Culture Of Human Pluripotent Stem Cells Research Articles

CD32 captures committed haemogenic endothelial cells during human embryonic development

During embryonic development, blood cells emerge from specialized endothelial cells, named haemogenic endothelial cells (HECs). As HECs are rare and only transiently found in early developing embryos, it remains difficult to distinguish them from endothelial cells. Here we performed transcriptomic analysis of 28- to 32-day human embryos and observed that the expression of Fc receptor CD32 (FCGR2B) is highly enriched in the endothelial cell population that contains HECs. Functional analyses using human embryonic and human pluripotent stem cell-derived endothelial cells revealed that robust multilineage haematopoietic potential is harboured within CD32+ endothelial cells and showed that 90% of CD32+ endothelial cells are bona fide HECs. Remarkably, these analyses indicated that HECs progress through different states, culminating in FCGR2B expression, at which point cells are irreversibly committed to a haematopoietic fate. These findings provide a precise method for isolating HECs from human embryos and human pluripotent stem cell cultures, thus allowing the efficient generation of haematopoietic cells in vitro.

Prediction of Acute Hepatotoxicity With Human Pluripotent Stem Cell-Derived Hepatic Organoids.

Recent development of hepatic organoids (HOs) derived from human pluripotent stem cells (hPSCs) provides an alternative in vitro model that can mimic the human liver detoxification pathway for drug safety assessment. By recapitulating the high level of maturity and drug-metabolizing capacity of the liver in a three-dimensional organoid culture, HOs may allow researchers to assess drug toxicity and metabolism more accurately than animal models or hepatocellular carcinoma cells. Although this promising potential has contributed to the development of various protocols, only a few protocols are available to generate functional HOs with guaranteed CYP450 enzymatic activity, the key feature driving toxic responses during drug metabolism. Based on previously published protocols, we describe an optimized culture method that can substantially increase the expression and activity of CYP450s, in particular CYP3A4, CYP2C9, and CYP2C19, in HOs. To generate mass-produced and highly reproducible HOs required as models for toxicity evaluation, we first generated hepatic endodermal organoids (HEOs) from hPSCs capable of in vitro proliferation and cryopreservation. The stepwise protocol includes generating HEOs as well as efficient methods to enhance CYP450 expression and activity in terminally differentiated HOs. Furthermore, we present a simple protocol for the assessment of HO cytotoxicity, one of the hallmarks of drug-induced acute hepatotoxicity. The protocols are relatively straightforward and can be successfully used by laboratories with basic experience in culturing hPSCs. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Generation of hepatic endodermal organoids from human pluripotent stem cells Basic Protocol 2: Expansion and cryopreservation of hepatic endodermal organoids Basic Protocol 3: Differentiation of hepatic organoids from hepatic endodermal organoids Basic Protocol 4: Evaluation of hepatotoxicity using hepatic organoids Support Protocol: Human pluripotent stem cell culture.

SALL3 mediates the loss of neuroectodermal differentiation potential in human embryonic stem cells with chromosome 18q loss

Human pluripotent stem cell (hPSC) cultures are prone to genetic drift, because cells that have acquired specific genetic abnormalities experience a selective advantage invitro. These abnormalities are highly recurrent in hPSC lines worldwide, but their functional consequences in differentiating cells are scarcely described. In this work, we show that the loss of chromosome 18q impairs neuroectoderm commitment and that downregulation of SALL3, a gene located in the common 18q loss region, is responsible for this failed neuroectodermal differentiation. Knockdown of SALL3 in control lines impaired differentiation in a manner similar to the loss of 18q, and transgenic overexpression of SALL3 in hESCs with 18q loss rescued the differentiation capacity of the cells. Finally, we show that loss of 18q and downregulation of SALL3 leads to changes in the expression of genes involved in pathways regulating pluripotency and differentiation, suggesting that these cells are in an altered state of pluripotency.

Derivation of human primordial germ cell-like cells in an embryonic-like culture

Primordial germ cells (PGCs) are the embryonic precursors of sperm and eggs. They transmit genetic and epigenetic information across generations. Given the prominent role of germline defects in diseases such as infertility, detailed understanding of human PGC (hPGC) development has important implications in reproductive medicine and studying human evolution. Yet, hPGC specification remains an elusive process. Here, we report the induction of hPGC-like cells (hPGCLCs) in a bioengineered human pluripotent stem cell (hPSC) culture that mimics peri-implantation human development. In this culture, amniotic ectoderm-like cells (AMLCs), derived from hPSCs, induce hPGCLC specification from hPSCs through paracrine signaling downstream of ISL1. Our data further show functional roles of NODAL, WNT, and BMP signaling in hPGCLC induction. hPGCLCs are successfully derived from eight non-obstructive azoospermia (NOA) participant-derived hPSC lines using this biomimetic platform, demonstrating its promise for screening applications.

Automated human induced pluripotent stem cell culture and sample preparation for 3D live-cell microscopy.

To produce abundant cell culture samples to generate large, standardized image datasets of human induced pluripotent stem (hiPS) cells, we developed an automated workflow on a Hamilton STAR liquid handler system. This was developed specifically for culturing hiPS cell lines expressing fluorescently tagged proteins, which we have used to study the principles by which cells establish and maintain robust dynamic localization of cellular structures. This protocol includes all details for the maintenance, passage and seeding of cells, as well as Matrigel coating of 6-well plastic plates and 96-well optical-grade, glass plates. We also developed an automated image-based hiPS cell colony segmentation and feature extraction pipeline to streamline the process of predicting cell count and selecting wells with consistent morphology for high-resolution three-dimensional (3D) microscopy. The imaging samples produced with this protocol have been used to study the integrated intracellular organization and cell-to-cell variability of hiPS cells to train and develop deep learning-based label-free predictions from transmitted-light microscopy images and to develop deep learning-based generative models of single-cell organization. This protocol requires some experience with robotic equipment. However, we provide details and source code to facilitate implementation by biologists less experienced with robotics. The protocol is completed in less than 10 h with minimal human interaction. Overall, automation of our cell culture procedures increased our imaging samples' standardization, reproducibility, scalability and consistency. It also reduced the need for stringent culturist training and eliminated culturist-to-culturist variability, both of which were previous pain points of our original manual pipeline workflow.

Plate-curving cell culture as a model for assessing curvature-induced cellular responses during neural tube morphogenesis

ABSTRACT Neurulation is an important shape-transforming event during embryonic development where a flat neural plate is converted into a neural tube. Failure in this morphogenetic process accounts for one of the most common birth defects. Mechanical biology has provided key insights into neural tube formation and curvature among many physical properties that are eliciting attention. However, the lack of a proper model to study the effect of curvature has limited the potential to reveal its role in neurulation. In this study, we introduce a novel cell culture method called plate-curving cell culture where a polydimethylsiloxane (PDMS) plate of desired physical properties is curved in either a concave or convex form while the human pluripotent stem cell culture induced to have early neural plate identity is placed on top of its surface. With this method, we observed the elongation of cell colony morphology, as well as the perpendicular alignment of the cell division axis in the concave surface; the oriented cell division does not seem to explain the colony elongation. Transcriptome comparison in search of alternate possibilities suggested selectively altered pathways in the concave surface culture. Our new method is widely available, easy-to-use and culture-friendly, facilitating future mechanobiological studies of neurulation.

Enrichment of FGF8-expressing cells from neurally induced human pluripotent stem cell cultures

In early vertebrate development, organizer regions-groups of cells that signal to and thereby influence neighboring cells by secreted morphogens-play pivotal roles in the establishment and maintenance of cell identities within defined tissue territories. The midbrain-hindbrain organizer drives regionalization of neural tissue into midbrain and hindbrain territories with fibroblast growth factor 8 (FGF8) acting as a key morphogen. This organizer has been extensively studied in chicken, mouse, and zebrafish. Here, we demonstrate the enrichment of FGF8-expressing cells from human pluripotent stem cells (hPSCs), cultured as attached embryoid bodies using antibodies that recognize "Similar Expression to Fgf" (SEF) and Frizzled proteins. The arrangement of cells in embryoid body subsets of these cultures and the gene expression profile of the FGF8-expressing population show certain similarities to the midbrain-hindbrain organizer in animal models. In the embryonic chick brain, the enriched cell population induces formation of midbrain structures, consistent with FGF8-organizing capability.

Label-free imaging of 3D pluripotent stem cell differentiation dynamics on chip

Massive, parallelized 3D stem cell cultures for engineering invitro human cell types require imaging methods with high time and spatial resolution to fully exploit technological advances in cell culture technologies. Here, we introduce a large-scale integrated microfluidic chip platform for automated 3D stem cell differentiation. To fully enable dynamic high-content imaging on the chip platform, we developed a label-free deep learning method called Bright2Nuc to predict in silico nuclear staining in 3D from confocal microscopy bright-field images. Bright2Nuc was trained and applied to hundreds of 3D human induced pluripotent stem cell cultures differentiating toward definitive endoderm on a microfluidic platform. Combined with existing image analysis tools, Bright2Nuc segmented individual nuclei from bright-field images, quantified their morphological properties,predicted stem cell differentiation state, and tracked the cells over time. Our methods are available in an open-source pipeline, enabling researchers to upscale image acquisition and phenotyping of 3D cell culture.

Evaluation of Neurotoxicity With Human Pluripotent Stem Cell–Derived Cerebral Organoids

The recent development of human cerebral organoids provides an invaluable in vitro model of human brain development to assess the toxicity of natural or man-made toxic substances. By recapitulating key aspects of early human neurodevelopment, investigators can evaluate with this three-dimensional (3D) model the effect of certain compounds on the formation of neuronal networks and their electrophysiological properties with more physiological relevance than neurons grown in monolayers and in cultures composed of a unique cell type. This promising potential has contributed to the development of a large number of diverse protocols to generate human cerebral organoids, making interlaboratory comparisons of results difficult. Based on a previously published protocol to generate human cortical organoids (herein called cerebral organoids), we detail several approaches to evaluate the effect of chemicals on neurogenesis, apoptosis, and neuronal function when exogenously applied to cultured specimens. Here, we take as an example 4-aminopyridine, a potassium channel blocker that modulates the activity of neurons and neurogenesis, and describe a simple and cost-effective way to test the impact of this agent on cerebral organoids derived from human induced pluripotent stem cells. We also provide tested protocols to evaluate neurogenesis in cerebral organoids with ethynyl deoxyuridine labeling and neuronal activity with live calcium imaging and microelectrode arrays. Together, these protocols should facilitate the implementation of cerebral organoid technologies in laboratories wishing to evaluate the effects of specific compounds or conditions on the development and function of human neurons with only basic cell culture equipment. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Generation of human cerebral organoids from pluripotent stem cells Support Protocol 1: Human pluripotent stem cell culture Basic Protocol 2: Evaluation of neurogenesis in cerebral organoids with ethynyl deoxyuridine labeling Basic Protocol 3: Calcium imaging in cerebral organoids Basic Protocol 4: Electrophysiological evaluation of cerebral organoids with microelectrode arrays Support Protocol 2: Immunostaining of cerebral organoids.

The isochromosome 20q abnormality of pluripotent cells interrupts germ layer differentiation.

Chromosome 20 abnormalities are some of the most frequent genomic changes acquired by human pluripotent stem cell (hPSC) cultures worldwide. Yet their effects on differentiation remain largely unexplored. We investigated a recurrent abnormality also found on amniocentesis, the isochromosome 20q (iso20q), during a clinical retinal pigment epithelium differentiation. Here we show that the iso20q abnormality interrupts spontaneous embryonic lineage specification. Isogenic lines revealed that under conditions that promote the spontaneous differentiation of wild-type hPSCs, the iso20q variants fail to differentiate into primitive germ layers and to downregulate pluripotency networks, resulting in apoptosis. Instead, iso20q cells are highly biased for extra-embryonic/amnion differentiation following inhibition of DNMT3B methylation or BMP2 treatment. Finally, directed differentiation protocols can overcome the iso20q block. Our findings reveal in iso20q a chromosomal abnormality that impairs the developmental competency of hPSCs toward germ layers but not amnion, which models embryonic developmental bottlenecks in the presence of aberrations.

Generating human blastoids modeling blastocyst-stage embryos and implantation.

Human early development sets the stage for embryonic and adult life but remains difficult to investigate. A solution came from the ability of stem cells to organize into structures resembling preimplantation embryos-blastocysts-that we termed blastoids. This embryo model is available in unlimited numbers and could thus support scientific and medical advances. However, its predictive power depends on how faithfully it recapitulates the blastocyst. Here, we describe how we formed human blastoids that (1) efficiently achieve the morphology of the blastocyst and (2) form lineages according to the pace and sequence of blastocyst development, (3) ultimately forming cells that transcriptionally reflect the blastocyst (preimplantation stage). We employ three different commercially available 96- and 24-well microwell plates with results similar to our custom-made ones, and show that blastoids form in clinical in vitro fertilization medium and can be cryopreserved for shipping. Finally, we explain how blastoids replicate the directional process of implantation into endometrial organoids, specifically when these are hormonally stimulated. It takes 4 d for human blastoids to form and 10 d to prepare the endometrial implantation assay, and we have cultured blastoids up to 6 d (time-equivalent of day 13). On the basis of our experience, we anticipate that a person with ~1 year of human pluripotent stem cell culture experience and of organoid culture should be able to perform the protocol. Altogether, blastoids offer an opportunity to establish scientific and biomedical discovery programs for early pregnancy, and an ethical alternative to the use of embryos.

Nanosheet coating improves stability of human pluripotent stem cell culture on glass substrates

High-resolution imaging analysis using various types of cells is an essential tool for dissecting cell functions. Generally, obtaining such images requires the cells to be cultured on glass substrates; however, it often results in the unstable status of cells. In this study, we report that coating the glass substrate using nanosheet composed of hydrophobic polystyrene, with Matrigel, significantly improves the viability of human pluripotent stem cells (hPSCs). Moreover, the nanosheet coating does not affect the transcriptome status of hPSC and enables researchers to perform the high-resolution imaging assay. These results indicate that the nanosheet coating is beneficial to the cells vulnerable to glass substrate culture. Using the nanosheet coating, we revealed that the spreading status of lnc RNA XIST, essential for X-chromosome inactivation (XCI) in female cells, in the nuclei significantly differs in each hPSC line. Taken together, our study provides a novel method to investigate biological questions using high-resolution imaging techniques.

Designed peptide-grafted hydrogels for human pluripotent stem cell culture and differentiation.

Human pluripotent stem cells (hPSCs) have the ability to differentiate into cells derived from three germ layers and are an attractive cell source for cell therapy in regenerative medicine. However, hPSCs cannot be cultured on conventional tissue culture flasks but can be cultured on biomaterials with specific hPSC integrin interaction sites. We designed hydrogels conjugated with several designed peptides that had laminin-β4 active sites, optimal elasticities and different zeta potentials. A higher expansion fold of hPSCs cultured on the hydrogels was found with the increasing zeta potential of the hydrogels conjugated with designed peptides, where positive amino acid (lysine) insertion into the peptides promoted higher zeta potentials of the hydrogels and higher expansion folds of hPSCs when cultured on the hydrogels using xeno-free protocols. The hPSCs cultured on hydrogels conjugated with the optimal peptides showed a higher expansion fold than those on recombinant vitronectin-coated plates, which are the gold standard of hPSC cultivation dishes. The hPSCs could differentiate into specific cell lineages, such as mesenchymal stem cells (MSCs) and MSC-derived osteoblasts, even after being cultivated on hydrogels conjugated with optimal peptides for long periods of time, such as 10 passages.

3D ECM-rich environment sustains the identity of naive human iPSCs.

The establishment of invitro naive human pluripotent stem cell cultures opened new perspectives for the study of early events in human development. The role of several transcription factors and signaling pathways have been characterized during maintenance of human naive pluripotency. However, little is known about the role exerted by the extracellular matrix (ECM) and its three-dimensional (3D) organization. Here, using an unbiased and integrated approach combining microfluidic cultures with transcriptional, proteomic, and secretome analyses, we found that naive, but not primed, hiPSC colonies are characterized by a self-organized ECM-rich microenvironment. Based on this, we developed a 3D culture system that supports robust long-term feeder-free self-renewal of naive hiPSCs and also allows direct and timely developmental morphogenesis simply by modulating the signaling environment. Our study opens new perspectives for future applications of naive hiPSCs to study critical stages of human development in 3D starting from a single cell.

Novel strategy to improve hepatocyte differentiation stability through synchronized behavior-driven mechanical memory of iPSCs.

Cellular homeostasis is assumed to be regulated by the coordination of dynamic behaviors. Lack of efficient methods for synchronizing large quantities of cells makes studying cell culture strategies for bioprocess development challenging. Here, we demonstrate a novel application of botulinum hemagglutinin (HA), an E-cadherin function-blocking agent, to synchronize behavior-driven mechanical memory in human induced pluripotent stem cell (hiPSC) cultures. Application of HA to hiPSCs resulted in a decrease in actin bundling and disruption of colony formation in a concentration-and time-dependent manner. Interestingly, cytoskeleton rearrangement in cells with prolonged exposure to HA resulted in mechanical memory synchronization with Yes-associated protein, which increased pluripotent cell homogeneity. Synchronized hiPSCs have higher capability to differentiate into functional hepatocytes than unsynchronized hiPSCs, resulting in improved efficiency and robustness of hepatocyte differentiation. Thus, our strategy for cell behavior synchronization before differentiation induction provides an approach against the instability of differentiation of pluripotent cells.

Micro and milli-chamber bioreactors for human induced pluripotent stem cell culture: Model and experimental validation

One of the main interests in developing microfluidic platforms is the lab-on-a-chip (LOC) applications, including the use of microdevices for the culture of prokaryotic and eukaryotic cells for different applications. In this context, the trapping and control of Micro/nano-scale bubbles have been considered as it becomes a field of growing concern addressing many challenges in LOC applications. In the present work, we present a novel microfluidic bioreactor based on the micropillar design that reduces stresses caused by bubbles on the cell growth in the microchip. The combination of one chamber with 3-pillars and 10-pillars design with the channel heights of 270 µm and 2 mm were evaluated. Computational fluid dynamics simulations (CFD) were conducted to investigate the flow dynamics in the new designs. Numerical values of velocity were compared with those obtained by experimental flow tests to evaluate the performance of the proposed microdevice. Finally, the functionality of the new milli-bioreactor design was validated by culturing human induced pluripotent stem cells (hiPSC) for 5 days. Cell growth, viability and sustain pluripotency were successfully proved using a new platform architecture. This multidisciplinary research provides new insights into the chemical engineering and operability of micro and milli-bioreactors with prospects for future industrial applications.

Key benefits of a microfluidic platform for cell culture at a clinically relevant scale

Watch the video or read the poster to learn:The capabilities of an automated cell therapy workstation for process development and manufacturing combining advanced end-to-end bioprocessing and analytical capabilities and seamless scale-up/downHighly efficient bioprocessing of primary T-cells, with 5-10x lower viral vector consumption, higher fold expansion, and tighter control of cell phenotype compared to conventional research cell culture vesselsBioprocessing of adherent mesenchymal stem cells in monolayer in the MicrofluidX platform, which has been shown to surpass the performance of conventional cell culture vessels with a 3x higher cell density while maintaining cell phenotypeLongitudinal studies over 6 passages of mesenchymal stem cells, which showed 50% higher average and 30% lower variability in cell densities compared to flask culture, while maintaining cell phenotype across all passagesJames Kusena is the VP Bioprocessing and Applications at MicrofluidX. James holds a PhD in human pluripotent stem cell culture and differentiation from Loughborough University, UK. He has 6 years of experience in cell therapy process development and manufacturing optimization. His background is in medicinal chemistry, international business and health economicsMohsen Shaeri is a Senior Scientist at the Cell and Gene Therapy Catapult, specializing in process development. He has 4 years of experience in microfluidic cell culture and over 12 years of experience in bioprocessing and automation, with a focus on cell therapies. He holds a PhD in Bioengineering from the University of Sheffield, UK.Pedro Costa is the Head of Operations at Stemmatters. Pedro holds a degree in Biochemistry from the University of Coimbra (Portugal) and a PhD in Biochemistry from the University of Coimbra in co-operation with Columbia University (NY, USA). He has over six years of experience in biomedical research, with a particular focus on nanocarrier development and functionalization, and in primary cell and stem cell isolation/culture, cell-based assays, and genome editing.

Generation of Human Ventral Midbrain Organoids Derived from Pluripotent Stem Cells.

Parkinson's disease (PD) is the second most common neurodegenerative disorder worldwide and is caused by the degeneration and loss of dopamine (DA) neurons in the ventral midbrain (VM). The focal and progressive degeneration of DA neurons in the VM makes PD a particularly attractive target for cell-based therapies. Human pluripotent stem cells (hPSCs) offer unprecedented opportunities to model the development and functional properties of human DA neurons in a dish. The use of human in vitro models based on hPSCs has empowered studies of VM development and provided access to neurons expressing a particular disease-specific phenotype. Currently, hPSC differentiation is most routinely carried out in monolayer cultures, which do not properly recapitulate cell-cell interactions and the structural complexity of the brain. Moreover, 2D cultures are challenging to maintain long term, as the cells tend to detach from the plate and lose their functional characteristics. This precludes the possibility of mimicking later phases of DA neurogenesis and recreating the complexity of functional neural circuitries. Here, we describe protocols showing how to maintain hPSCs in an undifferentiated state and how to then drive these hPSCs into 3D regionalized VM organoids. After long-term culture, these VM organoids exhibit mature and post-mitotic molecular features, including neuromelanin pigments similar to those released in primate VMs. We also report a protocol describing how to efficiently perform immunohistochemistry and how to detect neuromelanin-containing DA neurons in VM organoids. Together, these protocols provide a 3D in vitro platform that can be used to better understand the molecular mechanisms underlying DA neuron function and disease and may serve as a powerful tool for designing more targeted disease-modifying therapies. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Human pluripotent stem cell culture Basic Protocol 2: hPS cell differentiation for the generation of human ventral midbrain organoids Basic Protocol 3: Characterization of ventral midbrain organoids.

Controlling neural territory patterning from pluripotency using a systems developmental biology approach

SummarySuccessful manufacture of specialized human cells requires process understanding of directed differentiation. Here, we apply high-dimensional Design of Experiments (HD-DoE) methodology to identify critical process parameters (CPPs) that govern neural territory patterning from pluripotency—the first stage toward specification of central nervous system (CNS) cell fates. Using computerized experimental design, 7 developmental signaling pathways were simultaneously perturbed in human pluripotent stem cell culture. Regionally specific genes spanning the anterior-posterior and dorsal-ventral axes of the developing embryo were measured after 3 days and mathematical models describing pathway control were developed using regression analysis. High-dimensional models revealed particular combinations of signaling inputs that induce expression profiles consistent with emerging CNS territories and defined CPPs for anterior and posterior neuroectoderm patterning. The results demonstrate the importance of combinatorial control during neural induction and challenge the use of generic neural induction strategies such as dual-SMAD inhibition, when seeking to specify particular lineages from pluripotency.

Human 8-cell-like cells discovered.

Human naive pluripotent stem cells have the remarkable ability to generate blastoids comprising trophectoderm, epiblast, and hypoblast-like cells. In this issue, Taubenschmid-Stowers etal. (2022) show that human naive pluripotent stem cell cultures contain cells that resemble the 8-cell human embryo, providing a model to study zygotic genome activation.