficial effect of DS0384 cell-free supernatants on the intestinal maturation of hIOs. Experiments in an intestinal stem cell spheroid model and hIO-based intestinal inflamed model revealed that the cell-free supernatant from DS0384 comprising NCG promoted intestinal stem cell proliferation and was important for intestinal protection against cytokine-induced intestinal epithelial injury. The probiotic properties of DS0384 were also evaluated, including acid and bile tolerance and ability to adhere to human intestinal cells. Seven-day oral administration of DS0384 and cell-free supernatant promoted the intestinal development of newborn mice. Moreover, NCG exerted a protective effect on experimental colitis in mice. These results suggest that DS0384 is a useful agent for probiotic applications and therapeutic treatment for disorders of early gut development and for preventing intestinal barrier dysfunction.

SARS-CoV-2 infection of human pluripotent stem cell-derived liver organoids reveals potential mechanisms of liver pathology

Although respiratory symptoms are the most prevalent disease manifestation of infection by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), infection can also damage other organs, including the brain, gut, and liver. Symptoms of liver damage are observed in nearly half of patients that succumb to severe SARS-CoV-2 infection. Here we use human-induced pluripotent stem cell-derived liver organoids (HLOs) to recapitulate and characterize liver pathology following virus exposure. Utilizing single-cell sequencing technology, we identified robust transcriptomic changes that occur in SARS-CoV-2 infected liver cells as well as uninfected bystander cells. Our results show a significant induction of many inflammatory pathways, including IFN-α, INF-γ, and IL-6 signaling. Our results further identify IL-6 signaling as a potential mechanism for liver-mediated activation of circulating macrophages.

Induced pluripotent stem cell-derived brain organoids as potential human model system for chemotherapy induced CNS toxicity.

Neurotoxic phenomena are among the most common side effects of cytotoxic agents. The development of chemotherapy-induced polyneuropathy (CIPN) is a well-recognized adverse reaction in the peripheral nervous system, while changes of cognitive functions (post-chemotherapy cognitive impairment (PCCI)) are more diffuse and have only recently drawn scientific interest. PCCI in patients most often displays as short-term memory loss, reduced multitasking ability or deficits in language. Not least, due to a lack of preclinical human model systems, the underlying molecular mechanisms are poorly understood, and treatments are missing. We thus investigated whether induced pluripotent stem cell (iPSC)-derived brain organoids can serve as a human model system for the study of chemotherapy induced central nervous system toxicity. We robustly generated mature brain organoids from iPSC-derived neuronal precursor cells (NPC), which showed a typical composition with 1) dividing NPCs forming ventricle like structures 2) matured neurons and 3) supporting glial cells closer to the surface. Furthermore, upon stimulation the brain organoids showed functional signaling. When exposed to increasing concentrations of paclitaxel, a frequently used chemotherapy drug, we observed time dependent neurotoxicity with an EC50 of 153 nM, comparable to a published murine model system. Histological analysis after paclitaxel exposure demonstrated dose dependent apoptosis induction and reduced proliferation in the organoids with further Western blot analyses indicating the degradation of neuronal calcium sensor one protein (NCS-1) and activation of Caspase-3. We could also provide evidence that paclitaxel treatment negatively affects the pool of neuronal and astrocyte precursor cells as well as mature neurons. In summary our data suggests that human iPSC derived brain organoids are a promising preclinical model system to investigate molecular mechanisms underlying PCCI and to develop novel prevention and treatment strategies.

Modeling braf-induced thyroid cancer development and cell redifferentiation using pluripotent stem cell-derived organoids

Searchable abstracts of presentations at key conferences in endocrinology ISSN 1470-3947 (print) | ISSN 1479-6848 (online)

LP-36 Generation of Human pluripotent stem cell-derived hepatic organoids for drug metabolism and toxicity prediction

LP-36 Generation of Human pluripotent stem cell-derived hepatic organoids for drug metabolism and toxicity prediction

Technical advances in pluripotent stem cell-derived and tumorigenic organoids

Cell culture systems have been widely used to address fundamental questions in biology without sacrificing animals. Three-dimensional (3D) organoids provide more information on in vivo conditions than traditional culture systems because multiple cell types in organoids interact with each other in 3D structures. Despite extensive research and advances in the organoid field, some important limitations remain and need further consideration. In this review, we summarize how organoids are generated from pluripotent stem cells and describe the recent technical progress that has made organoids more similar to in vivo tissues for the application of organoids to modeling cancer. Lastly, we briefly discuss some limitations that have been raised in this field.

High-throughput bioengineering of homogenous and functional human-induced pluripotent stem cells-derived liver organoids via micropatterning technique.

Human pluripotent stem cell-derived liver organoids are emerging as more human-relevant in vitro models for studying liver diseases and hepatotoxicity than traditional hepatocyte cultures and animal models. The generation of liver organoids is based on the Matrigel dome method. However, the organoids constructed by this method display significant heterogeneity in their morphology, size, and maturity. Additionally, the formed organoid is randomly encapsulated in the Matrigel dome, which is not convenient for in situ staining and imaging. Here, we demonstrate an approach to generate a novel type of liver organoids via micropatterning technique. This approach enables the reproducible and high-throughput formation of bioengineered fetal liver organoids with uniform morphology and deterministic size and location in a multiwell plate. The liver organoids constructed by this technique closely recapitulate some critical features of human liver development at the fetal stage, including fetal liver-specific gene and protein expression, glycogen storage, lipid accumulation, and protein secretion. Additionally, the organoids allow whole-mount in-situ staining and imaging. Overall, this new type of liver organoids is compatible with the pharmaceutical industry’s widely-used preclinical drug discovery tools and will facilitate liver drug screening and hepatotoxic assessment.

Lung Organoids—The Ultimate Tool to Dissect Pulmonary Diseases?

Organoids are complex multicellular three-dimensional (3D) in vitro models that are designed to allow accurate studies of the molecular processes and pathologies of human organs. Organoids can be derived from a variety of cell types, such as human primary progenitor cells, pluripotent stem cells, or tumor-derived cells and can be co-cultured with immune or microbial cells to further mimic the tissue niche. Here, we focus on the development of 3D lung organoids and their use as disease models and drug screening tools. We introduce the various experimental approaches used to model complex human diseases and analyze their advantages and disadvantages. We also discuss validation of the organoids and their physiological relevance to the study of lung diseases. Furthermore, we summarize the current use of lung organoids as models of host-pathogen interactions and human lung diseases such as cystic fibrosis, chronic obstructive pulmonary disease, or SARS-CoV-2 infection. Moreover, we discuss the use of lung organoids derived from tumor cells as lung cancer models and their application in personalized cancer medicine research. Finally, we outline the future of research in the field of human induced pluripotent stem cell-derived organoids.

A Survey of the Metabolic Landscape of the Developing Cerebellum at Single-Cell Resolution

The use of cell-culture models to investigate development and disease of the cerebellum is a recent advance, facilitated by the discovery that patterning of precursors is capable of giving rise to cells with specific neuronal identity. Pluripotent stem cell-derived organoids, which exhibit self-organisational characteristics reminiscent of early cerebellar tissue, present a number of challenges including recapitulation of conditions resembling the mature brain. An understanding of the processes driving fetal and postnatal maturation is required to reproduce these conditions in vitro and advance the capability of the system to model adult-onset disease. A key tool for achieving this is single-cell RNA sequencing, which enables visualisation of key transcriptional features of subpopulations comprising tissues. Here, we explore and compare available single-cell RNA sequencing data derived from the developing human cerebellum and its synthetic, in vitro counterpart (stem cell-derived cerebellar organoids). We focus on performing a qualitative assessment of the expression of key metabolic pathway genes, given recent findings exemplifying tissue-specific metabolic activity, including hypoxia and metabolic shifts associated with neuronal expansion. Signatures indicative of known cell type-specific metabolic differences, such as the astrocyte-neuron lactate shuttle and glutamate-glutamine cycle were evident at a transcriptional level. Cerebellar tissue and cerebellar organoids showed a number of behavioural similarities, including HIF1 signalling, which may serve to drive expansion of granule cell progenitors in both settings. We further highlight numerous differences between cultured organoids and native tissue which may provide clarity on the state of metabolic state following differentiation of organoids, providing the future framework to test and further hypotheses regarding promoting maturation. Overall, this analysis provides insight into understanding the state of in vitro models of the cerebellum, a critical factor required for modelling susceptibility of various cell types to cerebellar disease.

Diabetes and SARS-CoV-2-Is There a Mutual Connection?

SARS-CoV-2, a newly emerged virus described for the first time in late 2019, affects multiple organs in humans, including the pancreas. Here, we present the bilateral link between the pathophysiology of diabetes and COVID-19, with diabetes being COVID-19 comorbidity, and a complication of SARS-CoV-2 infection. Analysis of clinical data indicates that patients with chronic conditions like diabetes are at increased risk of severe COVID-19, hospitalization, ICU admission, and death compared to the healthy subjects. Further, we show that SARS-CoV-2 infection might be also associated with the development of new-onset diabetes and diabetic ketoacidosis. We then discuss the options for studying SARS-CoV-2 infection in pancreatic settings, including the use of human pluripotent stem cell-derived pancreatic organoids. Further, we review the presence of SARS-CoV-2 receptors in different pancreatic cell types and the infection efficiency based on pancreatic sections from COVID-19 patients and primary human islet in vitro studies. Finally, we discuss the impact of SARS-CoV-2 infection on human pancreatic cell homeostasis, focusing on β-cells.

Modeling the Effects of Maternal Diabetes on the Developing Human Heart Using Pluripotent Stem Cell-Derived Heart Organoids.

Congenital heart defects (CHD) constitute the most common type of birth defect in humans. Maternal diabetes during the first trimester of pregnancy (pregestational diabetes, or PGD) is one of the most prominent factors contributing to CHD, and is present in a significant population of female patients with diabetes in reproductive age. PGD is challenging to manage clinically due to the extreme sensitivity of the developing embryo to glucose oscillations, and constitutes a critical health problem for the mother and the fetus. The prevalence of PGD‐induced CHD is increasing due to the ongoing diabetes epidemic. While studies using animal models and cells in culture have demonstrated that PGD alters critical cellular and developmental processes, the mechanisms remain obscure, and it is unclear to what extent these models recapitulate PGD‐induced CHD in humans. Clinical practice precludes direct studies in developing human embryos, further highlighting the need for physiologically relevant models. To bypass many of these technical and ethical limitations, we describe here a human pluripotent stem cell (hPSC)–based method to generate developmentally relevant self‐organizing human heart organoids. By using glucose and insulin to mimic the diabetic environment that the embryo faces in PGD, this system allows modeling critical features of PGD in a human system with relevant physiology, structure, and cell types. The protocol starts with the generation of hPSC‐derived embryoid bodies in a 96‐well plate, followed by a small molecule–based three‐step Wnt activation/inhibition/activation strategy. Organoids are then differentiated under healthy (normal insulin and glucose) and diabetic conditions (high insulin and glucose) over time, allowing for the study of the effects of pregestational diabetes on the developing human heart. We also provide an immunofluorescence protocol for comparing, characterizing, and analyzing the differences between the healthy and diabetic organoids, and comment on additional steps for preparing the organoids for analysis by other techniques after differentiation. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Generation of hPSC‐derived embryoid bodies Basic Protocol 2: Differentiation of EBs into heart organoids under healthy and diabetes‐like conditions Basic Protocol 3: Immunofluorescence and organoid preparation for other assays

Bioelectric Potential in Next-Generation Organoids: Electrical Stimulation to Enhance 3D Structures of the Central Nervous System.

Pluripotent stem cell-derived organoid models of the central nervous system represent one of the most exciting areas in in vitro tissue engineering. Classically, organoids of the brain, retina and spinal cord have been generated via recapitulation of in vivo developmental cues, including biochemical and biomechanical. However, a lesser studied cue, bioelectricity, has been shown to regulate central nervous system development and function. In particular, electrical stimulation of neural cells has generated some important phenotypes relating to development and differentiation. Emerging techniques in bioengineering and biomaterials utilise electrical stimulation using conductive polymers. However, state-of-the-art pluripotent stem cell technology has not yet merged with this exciting area of bioelectricity. Here, we discuss recent findings in the field of bioelectricity relating to the central nervous system, possible mechanisms, and how electrical stimulation may be utilised as a novel technique to engineer “next-generation” organoids.

Development of human pluripotent stem cell-derived hepatic organoids as an alternative model for drug safety assessment

Human in vitro hepatic models that faithfully recapitulate liver function are essential for successful basic and translational research. A limitation of current in vitro models, which are extensively used for drug discovery and toxicity testing, is the loss of drug metabolic function due to the low expression and activity of cytochrome P450 (CYP450) enzymes. Here, we aimed to generate human pluripotent stem cell-derived hepatic organoids (hHOs) with a high drug metabolic ability. We established a two-step protocol to produce hHOs from human pluripotent stem cells for long-term expansion and drug testing. Fully differentiated hHOs had multicellular composition and exhibited cellular polarity and hepatobiliary structures. They also displayed remarkable CYP450 activity and recapitulated the metabolic clearance, CYP450-mediated drug toxicity, and metabolism. Furthermore, hHOs successfully modeled Wilson's disease in terms of Cu metabolism, drug responses, and diagnostic marker expression and secretion. In conclusion, hHOs exhibit high capacity for drug testing and disease modeling. Hence, this hepatic model system provides an advanced tool for studying hepatic drug metabolism and diseases.

Human organoid models to study SARS-CoV-2 infection.

Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is one of the deadliest pandemics in history. SARS-CoV-2 not only infects the respiratory tract, but also causes damage to many organs. Organoids, which can self-renew and recapitulate the various physiology of different organs, serve as powerful platforms to model COVID-19. In this Perspective, we overview the current effort to apply both human pluripotent stem cell-derived organoids and adult organoids to study SARS-CoV-2 tropism, host response and immune cell-mediated host damage, and perform drug discovery and vaccine development. We summarize the technologies used in organoid-based COVID-19 research, discuss the remaining challenges and provide future perspectives in the application of organoid models to study SARS-CoV-2 and future emerging viruses.

State-matched organoid models to fight pancreatic cancer

As one of the deadliest cancers, pancreatic ductal adenocarcinoma (PDAC) requires sophisticated model systems to dissect disease onset, progression, and therapy resistance, as well as to personalize therapy. In recent years, patient- and pluripotent stem cell-derived organoids have become state-of-the-art systems to refine existing therapeutic strategies and deepen our knowledge of disease pathophysiology.

Culture of pluripotent stem cell-derived hepatocytes and organoids

Liver is one of the most important organs in the human body. Liver diseases are also a major threat to human health and longevity. Hepatic decompensation treatment is quite difficult due to multiple reasons. Extracorporeal liver support devices are unable to solve this problem, and there is a severe shortage of orthotopic liver transplant donors. Study of pluripotent stem cell-derived hepatocytes and organoids can determine not only hepatocyte fate, but also liver development, regeneration mechanisms, and pathophysiology. Furthermore, it can be used for drug screening in order to provide a stable source of functional hepatocytes for future transplantation therapy. Culture of pluripotent stem cell-derived hepatocytes and organoids has a self-organizing process similar to liver development, i.e., starting with changes in several key factors, and eventually forming functionally complex cells/organs. This paper introduces the main methods and progress of pluripotent stem cell-derived hepatocytes and organoids, with hope to provide clues for future research.

Epithelial-derived factors induce muscularis mucosa of human induced pluripotent stem cell-derived gastric organoids.

SummaryHuman gastric development has not been well studied. The generation of human pluripotent stem cell-derived gastric organoids (hGOs) comprising gastric marker-expressing epithelium without an apparent smooth muscle (SM) structure has been reported. We modified previously reported protocols to generate hGOs with muscularis mucosa (MM) from hiPSCs. Time course analyses revealed that epithelium development occurred prior to MM formation. Sonic hedgehog (SHH) and TGF-β1 were secreted by the epithelium. HH and TGF-β signal inhibition prevented subepithelial MM formation. A mechanical property of the substrate promoted SM differentiation around hGOs in the presence of TGF-β. TGF-β signaling was shown to influence the HH signaling and mechanical properties. In addition, clinical specimen findings suggested the involvement of TGF-β signaling in MM formation in recovering gastric ulcers. HH and TGF-β signaling from the epithelium to the stroma and the mechanical properties of the subepithelial environment may influence the emergence of MM in human stomach tissue.

DevKidCC allows for robust classification and direct comparisons of kidney organoid datasets

BackgroundWhile single-cell transcriptional profiling has greatly increased our capacity to interrogate biology, accurate cell classification within and between datasets is a key challenge. This is particularly so in pluripotent stem cell-derived organoids which represent a model of a developmental system. Here, clustering algorithms and selected marker genes can fail to accurately classify cellular identity while variation in analyses makes it difficult to meaningfully compare datasets. Kidney organoids provide a valuable resource to understand kidney development and disease. However, direct comparison of relative cellular composition between protocols has proved challenging. Hence, an unbiased approach for classifying cell identity is required.MethodsThe R package, scPred, was trained on multiple single cell RNA-seq datasets of human fetal kidney. A hierarchical model classified cellular subtypes into nephron, stroma and ureteric epithelial elements. This model, provided in the R package DevKidCC (github.com/KidneyRegeneration/DevKidCC), was then used to predict relative cell identity within published kidney organoid datasets generated using distinct cell lines and differentiation protocols, interrogating the impact of such variations. The package contains custom functions for the display of differential gene expression within cellular subtypes.ResultsDevKidCC was used to directly compare between distinct kidney organoid protocols, identifying differences in relative proportions of cell types at all hierarchical levels of the model and highlighting variations in stromal and unassigned cell types, nephron progenitor prevalence and relative maturation of individual epithelial segments. Of note, DevKidCC was able to distinguish distal nephron from ureteric epithelium, cell types with overlapping profiles that have previously confounded analyses. When applied to a variation in protocol via the addition of retinoic acid, DevKidCC identified a consequential depletion of nephron progenitors.ConclusionsThe application of DevKidCC to kidney organoids reproducibly classifies component cellular identity within distinct single-cell datasets. The application of the tool is summarised in an interactive Shiny application, as are examples of the utility of in-built functions for data presentation. This tool will enable the consistent and rapid comparison of kidney organoid protocols, driving improvements in patterning to kidney endpoints and validating new approaches.