ISSCR standards for the use of human stem cells in basic research

Sequential emergence and contraction of epithelial subtypes in the prenatal human choroid plexus revealed by a stem cell model

Despite the major roles of choroid plexus epithelial cells (CPECs) in brain homeostasis and repair, their developmental lineage and diversity remain undefined. In simplified differentiations from human pluripotent stem cells, derived CPECs (dCPECs) display canonical properties and dynamic motile multiciliated phenotypes that interact with Aβ uptake. Single dCPEC transcriptomes over time correlate well with human organoid and fetal CPECs, while pseudotemporal and cell cycle analyses highlight the direct CPEC origin from neuroepithelial cells. In addition, time series analyses define metabolic (type 1) and ciliogenic dCPECs (type 2) at early timepoints, followed by type 1 diversification into anabolic-secretory (type 1a) and catabolic-absorptive subtypes (type 1b) as type 2 cells contract. These temporal patterns are then confirmed in independent derivations and mapped to prenatal stages using human tissues. In addition to defining the prenatal lineage of human CPECs, these findings suggest dynamic models of ChP support for the developing human brain.

Opportunities and challenges for the use of human samples in translational cardiovascular research: a scientific statement of the ESC Working Group on Cellular Biology of the Heart, the ESC Working Group on Cardiovascular Surgery, the ESC Council on Basic Cardiovascular Science, the ESC Scientists of Tomorrow, the European Association of Percutaneous Cardiovascular Interventions of the ESC, and the Heart Failure Association of the ESC

Animal models offer invaluable insights into disease mechanisms but cannot entirely mimic the variability and heterogeneity of human populations, nor the increasing prevalence of multi-morbidity. Consequently, employing human samples-such as whole blood or fractions, valvular and vascular tissues, myocardium, pericardium, or human-derived cells-is essential for enhancing the translational relevance of cardiovascular research. For instance, myocardial tissue slices, which preserve crucial structural and functional characteristics of the human heart, can be used in vitro to examine drug responses. Human blood serves as a rich source of biomarkers, including extracellular vesicles, various types of RNA (miRNA, lncRNA, and circRNAs), circulating inflammatory cells, and endothelial colony-forming cells, facilitating detailed studies of cardiovascular diseases. Primary cardiomyocytes and vascular cells isolated from human tissues are invaluable for mechanistic investigations in vitro. In cases where these are unavailable, human induced pluripotent stem cells serve as effective substitutes, albeit with specific limitations. However, the use of human samples presents challenges such as ethical approvals, tissue procurement and storage, variability in patient genetics and treatment regimens, and the selection of appropriate control samples. Biobanks are central to the efficient use of these scarce and valuable resources. This scientific statement discusses opportunities to implement the use of human samples for cardiovascular research within specific clinical contexts, offers a practical framework for acquiring and utilizing different human materials, and presents examples of human sample applications for specific cardiovascular diseases, providing a valuable resource for clinicians, translational and basic scientists engaged in cardiovascular research.

Intestinal organoids in inflammatory bowel disease: advances, applications, and future directions

Inflammatory bowel disease (IBD), characterized by chronic gastrointestinal inflammation, is a significant global health challenge. Traditional models often fail to accurately reflect human pathophysiology, leading to suboptimal treatments. This review provides an overview of recent advancements in intestinal organoid technology and its role in IBD research. Organoids, derived from patient-specific or pluripotent stem cells, retain the genetic, epigenetic, and structural characteristics of the native gut, allowing for precise modeling of key aspects of IBD. Innovations in CRISPR editing, organoid-microbe co-cultures, and organ-on-a-chip systems have enhanced the physiological relevance of these models, facilitating drug discovery and personalized therapy screening. However, challenges such as vascularization deficits and the need for standardized protocols remain. This review underscores the need for interdisciplinary efforts to bridge the gap between models and the complex reality of IBD. Future directions include the development of scalable vascularized models and robust regulatory frameworks to accelerate therapeutic translation. Organoids hold promise for unraveling IBD heterogeneity and transforming disease management.

Advancing autism research: Insights from brain organoid modeling

Autism Spectrum Disorders (ASD) are characterized by a variety of behavioral symptoms and a complex genetic architecture, posing significant challenges in understanding the mechanistic processes underlying their pathology. Despite extensive research, the mechanisms linking genetic variations to the phenotypic outcomes associated with ASD remain elusive. Consistent evidence indicates disruptions in early brain development among individuals with ASD. The advent of brain organoids offers a unique opportunity for uncovering, how brain development changes in ASD patients. Brain organoids are three-dimensional in vitro model systems derived from pluripotent stem cells that recapitulate early human brain development across multiple biological levels. They have become an invaluable tool for studying human-specific brain development processes and neurodevelopmental disorders. In this review, we discuss recent findings using brain organoid technologies to model ASD and discuss, how these new technologies can enhance our understanding of ASD genetics and pathology at the molecular, cellular, and tissue levels.

Protocol for generating human assembloids to investigate thalamocortical and corticothalamic synaptic transmission and plasticity

Human induced pluripotent stem cells (hiPSCs) can be used to generate assembloids that recreate thalamocortical circuitry displaying short-term and long-term synaptic plasticity. Here, we describe a protocol for differentiating hiPSCs into thalamic and cortical organoids and then fusing them to generate thalamocortical assembloids. We detail the steps for using whole-cell patch-clamp electrophysiology to investigate the properties of synaptic transmission and synaptic plasticity in this model system. For complete details on the use and execution of this protocol, please refer to Patton et al.1.

Endocannabinoid system upregulates the enrichment and differentiation of human iPSC- derived spermatogonial stem cells via CB2R agonism

BACKGROUND

Male factor infertility (MFI) is responsible for 50% of infertility cases and in 15% of the cases sperm is absent due to germ cell aplasia. Human induced pluripotent stem cell (hiPSC)-derived spermatogonial stem cells (hSSCs) could serve as an autologous germ cell source for MFI in patients with an insufficient sperm yield for assisted reproductive technology (ART). The endocannabinoid system (ECS) has been implicated to play a role in mouse embryonic stem cells (mESCs) and the human testicular environment. However, the contribution of the ECS in hiPSCs and hiPSC-derived hSSCs is currently unknown. Here, we aimed to assess whether hiPSCs and hiPSC-derived hSSCs are regulated by components of the ECS and whether manipulation of the ECS could increase the yield of hiPSC-derived SSCs and serve as an autologous cell-based source for treatment of MFI.

METHODS

We reprogrammed human dermal fibroblasts (hDFs) to hiPSCs, induced differentiation of hSSC from hiPSCs and evaluated the presence of ECS ligands (AEA, 2-AG) by LC/MS, receptors (CB1R, CB2R, TRPV1, GPR55) by qPCR, flow cytometry and immunofluorescent labeling. We then examined the efficacy of endogenous and synthetic selective ligands (ACPA, CB65, CSP, ML184) on proliferation of hiPSCs using real-time cell analysis (RTCA) and assessed the effects of on CB2R agonism on hiPSC pluripotency and differentiation to hSSCs.

RESULTS

hiPSCs from hDFs expressed the pluripotency markers OCT4, SOX2, NANOG, SSEA4 and TRA-1-60; and could be differentiated into ID4+, PLZF + hSSCs. hiPSCs and hiPSC-derived hSSCs secreted AEA and 2-AG at 10- 10 - 10- 9 M levels. Broad expression of all ECS receptors was observed in both hiPSCs and hiPSC-derived hSSCs, with a higher CB2R expression in hSSCs in comparison to hiPSCs. CB2R agonist CB65 promoted proliferation and differentiation of hiPSCs to hiPSC-hSSCs in comparison to AEA, 2-AG, ACPA, CSP and ML184. The EC50 of CB65 was determined to be 2.092 × 10- 8 M for support of pluripotency and preservation of stemness on hiPSCs from 78 h. CB65 stimulation at EC50 also increased the yield of ID4 + hSSCs, PLZF + SSPCs and SCP3 + spermatocytes from day 10 to 12.

CONCLUSIONS

We demonstrated here for the first time that stimulation of CB2R results in an increased yield of hiPSCs and hiPSC-derived hSSCs. CB65 is a potent CB2R agonist that can be used to increase the yield of hiPSC-derived hSSCs offering an alternative source of autologous male germ cells for patients with MFI. Increasing the male germ/stem cell pool by CB65 supplementation could be part of the ART-associated protocols in MFI patients with complete germ cell aplasia.

A framework for neural organoids, assembloids and transplantation studies

As the field of neural organoids and assembloids expands, there is an emergent need for guidance and advice on designing, conducting and reporting experiments to increase the reproducibility and utility of these models. In this Perspective, we present a framework for the experimental process that encompasses ensuring the quality and integrity of human pluripotent stem cells, characterizing and manipulating neural cells in vitro, transplantation techniques and considerations for modelling human development, evolution and disease. As with all scientific endeavours, we advocate for rigorous experimental designs tailored to explicit scientific questions as well as transparent methodologies and data sharing to provide useful knowledge for current research practices and for developing regulatory standards.

Human iPSC Reprogramming Success: The Impact of Approaches and Source Materials

Since their discovery, human induced pluripotent stem cells (hiPSCs) have been instrumental in biomedical research, particularly in the fields of disease modelling, drug screening and regenerative therapies. Their use has significantly increased over recent years driven by the ability of hiPSCs to provide differentiated cell models without requiring embryonic stem cells. Furthermore, the transition from integrating to non-integrating reprogramming methodologies has contributed to the increase in utilisation. This shift minimises the risk of genomic alterations, enhancing the safety and reliability of hiPSCs. However, the factors that contribute to reprogramming success are still not well understood. In this study, we conducted a comparative analysis of the most prevalent non-integrating reprogramming methods across a range of starting source materials to assess their impact on reprogramming success rates. We found that while source material does not significantly impact success rates, the Sendai virus reprogramming method yields significantly higher success rates relative to the episomal reprogramming method. Our findings offer important insights from a biobanking perspective, for which long-term reliability, integrity and reproducibility of hiPSCs are crucial.

Harnessing the potential of human induced pluripotent stem cells, functional assays and machine learning for neurodevelopmental disorders

Neurodevelopmental disorders (NDDs) affect 4.7% of the global population and are associated with delays in brain development and a spectrum of impairments that can lead to lifelong disability and even mortality. Identification of biomarkers for accurate diagnosis and medications for effective treatment are lacking, in part due to the historical use of preclinical model systems that do not translate well to the clinic for neurological disorders, such as rodents and heterologous cell lines. Human-induced pluripotent stem cells (hiPSCs) are a promising in vitro system for modeling NDDs, providing opportunities to understand mechanisms driving NDDs in human neurons. Functional assays, including patch clamping, multielectrode array, and imaging-based assays, are popular tools employed with hiPSC disease models for disease investigation. Recent progress in machine learning (ML) algorithms also presents unprecedented opportunities to advance the NDD research process. In this review, we compare two-dimensional and three-dimensional hiPSC formats for disease modeling, discuss the applications of functional assays, and offer insights on incorporating ML into hiPSC-based NDD research and drug screening.

Considering future qualification for regulatory science in the early development of microphysiological systems: a case study of microthrombosis in a Vessel-on-Chip

Microphysiological systems (MPS) and Organs-on-Chips (OoCs) hold significant potential for replicating complex human biological processes in vitro. However, their widespread adoption by industry and regulatory bodies depends on effective qualification to demonstrate that these models are fit for purpose. Many models developed in academia are not initially designed with qualification in mind, which limits their future implementation in end-user settings. Here, we explore to which extent aspects of qualification can already be performed during early development stages of MPS and OoCs. Through a case study of our blood-perfused Vessel-on-Chip model, we emphasize key elements such as defining a clear context-of-use, establishing relevant readouts, ensuring model robustness, and addressing inherent limitations. By considering qualification early in development, researchers can streamline the progression of MPS and OoCs, facilitating their adoption in biomedical, pharmaceutical, and toxicological research. In addition, all in vitro methods must be independent of animal-derived materials to be considered fully fit for purpose. Ultimately, early qualification efforts can enhance the availability, reliability, and regulatory as well as ethical acceptance of these emerging New Approach Methodologies.

Heart and vessels from stem cells: A short history of serendipity and good luck

Stem cell research is the product of cumulative, integrated effort between and within laboratories and disciplines. The many collaborative steps that lead to that special "Eureka moment", when something that has been a puzzle perhaps for years suddenly become clear, is among the greatest pleasures of a scientific career. In this essay, the serendipitous pathway from first acquaintance with pluripotent stem cells to advanced cardiovascular models that emerged from studying development and disease will be described. Perhaps inspiration for later generations of stem cell researchers simply to follow whatever they find interesting.

Culture-acquired genetic variation in human pluripotent stem cells: Twenty years on

Genetic changes arising in human pluripotent stem cells (hPSC) upon culture may bestow unwanted or detrimental phenotypes to cells, thus potentially impacting on the applications of hPSCs for clinical use and basic research. In the 20 years since the first report of culture-acquired genetic aberrations in hPSCs, a characteristic spectrum of recurrent aberrations has emerged. The preponderance of such aberrations implies that they provide a selective growth advantage to hPSCs upon expansion. However, understanding the consequences of culture-acquired variants for specific applications in cell therapy or research has been more elusive. The rapid progress of hPSC-based therapies to clinics is galvanizing the field to address this uncertainty and provide definitive ways both for risk assessment of variants and reducing their prevalence in culture. Here, we aim to provide a timely update on almost 20 years of research on this fascinating, but a still unresolved and concerning, phenomenon.

Efficient generation of human induced pluripotent stem cells from urine samples of patients with Fragile X syndrome

Human induced pluripotent stem cells (iPSCs) are a valuable tool for studying human development and diseases. iPSCs can be generated by reprogramming from any somatic cells, however establishing primary cell cultures can involve invasive procedures (e.g., skin biopsy) and be labor-intensive. In this paper, we describe an efficient, reliable, and non-invasive method for cultivating primary urine-derived cells (UDCs) and efficiently reprogram them into iPSCs using a feeder-free and non-integrative system. This approach has several advantages: (i) UDCs collection and culture are non-invasive, straightforward, and do not require medical personnel; (ii) reprogramming UDCs using commercially available Sendai viruses is highly efficient and reliable; and (iii) iPSCs generated from UDCs demonstrate strong differentiation potential. To showcase the effectiveness of this method, we generated iPSC lines from UDCs of three control individuals and three patients with Fragile X syndrome.

Gain of 1q confers an MDM4-driven growth advantage to undifferentiated and differentiating hESC while altering their differentiation capacity

Gain of 1q is a highly recurrent chromosomal abnormality in human pluripotent stem cells. In this work, we show that gains of 1q impact the differentiation capacity to derivates of the three germ layers, leading to mis-specification to cranial placode and non-neural ectoderm during neuroectoderm differentiation. Also, we found a weaker expression of lineage-specific markers in hepatoblasts and cardiac progenitors. Competition assays show that the cells retain their selective advantage during differentiation, which is mediated by a higher expression of MDM4, a gene located in the common region of gain. MDM4 drives the winner phenotype of the mutant cells in both the undifferentiated and differentiating state by reducing the cells' sensitivity to DNA damage through decreased p53-mediated apoptosis. Finally, we found that cell density in culture plays a key role in promoting the competitive advantage of the cells by increasing DNA damage.

Consequences of trisomy 21 for brain development in Down syndrome

The appearance of cognitive deficits and altered brain morphology in newborns with Down syndrome (DS) suggests that these features are driven by disruptions at the earliest stages of brain development. Despite its high prevalence and extensively characterized cognitive phenotypes, relatively little is known about the cellular and molecular mechanisms that drive the changes seen in DS. Recent technical advances, such as single-cell omics and the development of induced pluripotent stem cell (iPSC) models of DS, now enable in-depth analyses of the biochemical and molecular drivers of altered brain development in DS. Here, we review the current state of knowledge on brain development in DS, focusing primarily on data from human post-mortem brain tissue. We explore the biological mechanisms that have been proposed to lead to intellectual disability in DS, assess the extent to which data from studies using iPSC models supports these hypotheses, and identify current gaps in the field.

Advancing stem cell technologies for conservation of wildlife biodiversity

Wildlife biodiversity is essential for healthy, resilient and sustainable ecosystems. For biologists, this diversity also represents a treasure trove of genetic, molecular and developmental mechanisms that deepen our understanding of the origins and rules of life. However, the rapid decline in biodiversity reported recently foreshadows a potentially catastrophic collapse of many important ecosystems and the associated irreversible loss of many forms of life on our planet. Immediate action by conservationists of all stripes is required to avert this disaster. In this Spotlight, we draw together insights and proposals discussed at a recent workshop hosted by Revive & Restore, which gathered experts to discuss how stem cell technologies can support traditional conservation techniques and help protect animal biodiversity. We discuss reprogramming, in vitro gametogenesis, disease modelling and embryo modelling, and we highlight the prospects for leveraging stem cell technologies beyond mammalian species.

SeqVerify: An accessible analysis tool for cell line genomic integrity, contamination, and gene editing outcomes

Over the last decade, advances in genome editing and pluripotent stem cell (PSC) culture have let researchers generate edited PSC lines to study a wide variety of biological questions. However, abnormalities in cell lines such as aneuploidy, mutations, on-target and off-target editing errors, and microbial contamination can arise during PSC culture or due to undesired editing outcomes. The ongoing decline of next-generation sequencing prices has made whole-genome sequencing (WGS) a promising option for detecting these abnormalities. However, this approach has been held back by a lack of easily usable data analysis software. Here, we present SeqVerify, a computational pipeline designed to take raw WGS data and a list of intended genome edits, and verify that the edits are present and that there are no abnormalities. We anticipate that SeqVerify will be a useful tool for researchers generating edited PSCs, and more broadly, for cell line quality control in general.

Guidelines for managing and using the digital phenotypes of pluripotent stem cell lines

Each pluripotent stem cell line has a physical entity as well as a digital phenotype, but linking the two unambiguously is confounded by poor naming practices and assumed knowledge. Registration gives each line a unique and persistent identifier that links to phenotypic data generated over the lifetime of that line. Registration is a key recommendation of the 2023 ISSCR Standards for the use of human stem cells in research. Here we consider how community adoption of stem cell line registration could facilitate the establishment of integrated digital phenotypes of specific human pluripotent stem cell (hPSC) lines.

Reassessment of marker genes in human induced pluripotent stem cells for enhanced quality control

Human induced pluripotent stem cells (iPSCs) have great potential in research, but pluripotency testing faces challenges due to non-standardized methods and ambiguous markers. Here, we use long-read nanopore transcriptome sequencing to discover 172 genes linked to cell states not covered by current guidelines. We validate 12 genes by qPCR as unique markers for specific cell fates: pluripotency (CNMD, NANOG, SPP1), endoderm (CER1, EOMES, GATA6), mesoderm (APLNR, HAND1, HOXB7), and ectoderm (HES5, PAMR1, PAX6). Using these genes, we develop a machine learning-based scoring system, "hiPSCore", trained on 15 iPSC lines and validated on 10 more. hiPSCore accurately classifies pluripotent and differentiated cells and predicts their potential to become specialized 2D cells and 3D organoids. Our re-evaluation of cell fate marker genes identifies key targets for future studies on cell fate assessment. hiPSCore improves iPSC testing by reducing time, subjectivity, and resource use, thus enhancing iPSC quality for scientific and medical applications.

Protocol for establishing inducible CRISPRd system for blocking transcription factor-binding sites in human pluripotent stem cells

Transcription factor (TF) gene knockout or knockdown experiments provide comprehensive downstream effects on gene regulation. However, distinguishing primary direct effects from secondary effects remains challenging. To assess the direct effect of TF binding events, we present a protocol for establishing a doxycycline (Dox)-inducible CRISPRd system in human pluripotent stem cells (hPSCs). We describe the steps for establishing CRISPRd host hPSCs, designing and preparing single-guide RNA (sgRNA) expression lentivirus vectors, generating CRISPRd hPSCs transduced with sgRNAs, and analyzing CRISPRd TF-block effects by chromatin immunoprecipitation (ChIP)-qPCR. For complete details on the use and execution of this protocol, please refer to Matsui et al.1.

Protocol for establishing inducible CRISPR interference system for multiple-gene silencing in human pluripotent stem cells

Inducible loss-of-function strategies are crucial for understanding gene function. However, creating inducible, multiple-gene knockout models is challenging and time-consuming. Here, we present a protocol for establishing a doxycycline-inducible CRISPR interference (CRISPRi) system to concurrently silence multiple genes in human induced pluripotent stem cells (hPSCs). We describe the steps for establishing host CRISPRi hPSCs, designing and cloning single-guide RNAs (sgRNAs) into a lentivirus plasmid, and establishing monoclonal CRISPRi hPSC lines transduced with sgRNAs. We also detail the procedures for selecting effective CRISPRi clones. For complete details on the use and execution of this protocol, please refer to Matsui et al.1.

Validating human induced pluripotent stem cell-specific quality control tests for the release of an intermediate drug product in a Good Manufacturing Practice quality system

One of the challenges in Good Manufacturing Practice (GMP)-compliant human induced pluripotent stem cell (hiPSC) production is the validation of quality control (QC) tests specific for hiPSCs, which are required for GMP batch release. This study presents a comprehensive description of the validation process for hiPSC-specific GMP-compliant QC assays; more specifically, the validation of assays to assess the potential presence of residual episomal vectors (REVs), the expression of markers of the undifferentiated state and the directed differentiation potential of hiPSCs. Critical aspects and specific acceptance criteria were formulated in a validation plan prior to assay validation. Assay specificity, sensitivity and reproducibility were tested, and the equipment used for each assay was subjected to performance qualification. A minimum input of 20 000 cells (120 ng of genomic DNA) was defined for accurate determination of the presence of REVs. Furthermore, since vector loss in hiPSC lines is a passage-dependent process, we advocate screening for REVs between passages eight and 10, as testing at earlier passages might lead to unnecessary rejection of hiPSC lines. The cutoff value for assessment of markers of the undifferentiated state was set to the expression of at least three individual markers on at least 75% of the cells. When multi-color flow cytometry panels are used, a fluorescence minus one control is advised to ensure the control for fluorescent spread. For the assay to assess the directed differentiation potential, the detection limit was set to two of three positive lineage-specific markers for each of the three individual germ layers. All of our assays proved to be reproducible and specific. Our data demonstrate that our implemented analytical procedures are suitable as QC assays for the batch release of GMP-compliant hiPSCs.

Australian researchers' perceptions and experiences with stem cell registration

The recently issued ISSCR standards in stem cell research recommend registration of human pluripotent stem cell lines (hPSCs). Registration is critical to establishing stem cell provenance and connecting cell lines to data derived on those lines. In this study, we sought to understand common barriers to registration by conducting interviews with forty-eight Australian stem cell stakeholders, including researchers, clinicians, and industry professionals. Australian stem cell researchers do not routinely register their lines, and only a third of those Australian lines captured by an international registry have fully completed the registration process. Most registered Australian cell lines lack complete information about their ethical provenance or key pluripotency characteristics. Incomplete registration is poorly aligned with the goals of open science on which registries are founded. Users also expressed concerns about the quality of the incomplete information provided to the resource. Registration was considered negatively, for instance as a hurdle or barrier to publication, which impacted on user perceptions of usefulness of registration and lowered the likelihood that they would engage with registries to find resources. Broader adoption of registration by journals, and continued advocacy by stem cell societies, will be important levers for awareness and engagement with registration. Although the Australian community represents a small fraction of potential registry users, the results of this study suggest ways for journals, registries, funders, and the international stem cell community to improve registration compliance.

STRAIGHT-IN: a platform for rapidly generating panels of genetically modified human pluripotent stem cell lines

Targeted integration of large DNA cargoes (>10 kb) or genomic replacements in mammalian cells, such as human pluripotent stem cells (hPS cells), remains challenging. Here we describe a platform termed serine and tyrosine recombinase-assisted integration of genes for high-throughput investigation (STRAIGHT-IN) to circumvent this. First, a landing pad cassette is precisely inserted or used to replace specific genomic regions. The site-specific integrase Bxb1 then enables DNA constructs, including those >50 kb, to be integrated into the genome, while Cre recombinase excises auxiliary DNA sequences to prevent postintegrative silencing. Using a strategy whereby the positive selection marker is only expressed if the donor plasmid carrying the payload is correctly targeted, we can obtain 100% enrichment for cells containing the DNA payload. Procedures for expressing Cre efficiently also mean that a clonal isolation step is no longer essential to derive the required genetically modified hPS cells containing the integrated DNA, potentially reducing clonal variability. Furthermore, STRAIGHT-IN facilitates rapid and multiplexed generation of genetically matched hPS cells when multiple donor plasmids are delivered simultaneously. STRAIGHT-IN has various applications, which include integrating complex genetic circuits for synthetic biology, as well as creating panels of hPS cells lines containing, as necessary, hundreds of disease-linked variants for disease modeling and drug discovery. After establishing the hPS cell line containing the landing pad, the entire procedure, including donor plasmid synthesis, takes 1.5-3 months, depending on whether single or multiple DNA payloads are integrated. This protocol only requires the researcher to be skilled in molecular biology and standard cell culture techniques.

The role of the International Society for Stem Cell Research (ISSCR) guidelines in disease modeling

Human stem cell-based modeling systems are valuable tools that can greatly improve the clinical translation of basic research. Importantly, the successful application of human stem cell-based models to biomedical research depends on the widespread adoption of ethical principles and practical standards. To achieve this outcome, the International Society for Stem Cell Research (ISSCR) provides a comprehensive set of recommendations that aim to promote the ethical usage of human stem cells and to ensure rigor and reproducibility within the field. Understanding and implementing these recommendations should be a top priority for investigators around the world.

Rigor and reproducibility in human brain organoid research: Where we are and where we need to go

Human brain organoid models have emerged as a promising tool for studying human brain development and function. These models preserve human genetics and recapitulate some aspects of human brain development, while facilitating manipulation in an in vitro setting. Despite their potential to transform biology and medicine, concerns persist about their fidelity. To fully harness their potential, it is imperative to establish reliable analytic methods, ensuring rigor and reproducibility. Here, we review current analytical platforms used to characterize human forebrain cortical organoids, highlight challenges, and propose recommendations for future studies to achieve greater precision and uniformity across laboratories.

A Standardized Nomenclature Design for Systematic Referencing and Identification of Animal Cellular Material

The documentation, preservation and rescue of biological diversity increasingly uses living biological samples. Persistent associations between species, biosamples, such as tissues and cell lines, and the accompanying data are indispensable for using, exchanging and benefiting from these valuable materials. Explicit authentication of such biosamples by assigning unique and robust identifiers is therefore required to allow for unambiguous referencing, avoid identification conflicts and maintain reproducibility in research. A predefined nomenclature based on uniform rules would facilitate this process. However, such a nomenclature is currently lacking for animal biological material. We here present a first, standardized, human-readable nomenclature design, which is sufficient to generate unique and stable identifying names for animal cellular material with a focus on wildlife species. A species-specific human- and machine-readable syntax is included in the proposed standard naming scheme, allowing for the traceability of donated material and cultured cells, as well as data FAIRification. Only when it is consistently applied in the public domain, as publications and inter-institutional samples and data are exchanged, distributed and stored centrally, can the risks of misidentification and loss of traceability be mitigated. This innovative globally applicable identification system provides a standard for a sustainable structure for the long-term storage of animal bio-samples in cryobanks and hence facilitates current as well as future species conservation and biomedical research.

A Review of the Evidence for Tryptophan and the Kynurenine Pathway as a Regulator of Stem Cell Niches in Health and Disease

Stem cells are ubiquitously found in various tissues and organs in the body, and underpin the body's ability to repair itself following injury or disease initiation, though repair can sometimes be compromised. Understanding how stem cells are produced, and functional signaling systems between different niches is critical to understanding the potential use of stem cells in regenerative medicine. In this context, this review considers kynurenine pathway (KP) metabolism in multipotent adult progenitor cells, embryonic, haematopoietic, neural, cancer, cardiac and induced pluripotent stem cells, endothelial progenitor cells, and mesenchymal stromal cells. The KP is the major enzymatic pathway for sequentially catabolising the essential amino acid tryptophan (TRP), resulting in key metabolites including kynurenine, kynurenic acid, and quinolinic acid (QUIN). QUIN metabolism transitions into the adjoining de novo pathway for nicotinamide adenine dinucleotide (NAD) production, a critical cofactor in many fundamental cellular biochemical pathways. How stem cells uptake and utilise TRP varies between different species and stem cell types, because of their expression of transporters and responses to inflammatory cytokines. Several KP metabolites are physiologically active, with either beneficial or detrimental outcomes, and evidence of this is presented relating to several stem cell types, which is important as they may exert a significant impact on surrounding differentiated cells, particularly if they metabolise or secrete metabolites differently. Interferon-gamma (IFN-γ) in mesenchymal stromal cells, for instance, highly upregulates rate-limiting enzyme indoleamine-2,3-dioxygenase (IDO-1), initiating TRP depletion and production of metabolites including kynurenine/kynurenic acid, known agonists of the Aryl hydrocarbon receptor (AhR) transcription factor. AhR transcriptionally regulates an immunosuppressive phenotype, making them attractive for regenerative therapy. We also draw attention to important gaps in knowledge for future studies, which will underpin future application for stem cell-based cellular therapies or optimising drugs which can modulate the KP in innate stem cell populations, for disease treatment.

A human neural crest model reveals the developmental impact of neuroblastoma-associated chromosomal aberrations

Early childhood tumours arise from transformed embryonic cells, which often carry large copy number alterations (CNA). However, it remains unclear how CNAs contribute to embryonic tumourigenesis due to a lack of suitable models. Here we employ female human embryonic stem cell (hESC) differentiation and single-cell transcriptome and epigenome analysis to assess the effects of chromosome 17q/1q gains, which are prevalent in the embryonal tumour neuroblastoma (NB). We show that CNAs impair the specification of trunk neural crest (NC) cells and their sympathoadrenal derivatives, the putative cells-of-origin of NB. This effect is exacerbated upon overexpression of MYCN, whose amplification co-occurs with CNAs in NB. Moreover, CNAs potentiate the pro-tumourigenic effects of MYCN and mutant NC cells resemble NB cells in tumours. These changes correlate with a stepwise aberration of developmental transcription factor networks. Together, our results sketch a mechanistic framework for the CNA-driven initiation of embryonal tumours.

Advancements in Human Embryonic Stem Cell Research: Clinical Applications and Ethical Issues

BACKGROUND

The development and use of human embryonic stem cells (hESCs) in regenerative medicine have been revolutionary, offering significant advancements in treating various diseases. These pluripotent cells, derived from early human embryos, are central to modern biomedical research. However, their application is mired in ethical and regulatory complexities related to the use of human embryos.

METHOD

This review utilized key databases such as ClinicalTrials.gov, EU Clinical Trials Register, PubMed, and Google Scholar to gather recent clinical trials and studies involving hESCs. The focus was on their clinical application in regenerative medicine, emphasizing clinical trials and research directly involving hESCs.

RESULTS

Preclinical studies and clinical trials in various areas like ophthalmology, neurology, endocrinology, and reproductive medicine have demonstrated the versatility of hESCs in regenerative medicine. These studies underscore the potential of hESCs in treating a wide array of conditions. However, the field faces ethical and regulatory challenges, with significant variations in policies and perspectives across different countries.

CONCLUSION

The potential of hESCs in regenerative medicine is immense, offering new avenues for treating previously incurable diseases. However, navigating the ethical, legal, and regulatory landscapes is crucial for the continued advancement and responsible application of hESC research in the medical field. Considering both scientific potential and ethical implications, a balanced approach is essential for successfully integrating hESCs into clinical practice.

Engineered T cells from induced pluripotent stem cells: from research towards clinical implementation

Induced pluripotent stem cell (iPSC)-derived T (iT) cells represent a groundbreaking frontier in adoptive cell therapies with engineered T cells, poised to overcome pivotal limitations associated with conventional manufacturing methods. iPSCs offer an off-the-shelf source of therapeutic T cells with the potential for infinite expansion and straightforward genetic manipulation to ensure hypo-immunogenicity and introduce specific therapeutic functions, such as antigen specificity through a chimeric antigen receptor (CAR). Importantly, genetic engineering of iPSC offers the benefit of generating fully modified clonal lines that are amenable to rigorous safety assessments. Critical to harnessing the potential of iT cells is the development of a robust and clinically compatible production process. Current protocols for genetic engineering as well as differentiation protocols designed to mirror human hematopoiesis and T cell development, vary in efficiency and often contain non-compliant components, thereby rendering them unsuitable for clinical implementation. This comprehensive review centers on the remarkable progress made over the last decade in generating functional engineered T cells from iPSCs. Emphasis is placed on alignment with good manufacturing practice (GMP) standards, scalability, safety measures and quality controls, which constitute the fundamental prerequisites for clinical application. In conclusion, the focus on iPSC as a source promises standardized, scalable, clinically relevant, and potentially safer production of engineered T cells. This groundbreaking approach holds the potential to extend hope to a broader spectrum of patients and diseases, leading in a new era in adoptive T cell therapy.

Optimized and Scalable Precoating-Free Reprogramming of Human Peripheral Blood Mononuclear Cells into iPSCs

Human disease modeling has been profoundly transformed by the introduction of human induced pluripotent stem cells (iPSCs), marking the onset of a new era. This ground-breaking development offers a tailored framework for generating pluripotent cells from any individual, effectively enabling the development of cellular models for the study of human physiology and diseases on an unprecedented scale. Although technologies for iPSCs generation have advanced rapidly over the past two decades, protocols for reprogramming patient-derived somatic cells into stem cells still pose a major challenge for the development of automated pipelines capable of generating iPSCs at scales that are cost-effective, reproducible, and easy to implement. Most methods commonly rely on extracellular matrix protein mixtures or synthetic substrates to promote efficient proliferation of iPSCs. Nonetheless, employing these substances entails a laborious and time-consuming process, as the culture surface requires coating treatments before cell seeding. Here we describe a method for reprogramming blood-derived mononucleated cells that eliminates the need to precoat culture surfaces for the entire experimental flow. This procedure is suitable for fresh or frozen purified peripheral blood mononuclear cells (PBMCs) and allows seeding of reprogrammed cells in a culture medium containing a fragment of laminin-511, regardless of the method of reprogramming employed. Our protocol incorporates a streamlined workflow that optimizes key factors, including cell density, culture medium composition, and iPSC culture propagation techniques. Using a precoating-free approach, we eliminate the time-consuming steps, while our optimized subcloning method improves the scalability of the protocol, making it suitable for large-scale applications. Additionally, the automation-friendly nature of our protocol allows for high-throughput processing, reducing the labor and costs associated with manual handling. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Miniaturized and time efficient precoating-free reprogramming of fresh or frozen PBMCs Alternate Protocol: Erythroid progenitor cells (EPCs) enrichment and reprogramming into iPSCs using Sendai viral vectors Basic Protocol 2: Picking and precoating-free optimized expansion of iPSC clones.