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Conditionally Reprogrammed Human Normal Airway Epithelial cells at ALI: A Physiological Model for Emerging Viruses

Virologica Sinica 2020年第3期35卷 280-289页

作者： Xuefeng Liu Yuntao Wu Lijun Rong Department of Pathology Center for Cell ReprogrammingGeorgetown University Medical CenterWashingtonDCUSA Department of Oncology Lombardi Comprehensive Cancer CenterGeorgetown University Medical CenterWashingtonDCUSA National Center for Biodefense and Infectious Diseases School of Systems BiologyGeorge Mason UniversityManassasVA 20110USA Department of Microbiology and Immunology University of Illinoi at ChicagoChicagoIL 60612USA

Cancer cell lines have been used widely in cancer biology, and as biological or functional cell systems in many biomedical research fields. These cells are usually defective for many normal activities or functions due to significant genetic and epigenetic changes. Normal primary cell yields and viability from any original tissue specimens are usually relatively low or highly variable. These normal cells cease after a few passages or population doublings due to very limited proliferative capacity. Animal models(ferret, mouse, etc.) are often used to study virus-host interaction. However, viruses usually need to be adapted to the animals by several passages due to tropism restrictions including viral receptors and intracellular restrictions. Here we summarize applications of conditionally reprogrammed cells(CRCs), long-term cultures of normal airway epithelial cells from human nose to lung generated by conditional cell reprogramming(CR) technology, as an ex vivo model in studies of emerging viruses. CR allows to robustly propagate cells from non-invasive or minimally invasive specimens, for example, nasal or endobronchial brushing. This process is rapid(2 days) and conditional. The CRCs maintain their differentiation potential and lineage functions, and have been used for studies of adenovirus, rhinovirus, respiratory syncytial virus, influenza viruses, parvovirus, and SARS-CoV. The CRCs can be easily used for airliquid interface(ALI) polarized 3 D cultures, and these coupled CRC/ALI cultures mimic physiological conditions and are suitable for studies of viral entry including receptor binding and internalization, innate immune responses, viral replications, and drug discovery as an ex vivo model for emerging viruses.

关键词： Normal cells cell senescence Conditional reprogramming Physiological conditions Functional models Air-liquid interface(ALI) Emerging viruses SARS-CoVs

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Label-free incoherent super-resolution optical microscopy

arXiv

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arXiv 2023年

作者： Jayakumar, Nikhil Villegas-Hernández, Luis E. Zhao, Weisong Mao, Hong Dullo, Firehun T. Tinguely, Jean-Claude Sagini, Krizia Llorente, Alicia Ahluwalia, Balpreet Singh Department of Physics and Technology UiT The Arctic University of Norway Tromsø9037 Norway Innovation Photonics and Imaging Center School of Instrumentation Science and Engineering Harbin Institute of Technology Harbin China Department of Microsystems and Nanotechnology SINTEF Digital Gaustadalleen 23C Oslo0373 Norway Department of Molecular Cell Biology Institute for Cancer Research Oslo University Hospital The Norwegian Radium Hospital Oslo0379 Norway Centre for Cancer Cell Reprogramming Faculty of Medicine University of Oslo Montebello Oslo0379 Norway Department for Mechanical Electronics and Chemical Engineering Oslo Metropolitan University Oslo Norway Department of Clinical Science Intervention and Technology Karolinska Institute Sweden

The photo-kinetics of fluorescent molecules have enabled the circumvention of far-field optical diffraction-limit. Despite its enormous potential, the necessity to label the sample may adversely influence the delicate biology under investigation. Thus, continued development efforts are needed to surpass the far-field labelfree diffraction barrier. The coherence of the detected light in label-free mode hinders the application of existing super-resolution methods based on incoherent fluorescence imaging. In this article, we present the physics and propose a methodology to circumvent this challenge by exploiting the photoluminescence of silicon nitride waveguides for near-field illumination of unlabeled samples. The technique is abbreviated EPSLON, Evanescently decaying Photoluminescence Scattering enables Label-free Optical Nanoscopy. We demonstrate that such an illumination has properties that mimic the photo-kinetics of nano-sized fluorescent molecules. This allows for developing a label-free incoherent system that is linear in intensity, and stable with time thereby permitting the application of techniques like structured illumination microscopy (SIM) and intensity-fluctuation-based optical nanoscopy (IFON) in label-free mode to circumvent the diffraction limit. We experimentally demonstrate labelfree super-resolution imaging of nanobeads (polystyrene and gold), extra-cellular vesicles, rat kidney sections, human kidney sections and human placenta tissue. In this proof-of-concept work, two-point resolution of ~180 nm on nanobeads, ~133 nm mean Fourier Ring Correlation (FRC) resolution (~1.92 times resolution gain) on rat kidney tissue sections, ~129 nm mean FRC resolution on human kidney tissue sections (~2.8 times resolution gain) and ~176 nm mean FRC resolution on human placenta tissue (~2.8 times resolution gain) is demonstrated. We believe EPSLON is a step forward within the field of incoherent far-field label-free super-resolution microscopy that holds a key t

关键词： Silicon nitride

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Peroxisomal core structures segregate diverse metabolic pathways

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Nature Communications 2025年第1期16卷 1-16页

作者： Bäcker, Nils Ast, Julia Martorana, Domenica Renicke, Christian Berger, Jil Mais, Cristopher-Nils Christ, Marvin Stehlik, Thorsten Heimerl, Thomas Wernet, Valentin Taxis, Christof Pané-Farré, Jan Bölker, Michael Klatt, Judith M. Sandrock, Björn Schink, Kay Oliver Bange, Gert Freitag, Johannes Center for Synthetic Microbiology (SYNMIKRO) Philipps-University Marburg Marburg Germany Department of Biology Philipps-University Marburg Marburg Germany Department of Genetics Stanford University School of Medicine Stanford CA United States Department of Chemistry Philipps-University Marburg Marburg Germany Department of Microbiology Institute for Applied Biosciences KIT Karlsruhe Germany Health and Medical University Erfurt Erfurt Germany Microcosm Earth Center Philipps-University Marburg & Max-Planck-Institute for terrestrial Microbiology Marburg Germany Centre for Cancer Cell Reprogramming Faculty of Medicine University of Oslo Montebello Oslo Norway Department of Molecular Cell Biology Institute for Cancer Research Oslo University Hospital Montebello Oslo Norway Department of Molecular Medicine Institute of Basic Medical Sciences Faculty of Medicine University of Oslo Oslo Norway Max-Planck-Institute for terrestrial Microbiology Molecular Physiology of Microbes Marburg Germany

Peroxisomes are single membrane-bounded oxidative organelles with various metabolic functions including β-oxidation of fatty acids. Peroxisomes of many species confine certain metabolic enzymes into sub-compartments sometimes visible as electron dense cores. Why these structures form is largely unknown. Here, we report that in the smut fungus Ustilago maydis detergent resistant core structures are enriched for different enzymes excluding several key enzymes of the β-oxidation pathway. This confinement contributes to generation of peroxisome subpopulations that differ in their enzyme content. We identify short amino acid motifs necessary and sufficient for protein self-assembly into aggregates in vitro. The motifs trigger enrichment in cores in vivo and are active in mammalian cells. Perturbation of core assembly via variation of such motifs affects peroxisome function in U. maydis strains challenged with fatty acids. Thus, protein core structures serve to compartmentalize the lumen of peroxisomes thereby preventing interference of biochemical reactions. Metabolic compartmentalization of peroxisomes via assembly of specific proteins may occur in other organisms as well. © The Author(s) 2025.

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Advances in lacrimal gland organoid development: Techniques and therapeutic applications

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Biomedicine and Pharmacotherapy 2025年 183卷 117870-117870页

作者： Abdal Dayem, Ahmed Bin Jang, Soo Lim, Nahee Yeo, Han Cheol Kwak, Yeonjoo Lee, Shin-Hyo Shin, Hyun Jin Cho, Sang-Goo Department of Stem Cell and Regenerative Biotechnology School of Advanced Biotechnology Molecular & Cellular Reprogramming Center Institute of Advanced Regenerative Science and Institute of Health Aging & Society Konkuk University 120 Neungdong-ro Gwangjin-gu Seoul 05029 South Korea Department of Anatomy Wonkwang University School of Medicine Iksan South Korea Jesaeng-Euise Clinical Anatomy Center Wonkwang University School of Medicine Iksan South Korea Konkuk University School of Medicine Chungju city South Korea Department of Ophthalmology Konkuk University Medical Center Seoul South Korea Research Institute of Medical Science Konkuk University School of Medicine Seoul South Korea Institute of Biomedical Science & Technology Konkuk University Seoul South Korea R&D Team StemExOne Co. Ltd Seoul South Korea

The human lacrimal gland (LG), located above the outer orbital region within the frontal bone socket, is essential in maintaining eye surface health and lubrication. It is firmly anchored to the orbital periosteum by the connective tissue, and it is vital for protecting and lubricating the eye by secreting lacrimal fluid. Disruption in the production, composition, or secretion of lacrimal fluid can lead to dry eye syndrome, a condition characterized by ocular discomfort and potential eye surface damage. This review explores the recent advancements in LG organoid generation using tissues and stem cells, highlighting cutting-edge techniques in biomaterial-based and scaffold-free technologies. Additionally, we shed light on the complex pathophysiology of LG dysfunction, providing insights into the LG physiological roles while identifying strategies for generating LG organoids and exploring their potential clinical applications. Alterations in LG morphology or secretory function can affect the tear film stability and quality, leading to various ocular pathological conditions. This comprehensive review underlines the critical crosslink of LG organoid development with disease modeling and drug screening, underscoring their potential for advancing therapeutic applications. © 2025

关键词： Lacrimal gland Organoids Regeneration Stem cells

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Role of the NLRP3 inflammasome in myocarditis induced by immune checkpoint inhibitors cancer immunotherapy

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Archives of Cardiovascular Diseases 2024年第6期117卷 S191-S191页

作者： Samantha Conte Thi Thom Tran Isaure Firoaguer Stéphanie Simoncini Stéphane Robert Claire El Yazidi Frédérique Magdinier Denis Puthier Franck Thuny Jennifer Cautela Nathalie Lalevée Équipe 5 C2VN INSERM 1263 Marseille France Équipe 3 C2VN INSERM 1263 Marseille France Plateforme AMUTICYT C2VN Marseille France Cell reprogramming and differenciation facitily Marseille Medical Genetics Marseille France U1090 TAGC Marseille France Mediterranean Center of Cardio-Oncology Aix-Marseille Université Marseille France

Introduction The inflammasome NLRP3 is involved in the inflammatory processes of several cardiac diseases. Recently, GBP5 and 6 transcripts have been found to be specifically deregulated in immune-related myocarditis, but the mechanism of action remains unclear. Cardiomyocyte dysfunction during the cardiotoxic reaction probably results from the combined action of cytokines secreted by T lymphocytes reactivated by ICIs and inflammatory molecules released by endocardial and vascular endothelial cells. Our hypothesis is that cardiac dysfunction in immune-mediated myocarditis is linked to activation of the NLRP3 inflammasome in cardiac cells in this inflammatory context. Objective Our aim is to unravel the regulatory mechanisms of the NLRP3 inflammasome in response to cytokines known to be secreted during ICI-related myocarditis, and to characterise the role of paracrine effects of endothelial cells in cardiomyocyte dysfunction. Method hiPSC-derived cardiomyocytes (hiPSC-CM) and endothelial cells (hiPSC-EC) were stimulated by different inflammatory cytokines (IFN-γ, RANTES, Granzyme B and IL-1β). We studied several groups: healthy individual (1 clone from 1 individual), melanoma patients who reported immuno-mediated myocarditis (13 clones from 5 patients), and melanoma patients who did not report cardiotoxicity after immunotherapy (7 clones from 3 patients). Results IFN-γ affects the viability of cardiac cells by activating the JAK/STAT inflammatory pathway, and by overexpressing NLRP3 inflammasome transcripts such as nlrp3, nlrc5 and caspase-1. This effect is associated to overexpression of the MHC and PD-L1 proteins, as described in humans. IFN-γ alone did not induce significant differences between groups on these targets. We have developed a flow cytometry multiplexing protocol to characterise apoptosis associated with caspase activity, in particular NLRP3 inflammasome-associated caspase-1, metabolic deregulation and oxidative stress. The results are currently being

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OncoEnrichR: cancer-dedicated gene set interpretation

arXiv

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arXiv 2021年

作者： Nakken, Sigve Gundersen, Sveinung Bernal, Fabian L.M. Polychronopoulos, Dimitris Hovig, Eivind Wesche, Jørgen Department of Tumor Biology Institute for Cancer Research Oslo University Hospital Norway Centre for Cancer Cell Reprogramming Institute of Clinical Medicine Faculty of Medicine University of Oslo Norway Centre for Bioinformatics Department of Informatics University of Oslo Norway University Center for Information Technology University of Oslo Norway Early Data Science and Computational Oncology Research and Early Development Oncology R&D AstraZeneca Cambridge United Kingdom

Genome-scale screening experiments in cancer produce long lists of candidate genes that require extensive interpretation for biological insight and prioritization for follow-up studies. Interrogation of gene lists frequently represents a significant and time-consuming undertaking, in which experimental biologists typically combine results from a variety of bioinformatics resources in an attempt to portray and understand cancer relevance. As a means to simplify and strengthen the support for this endeavor, we have developed oncoEnrichR, a flexible bioinformatics tool that allows cancer researchers to comprehensively interrogate a given gene list along multiple facets of cancer relevance. oncoEnrichR differs from general gene set analysis frameworks through the integration of an extensive set of prior knowledge specifically relevant for cancer, including ranked gene-tumor type associations, literature-supported proto-oncogene and tumor suppressor gene annotations, target druggability data, regulatory interactions, synthetic lethality predictions, as well as prognostic associations, gene aberrations, and co-expression patterns across tumor types. The software produces a structured and user-friendly analysis report as its main output, where versions of all underlying data resources are explicitly logged, the latter being a critical component for reproducible science. We demonstrate the usefulness of oncoEnrichR through interrogation of two candidate lists from proteomic and CRISPR screens. oncoEnrichR is freely available as a web-based workflow hosted by the Galaxy platform (https://***), and can also be accessed as a stand-alone R package (https://***/sigven/oncoEnrichR). © 2021, CC BY-NC-SA.

关键词： Tumors

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Corrigendum to "Advances in lacrimal gland organoid development: Techniques and therapeutic applications" [Biomed. Pharmacother. 183 (2025) 117870]

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Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie 2025年 184卷 117888页

作者： Ahmed Abdal Dayem Soo Bin Jang Nahee Lim Han Cheol Yeo Yeonjoo Kwak Shin-Hyo Lee Hyun Jin Shin Ssang-Goo Cho Department of Stem Cell and Regenerative Biotechnology School of Advanced Biotechnology Molecular & Cellular Reprogramming Center Institute of Advanced Regenerative Science and Institute of Health Aging & Society Konkuk University 120 Neungdong-ro Gwangjin-gu Seoul 05029 Republic of Korea. Department of Anatomy Wonkwang University School of Medicine Iksan Republic of Korea Jesaeng-Euise Clinical Anatomy Center Wonkwang University School of Medicine Iksan Republic of Korea. Konkuk University School of Medicine Chungju city Republic of Korea Department of Ophthalmology Konkuk University Medical Center Seoul Republic of Korea Research Institute of Medical Science Konkuk University School of Medicine Seoul Republic of Korea Institute of Biomedical Science & Technology Konkuk University Seoul Republic of Korea. Department of Stem Cell and Regenerative Biotechnology School of Advanced Biotechnology Molecular & Cellular Reprogramming Center Institute of Advanced Regenerative Science and Institute of Health Aging & Society Konkuk University 120 Neungdong-ro Gwangjin-gu Seoul 05029 Republic of Korea R&D Team StemExOne Co. Ltd. Seoul Republic of Korea. Electronic address: ssangoo@konkuk.ac.kr.

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Cardiotoxicity is mediated by the NLRP3 inflammasome in hiPSC-derived endothelial cells from patients with immune checkpoint inhibitor-related myocarditis

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Archives of Cardiovascular Diseases Supplements 2023年第2期15卷 212-212页

作者： Samantha Conte Thi Thom Tran Stéphane Robert Claire El Yazidi Frédérique Magdinier Denis Puthier Franck Thuny Jennifer Cautela Nathalie Lalevée Équipe 5 C2VN Inserm 1263 Marseille France Institut MarMaRa Aix-Marseille université Marseille France Plateforme AMUTICYT C2VN Marseille France Cell reprogramming and differenciation facitily Marseille Medical Genetics Marseille France Umr 1090 TAGC Marseille France University Mediterranean Center of Cardio-Oncology Aix-Marseille université Marseille France

Introduction In association with immune checkpoint inhibitors (ICI) anticancer therapy , myocarditis (ICI-M), have emerged with a mortality rate reaching 50%. The IFN-γ pathway and inflammasome regulatory proteins seem to be specifically involved in ICI-M, but the mechanism of action remains unclear. In the cardiovascular system, the endocardial and vascular endothelium is involved in the regulation of the contractile function of cardiomyocytes . Our hypothesis is that the cardiotoxicity induced by the infiltration of immune cells into the myocardium is partly due to an exacerbation of inflammasome activation in endothelial cells , which subsequently affects the cardiomyocytes function. Objective Our aim is to characterize the role of endothelial cells in ICI-related myocarditis in a unique model of induced pluripotent stem cells (hiPSC)-derived cardiac cells. Method The hiPSC were generated from melanoma patients who received anti-PD-1/anti-CTLA-4 immunotherapy and followed at the Cardio-Oncology Centre (North Hospital , Marseille). Twelve hiPSC clones were generated from patients who developed myocarditis (ICI-M, 6 clones from 3 patients), and patients who did not develop cardiotoxicity (non-ICI-M, 6 clones from 3 patients). hiPSC-derived endothelial cells (hiPSC-EC) were differentiated from hiPSC clones and stimulated by 10 ng/mL of IFN-γ during 48 h. Results IFN-γ induced a decrease in cell viability , as well as an increase in the expression of transcripts of genes associated with the JAK/STAT and NLRP3 inflammasome pathways in hiPSC-EC. However, the decrease in cell viability was significantly greater in hiPSC-EC from the ICI-M group compared to the non-ICI-M group. IFN-γ activation of inflammatory intracellular signalling is greater in the ICI-M group, in particular overexpression of the jak1, jak2, stat3 and gbp6 transcripts. At the protein level, in this ICI-M group, the IFN-γ-induced increase of MHC-I and PD-L1 is greater than in the non-ICI-M group. C

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Orchestrating stem cell fate: Novel tools for regenerative medicine

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World Journal of Stem cells 2019年第8期11卷 464-475页

作者： Sara Cruciani Sara Santaniello Andrea Montella Carlo Ventura Margherita Maioli Department of Biomedical Sciences University of Sassari Sassari 07100 Italy Laboratory of Molecular Biology and Stem Cell Engineering National Institute of Biostructures and Biosystems – Eldor Lab Innovation Accelerator Consiglio Nazionale delle Ricerche Bologna 40129 Italy Operative Unit of Clinical Genetics and Developmental Biology Sassari 07100 Italy Istituto di Ricerca Genetica e Biomedica Consiglio Nazionale delle Ricerche Cagliari 09042 Italy Center for Developmental Biology and Reprogramming-CEDEBIOR Department of Biomedical Sciences University of Sassari Sassari 07100 Italy

Mesenchymal stem cells are undifferentiated cells able to acquire different phenotypes under specific stimuli. In vitro manipulation of these cells is focused on understanding stem cell behavior, proliferation and pluripotency. Latest advances in the field of stem cells concern epigenetics and its role in maintaining self-renewal and differentiation capabilities. Chemical and physical stimuli can modulate cell commitment, acting on gene expression of Oct-4, Sox-2 and Nanog, the main stemness markers, and tissue-lineage specific genes. This activation or repression is related to the activity of chromatin-remodeling factors and epigenetic regulators, new targets of many cell therapies. The aim of this review is to afford a view of the current state of in vitro and in vivo stem cell applications, highlighting the strategies used to influence stem cell commitment for current and future cell therapies. Identifying the molecular mechanisms controlling stem cell fate could open up novel strategies for tissue repairing processes and other clinical applications.

关键词： Stem cells Epigenetics Self-renewal In vitro differentiation Physical stimuli Stem cell fate Clinical practice cell transplantation

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Cover Image, Volume 92, Number 11, November 2020

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Journal of Medical Virology 2020年第11期92卷

作者： Xuefeng Liu Abdul M. Mondal Department of Pathology Center for Cell Reprogramming Georgetown University Medical Center Washington DC Department of Oncology Lombardi Comprehensive Cancer Center Georgetown University Medical Center Washington DC

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