Cell Biology Research Research Articles

Applications of Flow Cytometry in Drug Discovery and Translational Research.

Flow cytometry is a mainstay technique in cell biology research, where it is used for phenotypic analysis of mixed cell populations. Quantitative approaches have unlocked a deeper value of flow cytometry in drug discovery research. As the number of drug modalities and druggable mechanisms increases, there is an increasing drive to identify meaningful biomarkers, evaluate the relationship between pharmacokinetics and pharmacodynamics (PK/PD), and translate these insights into the evaluation of patients enrolled in early clinical trials. In this review, we discuss emerging roles for flow cytometry in the translational setting that supports the transition and evaluation of novel compounds in the clinic.

More than just Alkene Construction – Re‐using Wittig Reactions/Reagents in Biomacromolecular Labeling, Imaging, Sequencing and Modification

AbstractClassical organic chemical reactions are essential for modern synthetic chemistry and offer valuable insights for chemical biology research. The pioneering bioorthogonal chemistry, based on the Staudinger reaction, is a prime example. However, the biocompatibility of classic “name” reactions like the Wittig reaction is still not fully explored. This versatile reaction efficiently converts carbonyl groups into olefins using phosphorus ylides, making it valuable in synthetic chemistry. Despite being in the early stages of development, the Wittig reaction and its reagents have various applications in peptide, protein, DNA, and RNA research. However, they have limitations such as low activity and efficiency, requiring organic solvents. Future directions may include developing Wittig reagents with improved biostability, simplifying the method, and creating multi‐labeling methods. Improving light‐activated Wittig reactions and interdisciplinary integration can further advance bioorthogonal chemistry. As technology advances, the Wittig reaction is poised to make greater contributions to molecular biology, cell biology, and biochemical modification research.

High biocompatible FITC-conjugated silica nanoparticles for cell labeling in both in vitro and in vivo models

Fluorescence nanosilica-based cell tracker has been explored and applied in cell biological research. However, the aggregation of these nanoparticles at physiological pH is still the main limitation. In this research, we introduced a novel fluorescence nano-based cell tracker suitable for application in live cells. The silica-coated fluorescein isothiocyanate isomer (FITC-SiO2) nanoparticles (NPs) were modified with carboxymethylsilanetriol disodium salt (FITC-SiO2-COOH), integrating the dianion form of FITC molecules. This nanosystem exhibited superior dispersion in aqueous solutions and effectively mitigated dye leakage. These labeled NPs displayed notable biocompatibility and minimal cytotoxicity in both in vitro and in vivo conditions. Significantly, the NPs did not have negative implications on cell migration or angiogenesis. They successfully penetrated primary fibroblasts, human umbilical vein endothelial cells and HeLa cells in both 2D and 3D cultures, with the fluorescence signal enduring for over 72 h. Furthermore, the NP signals were consistently observed in the developing gastrointestinal tract of live medaka fish larvae for extended periods during phases of subdued digestive activity, without manifesting any apparent acute toxicity. These results underscore the promising utility of FITC-SiO2-COOH NPs as advanced live cell trackers in biological research.

Mesenchyme instructs growth while epithelium directs branching in the mouse mammary gland.

The mammary gland is a unique organ that undergoes dynamic alterations throughout a female's reproductive life, making it an ideal model for developmental, stem cell and cancer biology research. Mammary gland development begins in utero and proceeds via a quiescent bud stage before the initial outgrowth and subsequent branching morphogenesis. How mammary epithelial cells transit from quiescence to an actively proliferating and branching tissue during embryogenesis and, importantly, how the branch pattern is determined remain largely unknown. Here, we provide evidence indicating that epithelial cell proliferation and onset of branching are independent processes, yet partially coordinated by the Eda signaling pathway. Through heterotypic and heterochronic epithelial-mesenchymal recombination experiments between mouse mammary and salivary gland tissues and ex vivo live imaging, we demonstrate that unlike previously concluded, the mode of branching is an intrinsic property of the mammary epithelium whereas the pace of growth and the density of ductal tree are determined by the mesenchyme. Transcriptomic profiling and ex vivo and in vivo functional studies in mice disclose that mesenchymal Wnt/ß-catenin signaling, and in particular IGF-1 downstream of it critically regulate mammary gland growth. These results underscore the general need to carefully deconstruct the different developmental processes producing branched organs.

Single-Nucleotide-Specific Lipidic Nanoflares for Precise and Visible Detection of KRAS Mutations via Toehold-Initiated Self-Priming DNA Polymerization.

Accurate identification of single-nucleotide mutations in circulating tumor DNA (ctDNA) is critical for cancer surveillance and cell biology research. However, achieving precise and sensitive detection of ctDNAs in complex physiological environments remains challenging due to their low expression and interference from numerous homologous species. This study introduces single-nucleotide-specific lipidic nanoflares designed for the precise and visible detection of ctDNA via toehold-initiated self-priming DNA polymerization (TPP). This system can be assembled from only a single cholesterol-conjugated multifunctional molecular beacon (MMB) via hydrophobicity-mediated aggregation. This results in a compact, high-density, and nick-hidden arrangement of MMBs on the surface of lipidic micelles, thereby enhancing their biostability and localized concentrations. The assay commences with the binding of frequently mutated regions of ctDNA to the MMB toehold domain. This domain is the proximal holding point for initiating the TPP-based strand-displacement reaction, which is the key step in enabling the discrimination of single-base mutations. We successfully detected a single-base mutation in ctDNA (KRAS G12D) in its wild-type gene (KRAS WT), which is one of the most frequently mutated ctDNAs. Notably, coexisting homologous species did not interfere with signal transduction, and small differences in these variations can be visualized by fluorescence imaging. The limit of detection was as low as 10 amol, with the system functioning well in physiological media. In particular, this system allowed us to resolve genetic mutations in the KRAS gene in colorectal cancer, suggesting its high potential in clinical diagnosis and personalized medicine.

"Bioelectricity in Development, Regeneration, and Cancers" Cell Bio 2023: A Joint Meeting of the American Society of Cell Biology and European Molecular Biology Organization December 2-6, 2023, in Boston, MA, USA.

Cell Bio conferences-organized jointly by the American Society of Cell Biology (ASCB) and European Molecular Biology Organization (EMBO)-showcase a diverse global community of the brightest researchers in Cell Biology and in emerging interdisciplinary topics, including bioelectricity. In this report, we briefly overview the Cell Bio 2023 subgroup meeting "Bioelectricity in Development, Regeneration, and Cancers." This subgroup meeting featured 12 talks (7 Principal Investigators and 5 junior scientists) exploring the role of bioelectricity in endogenous and diseased states in model systems ranging from cells in culture to single-cell organisms such as yeast all the way to mammalian systems (including tools and technology developed for exploring bioelectricity and electrotaxis in cells and tissues). The subgroup meeting concluded with a discussion on the current challenges and opportunities for the field of bioelectricity.

[Therapeutics in cystic fibrosis: Clinical revolution and new challenges].

Over time, cystic fibrosis has become a model of synergy between research in pathophysiology and cell biology, and clinical advances. Therapies targeting the CFTR protein, in particular CFTR modulators, have transformed the prognosis of patients, bringing the hope of a normal life with the possibility of starting a family and growing old, challenging established statistics. However, patients are not yet cured, and side effects remain insufficiently documented. Epidemiological changes create new challenges for the management of cystic fibrosis. Approximately 10 % of patients still lack a therapeutic option. The community of researchers, pharmaceutical industries, patient associations, and health authorities remains committed to monitor the long-term effects of these still poorly characterised treatments, and to explore new pharmacological approaches, such as gene therapies.

Xylella fastidiosa en Costa Rica: Impacto económico, relevancia agrícola y una visión general de la investigación nacional

Xylella fastidiosa is a phytopathogenic bacterium considered a quarantine pest in crops of agricultural importance. It is associated with various diseases in crops such as: coffee, citrus, grapes, olive and ornamental species. This bacterium has negative repercussions on the export market of Costa Rica, due to phytosanitary restrictions imposed especially on the phoenix palm (Phoenix spp.). In addition, its high dispersion capacity, the existence of genetic variants and its interaction with other microorganisms make X. fastidiosa a bacterium of interest to agriculture. Currently, different research efforts are being conducted to expand the understanding about X. fastidiosa and involve the general population in the subject. This article describes the economic and social impact of X. fastidiosa on national agricultural production. Information was collected through a bibliographic review and was complemented by contributions from professionals from the Center for Cell and Molecular Biology Research (CIBCM) who currently lead research on the subject.

Enzyme-immobilized nanoclay hydrogel simultaneously reduces inflammation and scar deposition to treat spinal cord injury

Spinal cord injury (SCI) is a severely disabling pathological condition and always results in sensory and motor functions loss. After SCI, inflammation-mediated secondary tissue damage and subsequent formation of neuroglial scar suppress neuron survival and regeneration, therefore resulting in severe neurofunctional dysfunction. Although nanoclay biomaterials demonstrated useful immunomodulation feature in non-neuronal tissue, it is unclear if they can inhibit inflammation in SCI lesions and promote neurofunctional recovery. In this study, we immobilized chondroitinase ABC enzyme (ChABC), which can degrade chondroitin sulfate proteoglycans (CSPGs) of neuroglial scar, inside nanoclay (Laponite®, Lap) hydrogel through electrostatic interaction. The presented ChABC-immobilized Lap hydrogel (ChABC@Lap) exhibited shear-thinning properties and excellent injectability, allowing to locally deliver it into injured area through a non-invasive manner. Cell biological experiments and SCI rat model research revealed that both pure Lap (without ChABC) and ChABC@Lap hydrogels significantly reduced pro-inflammatory macrophage marker (iNOS) intensity. Importantly, compared with Lap hydrogel, ChABC@Lap hydrogel significantly decreased GFAP and CS-56 marked scar deposition, increased Tuj-1+ neurons regeneration, and promoted NF200+ neurons survival, thereby improving SCI rat of electrophysiological characteristics and motor function. In summary, the designed enzyme-immobilized nanoclay hydrogel offers a promising strategy for SCI therapy through modulating simultaneously inflammation and glial scar deposition.

Facilitating long-term cell examinations and time-lapse recordings in cell biology research with CO2 mini-incubators

In recent years, microscopy has revolutionized the study of dynamic living cells. However, performing long-term live cell imaging requires stable environmental conditions such as temperature, pH, and humidity. While standard incubators have traditionally provided these conditions, other solutions, like stagetop incubators are available. To further enhance the accessibility of stable cell culture environments for live cell imaging, we developed a portable CO2 cell culture mini-incubator that can be easily adapted to any x–y inverted microscope stage, enabling long-term live cell imaging. This mini-incubator provides and maintains stable environmental conditions and supports cell viability comparable to standard incubators. Moreover, it allows for parallel experiments in the same environment, saving both time and resources. To demonstrate its functionality, different cell lines (VERO and MDA-MB-231) were cultured and evaluated using various assays, including crystal violet staining, MTT, and flow cytometry tests to assess cell adhesion, viability, and apoptosis, respectively. Time-lapse imaging was performed over an 85-h period with MDA-MB-231 cells cultured in the mini-incubator. The results indicate that this device is a viable solution for long-term imaging and can be applied in developmental biology, cell biology, and cancer biology research where long-term time-lapse recording is required.

Electroactive 4D Porous Scaffold Based on Conducting Polymer as a Responsive and Dynamic In Vitro Cell Culture Platform.

In vivo, cells reside in a 3D porous and dynamic microenvironment. It provides biochemical and biophysical cues that regulate cell behavior in physiological and pathological processes. In the context of fundamental cell biology research, tissue engineering, and cell-based drug screening systems, a challenge is to develop relevant in vitro models that could integrate the dynamic properties of the cell microenvironment. Taking advantage of the promising high internal phase emulsion templating, we here designed a polyHIPE scaffold with a wide interconnected porosity and functionalized its internal 3D surface with a thin layer of electroactive conducting polymer poly(3,4-ethylenedioxythiophene) (PEDOT) to turn it into a 4D electroresponsive scaffold. The resulting scaffold was cytocompatible with fibroblasts, supported cellular infiltration, and hosted cells, which display a 3D spreading morphology. It demonstrated robust actuation in ion- and protein-rich complex culture media, and its electroresponsiveness was not altered by fibroblast colonization. Thanks to customized electrochemical stimulation setups, the electromechanical response of the polyHIPE/PEDOT scaffolds was characterized in situ under a confocal microscope and showed 10% reversible volume variations. Finally, the setups were used to monitor in real time and in situ fibroblasts cultured into the polyHIPE/PEDOT scaffold during several cycles of electromechanical stimuli. Thus, we demonstrated the proof of concept of this tunable scaffold as a tool for future 4D cell culture and mechanobiology studies.

A Century Journey of Organelles Research in the Plant Endomembrane System.

We are entering an exciting century in the study of the plant organelles in the endomembrane system. Over the past century, especially within the past 50 years, tremendous advancements have been made in the complex plant cell to generate a much clearer and informative picture of plant organelles, including the molecular/morphological features, dynamic/spatial behavior, and physiological functions. Importantly, all these discoveries and achievements in the identification and characterization of organelles in the endomembrane system would not have been possible without: 1) the innovations and timely applications of various state-of-art cell biology tools and technologies for organelle biology research, 2) the continuous efforts in developing and characterizing new organelle markers by the plant biology community; and 3) the landmark studies on the identification and characterization of the elusive organelles. While molecular aspects and results for individual organelles have been extensively reviewed, the development of the techniques for organelle research in plant cell biology is less appreciated. As one of the ASPB Centennial Reviews on "organelle biology", here we aim to take a journey across a century of organelle biology research in plants by highlighting the important tools (or landmark technologies) and key scientists that contributed to visualize organelles. We then highlight the landmark studies leading to the identification and characterization of individual organelles in the plant endomembrane systems.

Protein Isolation from 3D Hydrogel Scaffolds.

Protein isolation is an essential tool in cell biology to characterize protein abundance under various experimental conditions. Several protocols exist, tailored to cell culture or tissue sections, and have been adapted to particular downstream analyses (e.g., western blotting or mass spectrometry). An increasing trend in bioengineering and cell biology is to use three-dimensional (3D) hydrogel-based scaffolds for cell culture. In principle, the same protocols can be used to extract protein from hydrogel-based cell and tissue constructs. However, in practice the yield and quality of the recovered protein pellet is often substantially lower when using standard protocols and requires tuning of multiple steps, including the selected lysis buffer and the scaffold homogenization strategy, as well as the methods for protein purification and reconstitution. We present here specific protocols tailored to common 3D hydrogels to help researchers using hydrogel-based 3D cell culture improve the quantity and quality of their extracted protein. We focus on three materials: protease-degradable PEG-based hydrogels, collagen hydrogels, and alginate hydrogels. We discuss how the protein extraction procedure can be adapted to the scaffold of interest (degradable or non-degradable gels), proteins of interests (soluble, matrix-bound, or phosphoproteins), and downstream biochemical assays (western blotting or mass spectrometry). With the growing interest in 3D cell culture, the protocols presented should be useful to many researchers in cell biology, protein science, biomaterials, and bioengineering communities. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Isolating proteins from PEG-based hydrogels Basic Protocol 2: Isolating proteins from collagen hydrogels Basic Protocol 3: Isolating proteins from alginate hydrogels Alternate Protocol: Isolating protein from alginate gels using EDTA to dissolve the gel Support Protocol: Isolating protein and RNA simultaneously from the same samples.

3D Cell Culture: Techniques For and Beyond Organoid Applications.

In the rapidly evolving landscape of cell biology and biomedical research, three-dimensional (3D) cell culture has contributed not only to the diversification of experimental tools available but also to their improvement toward greater physiological relevance. 3D cell culture has emerged as a revolutionary technique that bridges the long-standing gap between traditional two-dimensional (2D) cell culture and the complex microenvironments found in living organisms. By providing conditions for establishing critical features of in vivo environment, such as cell-cell and cell-extracellular matrix interactions, 3D cell culture enables proper tissue-like architecture and differentiated function of cells. Since the early days of 3D cell culture in the 1970s, the field has witnessed remarkable progress, with groundbreaking discoveries, novel methodologies, and transformative applications. One particular 3D cell culture technique has caught the attention of many scientists and has experienced an unprecedented boom and enthusiastic application in both basic and translational research over the past decade - the organoid technology. This book chapter provides an introduction to the fundamental concepts of 3D cell culture including organoids, an overview of 3D cell culture techniques, and an overview of methodological- and protocol-oriented chapters in the book 3D Cell Culture.

Ultrasound-propelled nanomotors for efficient cancer cell ferroptosis.

Ferroptosis is a non-apoptotic form of cell death that is dependent on the accumulation of intracellular iron that causes elevation of toxic lipid peroxides. Therefore, it is crucial to improve the levels of intracellular iron and reactive oxygen species (ROS) in a short time. Here, we first propose ultrasound (US)-propelled Janus nanomotors (Au-FeOx/PEI/ICG, AFPI NMs) to accelerate cellular internalization and induce cancer cell ferroptosis. This nanomotor consists of a gold-iron oxide rod-like Janus nanomotor (Au-FeOx, AF NMs) and a photoactive indocyanine green (ICG) dye on the surface. It not only exhibits accelerating cellular internalization (∼4-fold) caused by its attractive US-driven propulsion but also shows good intracellular motion behavior. In addition, this Janus nanomotor shows excellent intracellular ROS generation performance due to the synergistic effect of the "Fenton or Fenton-like reaction" and the "photochemical reaction". As a result, the killing efficiency of actively moving nanomotors on cancer cells is 88% higher than that of stationary nanomotors. Unlike previous passive strategies, this work is a significant step toward accelerating cellular internalization and inducing cancer-cell ferroptosis in an active way. These novel US-propelled Janus nanomotors with strong propulsion, efficient cellular internalization and excellent ROS generation are suitable as a novel cell biology research tool.

Reversibly immortalization establishes a hair follicle stem cell line with hair follicle reconstruction ability.

Hair follicle stem cells (HFSCs) play critical roles in the periodic regeneration of hair follicles. HFSCs are also a good model for stem cell biology research. However, no stable mouse HFSC cell line has been reported, which restricts the research and application of HFSCs. We isolated HFSCs from mouse hair follicles and immortalized them by inducing a reversible SV40 large T antigen. Through monoclonal screening, we identified a reversibly immortalized cell line, immortalized HFSC (iHFSC2). RNA sequencing, fluorescence-activated cell sorting, western blotting and immunofluorescence experiments revealed that the expression patterns of iHFSC2 and HFSC were similar at the protein and mRNA levels. After that, iHFSC2s were passaged and morphologically monitored for up to 40 times to detect their long-term culture potential. The long-term cultured iHFSC2 could regenerate hair follicles with complete hair follicle structure and HFSCs in the bulge area. This work successfully established an HFSC cell line with the ability of hair follicle reconstruction.

Interview with Journal of Cell Science Editor Renata Basto

ABSTRACT Renata Basto is a Centre National de la Recherche Scientifique (CNRS) Team Leader at the Institut Curie and Deputy Director of the Cell Biology and Cancer Research Unit in Paris, France. Renata completed her undergraduate degree at the University of Lisbon, Portugal, before moving abroad to Gif-sur-Yvette, France for her doctoral studies on mitotic spindle assembly checkpoint proteins in Drosophila, mentored by Prof. Rui Gomes and Prof. Roger Karess. She then received a postdoctoral fellowship with Prof. Jordan Raff at the University of Cambridge, UK, where her work helped identify centrosome amplification as a tumour-initiating mechanism. In 2008, she joined the Department of Cell Biology at CNRS and the Institut Curie, where her laboratory studies the roles of centrosomes, and mechanisms of mitotic spindle assembly, polyploidy and genetic instability in development, health and disease. Renata joined Journal of Cell Science as an Editor in August 2023, bringing to the journal her significant expertise in the cell biology of centrosomes, spindle proteins, microtubules and mitosis. We spoke with Renata over Zoom to learn about her fascinating career, her advice for young scientists and the impact she hopes to make as an Editor.

Role of mitochondria in the regulation of ferroptosis and disease.

Ferroptosis is a distinctive form of iron-dependent cell death characterized by significant ultrastructural changes in mitochondria. Given the crucial involvement of mitochondria in various cellular processes such as reactive oxygen species production, energy metabolism, redox status, and iron metabolism, mounting evidence suggests a vital role of mitochondria in the regulation and execution of ferroptosis. Furthermore, there exists a strong correlation between ferroptosis and various diseases. In this review, we aim to summarize the mechanisms underlying the induction and defense of ferroptosis, emphasizing the influence of mitochondria on this intricate process. Additionally, we provide an overview of the role of ferroptosis in disease, particularly cancer, and elucidate the mechanisms by which drugs targeting mitochondria impact ferroptosis. By presenting a theoretical foundation and reference point, this review aims to contribute to both basic cell biology research and the investigation of clinically relevant diseases.

Microfluidic-Based Reconstitution of Functional Lymphatic Microvasculature: Elucidating the Role of Lymphatics in Health and Disease.

The knowledge of the blood microvasculature and its functional role in health and disease has grown significantly attributable to decades of research and numerous advances in cell biology and tissue engineering; however, the lymphatics (the secondary vascular system) has not garnered similar attention, in part due to a lack of relevant in vitro models that mimic its pathophysiological functions. Here, a microfluidic-based approach is adopted to achieve precise control over the biological transport of growth factors and interstitial flow that drive the in vivo growth of lymphatic capillaries (lymphangiogenesis). The engineered on-chip lymphatics with in vivo-like morphology exhibit tissue-scale functionality with drainage rates of interstitial proteins and molecules comparable to in vivo standards. Computational and scaling analyses of the underlying transport phenomena elucidate the critical role of the three-dimensionalgeometry and lymphatic endothelium in recapitulating physiological drainage. Finally, the engineered on-chip lymphatics enabled studies of lymphatic-immune interactions that revealed inflammation-driven responses by the lymphatics to recruit immune cells via chemotactic signals similar to in vivo, pathological events. This on-chip lymphatics platform permits the interrogation of various lymphatic biological functions, as well as screening of lymphatic-based therapies such as interstitial absorption of protein therapeutics and lymphatic immunomodulation for cancer therapy.

Microfluidic technology for cell biology-related applications: a review.

Fluid flow at the microscale level exhibits a unique phenomenon that can be explored to fabricate microfluidic devices integrated with components that can perform various biological functions. In this manuscript, the importance of physics for microscale fluid dynamics using microfluidic devices has been reviewed. Microfluidic devices provide new opportunities with regard to spatial and temporal control over cell growth. Furthermore, the manuscript presents an overview of cellular stimuli observed by combining surfaces that mimic the complex biochemistries and different geometries of the extracellular matrix, with microfluidic channels regulating the transport of fluids, soluble factors, etc. We have also explained the concept of mechanotransduction, which defines the relation between mechanical force and biological response. Furthermore, the manipulation of cellular microenvironments by the use of microfluidic systems has been highlighted as a useful device for basic cell biology research activities. Finally, the article focuses on highly integrated microfluidic platforms that exhibit immense potential for biomedical and pharmaceutical research as robust and portable point-of-care diagnostic devices for the assessment of clinical samples.