Correction to “Bifurcation in a G 0 Model of Hematological Stem Cells With Delay”

Translation: Screening for Novel Therapeutics With Disease-Relevant Cell Types Derived from Human Stem Cell Models

With recent advances in stem cell technology, there has been an expansion of human stem and progenitor cell models of pediatric brain tumors, including use of human pluripotent and embryonic stem cells both in organoid cultures and following xenotransplantation in mice. In this review, we discuss the current approaches to modelling pediatric brain cancers using stem cells. While brain tumors describe a broad set of disease entities, we focus on glioma, medulloblastoma and ependymoma, as these are not only the most common malignant brain tumor types but also have the most stem cell models currently available. We examine human stem cell-based modeling approaches and discuss the biological questions that are being addressed using these state-of-the-art tools. Specifically, we focus on the unique advantage of using these cells to understand the functional consequences of gene mutations and their downstream growth-promoting pathways within the cell in a human context. These approaches are needed to ascertain the key players that are functionally relevant in the initiation and propagation of these tumors at the gene and protein level and to identify new drug targets. Moreover, human stem cell-based modeling approaches may complement studies in genetically engineered mouse models to address fundamental questions in tumor biology, particularly the early stages of tumorigenesis.

The periodical dynamics of a G0 cell cycle model of pluripotential stem cells is analyzed by DDE‐Biftool software. The cell cycle model is impressed by modeling the optional choice of Hill function, which is benefited by Fourier transformation. The cell cycle is based on DDEs with distributed time delay, in which the kernel function is denoted by Gamma‐distribution expression. Hopf bifurcation of the linear version of the cell cycle model with distribution time delay is analyzed analytically. The periodical solution continuation is simulated by the artificial handbook of DDE‐Biftool software. With the discrete time delay, the complex behavior of adding‐period bifurcation and period‐doubling bifurcation are simulated. With distribution time delay, the continuation work of the homoclinic solution is done, and the homoclinic bifurcation line crosses the generalized Hopf point nearly.JEL Classification: 34C25, 34K18, 37G15

Both theoretical and experimental evidence support the concept of a tumor stem cell (TSC) model - a rare population of self-renewing stem cells among the heterogeneous mixture of tumor cells essential for solid tumor growth and progression. However, this growing evidence is not by itself convincing without an adequate molecular mechanism explaining how these TSCs maintain their stemness, since there is always a possibility that the so-called solid tumor TSCs may be a highly tumorigenic fraction of the heterogeneous mixture of tumor cells. The lack of knowledge of how TSCs maintain their state of stemness is therefore a major limitation that requires attention in order to improve our understanding on the stem cell model of tumor growth. An emerging and provocative concept in tumor biology is that a rare population of tumor stem cells exists among the heterogeneous population of cells within tumors. The TSC model suggests that proliferative potential and growth patterns of many human tumors may depend upon a small proportion of tumor stem cells that lead to repopulation following cytotoxic therapy. In this review, we will briefly discuss the basic concept of the TSC model and the emerging findings of the existence of the TSC fraction, even in established tumor cell lines.

Modeling motor neuron disease: the matter of time

<bold xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Objectives:</b> in recent biomedical applications for regenerative and tissue engineering, the use of electric and magnetic fields is increasingly exploited. Among the wide application range, an innovative treatment for Spinal Cord Injury (SCI) is urgent. The European project RISEUP proposes a novel device development, that will provide highly intense microsecond pulsed electric fields (μsPEFs) to stimulate stem cells differentiation towards neuronal phenotypes, through an electroporation-driven process, and regenerate the lesioned tissue. Within RISEUP the use of advanced computational models is crucial to predict the cellular functional response through microdosimetry studies. <bold xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Technology or Method:</b> a multiphysic neuro-functionalized computational model has been built, using a realistic induced Neuronal Stem Cell (iNSC) model (a iNSC digital twin), to predict the effect of μsPEFs stimulation on both neuronal response and pore formation dynamics. <bold xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Results:</b> considering a 100-μsPEF and an intensity of 30 kV/m, the pore density can reach up to 10<sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">14</sup> m<sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−2</sup> over the plasma membrane, with a consequent hyperpolarization and a phase shift of the neuronal firing. Whereas, where the pore density remains at its default value 10<sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">9</sup> m<sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−2</sup>, the neuronal response is slightly affected in spikes frequency and shape, but still maintaining its firing functions. <bold xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Conclusions</b>: this study provides an innovative multiphysics implementation on a realist 2D iNSC model, that has demonstrated the 100-μsPEF influence on the neurodynamic response. <bold xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Clinical or Biological Impact:</b> the results obtained give powerful insights for further <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">in vitro</i> and <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">in vivo</i> experiments, that will validate the use of the device proposed within RISEUP for SCI regeneration.

Dissecting the key molecular mechanism of embryonic development provides novel insights into embryogenesis and potential intervention strategies for clinical practices. However, the ability to study the molecular mechanisms of early embryo development in humans, such as zygotic genome activation and lineage segregation, is meaningfully constrained by methodological limitations and ethical concerns. Totipotent stem cells have an extended developmental potential to differentiate into embryonic and extraembryonic tissues, providing a suitable model for studying early embryo development. Recently, a series of ground-breaking results on stem cells have identified totipotent-like cells or induced pluripotent stem cells into totipotent-like cells. This review followed the PRISMA guidelines, surveys the current works of literature on totipotent, naive, and formative pluripotent stem cells, introduces the molecular and biological characteristics of those stem cells, and gives advice for future research. The search method employed the terms 'totipotent' OR 'naive pluripotent stem cell' OR 'formative pluripotent stem cell' for unfiltered search on PubMed, Web of Science, and Cochrane Library. Papers included were those with information on totipotent stem cells, naive pluripotent stem cells, or formative pluripotent stem cells until June 2024 and were published in the English language. Articles that have no relevance to stem cells, or totipotent, naive pluripotent, or formative pluripotent cells were excluded. There were 152 records included in this review. These publications were divided into four groups according to the species of the cells included in the studies: 67 human stem cell studies, 70 mouse stem cell studies, 9 porcine stem cell studies, and 6 cynomolgus stem cell studies. Naive pluripotent stem cell models have been established in other species such as porcine and cynomolgus. Human and mouse totipotent stem cells, e.g. human 8-cell-like cells, human totipotent blastomere-like cells, and mouse 2-cell-like cells, have been successfully established and exhibit high developmental potency for both embryonic and extraembryonic contributions. However, the observed discrepancies between these cells and real embryos in terms of epigenetics and transcription suggest that further research is warranted. Our results systematically reviewed the established methods, molecular characteristics, and developmental potency of different naive, formative pluripotent, and totipotent stem cells. Furthermore, we provide a parallel comparison between animal and human models, and offer recommendations for future applications to advance early embryo research and assisted reproduction technologies. Totipotent cell models provide a valuable resource to understand the underlying mechanisms of embryo development and forge new paths toward future treatment of infertility and regenerative medicine. However, current in vitro cell models exhibit epigenetic and transcriptional differences from in vivo embryos, and many cell models are unstable across passages, thus imperfectly recapitulating embryonic development. In this regard, standardizing and expanding current research on totipotent stem cell models are essential to enhance our capability to resemble and decipher embryogenesis.

The existence of cancer stem cell (CSC) has been considered as one of the important reason as to why patients have a poor prognosis. However, heterotopic transplantation of embryonic stem cells and induced pluripotent stem cells has been shown to form teratoma, but not malignant teratoma. Since the microenvironment niche is playing a significant role for the proper differentiation of stem cells, the cancerous niche should drive stem cells into malignant cells in vivo. According to this hypothesis, we tried to generate cancer cells from human induced pluripotent stem (hiPS) cells. For the conversion into CSC, the conditioned medium from different human cancer cell lines was collected from confluent dishes and filtered using 0.22 micrometer filter. Then, hiPS cells, without MEF feeder cells, were maintained in the conditioned medium (CM) in the ratio of 1:1. The medium was changed every day with CM for 4 weeks. hiPS cells with the complete medium were used as control. For transplantation studies, 10^4 cells were suspended in HBSS and were xenotransplantated into NOD-SCID mice. After 3 months, tumors were excised and fixed in 10% neutral formalin buffer solution, or subjected to primary culture. The converted cells and primary cultured cells formed spheroids in suspension culture, and had tumorigenicity in vivo. The stemness of living cells was checked under fluorescent microscopy observation with rBC2LCN-FITC staining. The RNAs were extracted from converted cells and microarray analysis was perfomed. The RNA expression patterns of cell lines were visualized by sphered self-organizing map (sSOM) analysis. The sSOM analysis perfomed based upon various parameters shows the converted CSCs can be characterized into various cell types. Utilizing this method, we successfully established two different hiPS-CSC lines using CM from A172 and RERF-LC-KJ. The comprehensive understanding of cancer could be realized as the heterogeneity of cancer tissues is clarified and their component cells are identified. This study will lead to the development of the true personalized therapy of cancer in the future. Citation Format: Tomonari Kasai, Kenta Hoshikawa, Shuto Takejiri, Masashi Ikeda, Kazuki Kumon, Anna Sanchez Calle, Arun Vaidyanath, Akifumi Mizutani, Chen Ling, Masaharu Seno. Derivation of a model of cancer stem cell from human induced pluripotent stem cells. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-144. doi:10.1158/1538-7445.AM2015-LB-144

Although significant progresses in molecular oncology are being made using conventional cell lines, most therapies still fail in phase III clinical trials. Patient-derived models are being used more frequently as they are more faithfully representing the genomic features of primary tumors. However, one by one test of each model from large biobanks is extremely economy and time consuming. In this study, each of a panel of patient-derived glioblastoma stem cell (GSC) models was uniquely tagged by a lentiviral Cas9D10A and paired-gRNA targetable unique reporter (CAPTURE) barcoding system. Barcoded GSCs were then pooled evenly and following by radiation treatment (RT) in vitro. Amplicon sequencing was employed to count the barcodes distribution, which represent the relative cell number. The results showed that this approach faithfully identified the RT resistant GSCs from a mixing pool when comparing to the results from canonical clonogenic assay. In addition, a fluorescence marker will be switched by delivery of corresponding barcodes targeting CRISPR so that we can re-isolate interested cell models from the treated pool for investigating the treatment sensitivity and resistance mechanism. This study will provide a robust approach for therapeutic discovery take advantage of patient-derived models from large biobanks. Citation Format: Ze-yan Zhang, Yingwen Ding, Ravesanker Ezhilarasan, Jie Yang, Lihong Long, Lawrence Bronk, Qianghu Wang, Erik P. Sulman. High-throughput evaluation of treatment response in patient-derived glioma stem cell models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1917.

Over recent years, constraint-based modelling of metabolic networks has become increasingly popular; the models are suitable for system-level modelling of cell physiology. The goal of the present work was to reconstruct a constraint-based metabolic network model of bone marrow-derived mesenchymal stem cells (BMMSCs). To reconstruct a BMMSC-specific metabolic model, transcriptomic data of BMMSCs, and additionally, the human generic metabolic network model (Recon1) were used. Then, using the mCADRE algorithm, a draft metabolic network was reconstructed. Literature and proteomic data were subsequently used to refine and improve the draft. From this, iMSC1255 was derived to be the metabolic network model of BMMSCs. iMSC1255 has 1255 genes, 1850 metabolites and 2288 reactions. After including additional constraints based on previously reported experimental results, our model successfully predicted BMMSC growth rate and metabolic phenotypes. Here, iMSC1255 is introduced to be the metabolic network model of bone marrow-derived mesenchymal stem cells. Based on current knowledge, this is the first report on genome-scale reconstruction and validation of a stem cell metabolic network model.

Epithelial stem cells are regulated through a complex interplay of signals from diffusible ligands, cellular interactions, and attachment to the extracellular matrix. The development of Drosophila models of epithelial stem cells and their associated niche has made it possible to dissect the contribution of each of these factors in vivo, during both basal homeostasis and in response to acute damage such as infection. Studies of Drosophila epithelial stem cells have also provided insight into the mechanisms by which a healthy population of stem cells are maintained throughout adulthood by demonstrating, for example, that stem cells have a finite lifespan and may be displaced by replacement cells competing for niche occupancy. Here, we summarize the literature on each of the known Drosophila epithelial stem cells, with a focus on the two most well-characterized types, the follicle stem cells (FSCs) in the ovary and the intestinal stem cells (ISCs) in the posterior midgut. Several themes have emerged from these studies, which suggest that there may be a common set of features among niches in a variety of epithelia. For example, unlike the simpler Drosophila germline stem cell niches, both the FSC and ISC niches produce multiple, partially redundant, niche signals, some of which activate pathways such as Wnt/Wingless, Hedgehog, and epidermal growth factor (EGF) that also regulate mammalian epithelial tissue renewal. Further study into these relatively new stem cell models will be of use in understanding both the specifics of epithelial regeneration and the diversity of mechanisms that regulate adult stem cells in general.

Tissue turnover, regeneration, and repair take place throughout life. Stem cells are key players in these processes. The characteristics and niches of the stem cell populations in different tissues, and even in related tissues, vary extensively. In this review, stem cell differentiation and stem cell contribution to tissue maintenance and regeneration is compared in the epithelia of the skin, the cornea, the lung, and the intestine. A hierarchical model for adult stem cells is proposed, based on the potency of stem cell subpopulations in a specific tissue. The potency is defined in terms of the maintenance, the repair, and the regeneration of the tissue. The niche supplies cues to maintain the specific stem cell potency.

Stem cells are fundamental to tissue maintenance and repair; they also play a critical role in cancer development and in determining the outcomes of cancer treatment. This review explores recent mathematical and computational models that address stem cell dynamics in the context of normal tissue regulation and cancer. Quantitative approaches have yielded significant insight into the processes of tissue regulation in normal hierarchically organized tissues. Modeling of cancer stem cells has also illuminated important mechanisms involved in cancer initiation and progression. In particular, mathematical studies have been instrumental to our current understanding of the role of stem cells in cancer therapy, resistance, and relapse. The use of quantitative methods to understand stem cell behavior has greatly expanded in recent years. In the future, mathematics will be an increasingly important and necessary tool necessary to fully unravel the complexity of stem cell dynamics.

In vitro investigations of host-virus interactions are reliant on suitable cell and tissue culture models. Results are only as good as the model they are generated in. However, choosing cell models for in vitro work often depends on availability and previous use alone. Despite the vast increase in coronavirus research over the past few years, scientists are still heavily reliant on: non-human, highly heterogeneous or not fully differentiated, or naturally unsusceptible cells requiring overexpression of receptors and other accessory factors. Complex primary or stem cell models are highly representative of human tissues but are expensive and time-consuming to develop and maintain with limited suitability for high-throughput experiments.Using tissue-specific expression patterns, we identified human kidney cells as an ideal target for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and broader coronavirus infection. We show the use of the well-characterized human kidney cell line Caki-1 for infection with three human coronaviruses (hCoVs): Betacoronaviruses SARS-CoV-2 and Middle Eastern respiratory syndrome coronavirus and Alphacoronavirus hCoV 229E. Caki-1 cells show equal or superior susceptibility to all three coronaviruses when compared to other commonly used cell lines for the cultivation of the respective virus. Antibody staining against SARS-CoV-2 N protein shows comparable replication rates. A panel of 26 custom antibodies shows the location of SARS-CoV-2 proteins during replication using immunocytochemistry. In addition, Caki-1 cells were found to be susceptible to two other human respiratory viruses, influenza A virus and respiratory syncytial virus, making them an ideal model for cross-comparison for a broad range of respiratory viruses. IMPORTANCE Cell lines remain the backbone of virus research, but results are only as good as their originating model. Despite increased research into human coronaviruses following the COVID-19 pandemic, researchers continue to rely on suboptimal cell line models of: non-human origin, incomplete differentiation, or lacking active interferon responses. We identified the human kidney Caki-1 cell line as a potential target for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). This cell line could be shown to be infectable with a wide range of coronaviruses including common cold virus hCoV-229E, epidemic virus MERS-CoV, and SARS-CoV-2 as well as other important respiratory viruses influenza A virus and respiratory syncytial virus. We could show the localization of 26 SARS-CoV-2 proteins in Caki-1 cells during natural replication and the cells are competent of forming a cellular immune response. Together, this makes Caki-1 cells a unique tool for cross-virus comparison in one cell line.

Contributions of Mouse and Human Hematopoietic Cells to Remodeling of the Adult Auditory Nerve After Neuron Loss.