Cell Biology Research Research Articles

Generation of a highly specific and potent antibody against Ce-lamin/LMN-1.

High quality antibodies are useful tools for research in cell and developmental biology. We have obtained highly specific and potent guinea pig-derived polyclonal antibodies against Ce-lamin/ LMN-1 . Western blotting experiments using these antibodies demonstrated that maternally loaded Ce-lamin/ LMN-1 protein is very stable, can perdure through embryonic and larval development and remain detectable in homozygous null lmn-1 mutant adults.

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.

Establishment of the microscope incubation system and its application in evaluating tumor treatment effects through real-time live cellular imaging.

Introduction: Long-term imaging of live cells is commonly used for the study of dynamic cell behaviors. It is crucial to keep the cell viability during the investigation of physiological and biological processes by live cell imaging. Conventional incubators that providing stable temperature, carbon dioxide (CO2) concentration, and humidity are often incompatible with most imaging tools. Available commercial or custom-made stage-top incubators are bulky or unable to provide constant environmental conditions during long time culture. Methods: In this study, we reported the development of the microscope incubation system (MIS) that can be easily adapted to any inverted microscope stage. Incremental PID control algorithm was introduced to keep stable temperature and gas concentration of the system. Moreover, efficient translucent materials were applied for the top and bottom of the incubator which make it possible for images taken during culture. Results: The MIS could support cell viability comparable to standard incubators. When used in real time imaging, the MIS was able to trace single cell migration in scratch assay, T cell mediated tumor cells killing in co-culture assay, inflation-collapse and fusion of organoids in 3D culture. And the viability and drug responses of cells cultured in the MIS were able to be calculated by a label-free methods based on long term imaging. Discussion: We offer new insights into monitoring cell behaviors during long term culture by using the stage adapted MIS. This study illustrates that the newly developed MIS is a viable solution for long-term imaging during in vitro cell culture and demonstrates its potential in cell biology, cancer biology and drug discovery research where long-term real-time recording is required.

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.

Toward quantitative super-resolution microscopy: molecular maps with statistical guarantees.

Quantifying the number of molecules from fluorescence microscopy measurements is an important topic in cell biology and medical research. In this work, we present a consecutive algorithm for super-resolution (stimulated emission depletion (STED)) scanning microscopy that provides molecule counts in automatically generated image segments and offers statistical guarantees in form of asymptotic confidence intervals. To this end, we first apply a multiscale scanning procedure on STED microscopy measurements of the sample to obtain a system of significant regions, each of which contains at least one molecule with prescribed uniform probability. This system of regions will typically be highly redundant and consists of rectangular building blocks. To choose an informative but non-redundant subset of more naturally shaped regions, we hybridize our system with the result of a generic segmentation algorithm. The diameter of the segments can be of the order of the resolution of the microscope. Using multiple photon coincidence measurements of the same sample in confocal mode, we are then able to estimate the brightness and number of molecules and give uniform confidence intervals on the molecule counts for each previously constructed segment. In other words, we establish a so-called molecular map with uniform error control. The performance of the algorithm is investigated on simulated and real data.

Stretchable Sponge-Based Electrochemical Biosensor for Real-Time Sensing of Cells in Three-Dimensional Culture.

For the study of cell biology, real-time information on cell physiological processes will be more accurate and closer to the in vivo condition in a three-dimensional (3D) culture system. Although most reported 3D cell culture scaffolds can better mimic the in vivo dynamic microenvironment, the real-time analysis technique is deficient or lacking. Herein, a stretchable and conductive 3D scaffold is developed to construct an electrochemical biosensor for real-time monitoring of cell release in 3D culture under stimulation of drug stimulant and mechanical force. In our design, the polyurethane sponge (PU) dipped with conductive carbon ink (CC/PU) was used as a conductive scaffold, and gold nanoparticles (nano-Au) were electrodeposited on the CC/PU (nano-Au CC/PU) to improve the electrochemical sensing performance. The prepared nano-Au CC/PU scaffold exhibits a good electrocatalytic ability to H2O2 with a linear range from 20 nM to 43 μM. Due to the great biocompatibility, HeLa cells can be cultured directly on the nano-Au CC/PU and the in situ and real-time tracking of H2O2 secretion from cells was achieved. The results demonstrate that both the drug stimulant and mechanical force can rapidly activate the release of reactive oxygen species. This study indicates that the stretchable 3D sensing scaffold has good potential for cell biology research in an in vivo-like microenvironment and can be extensively used in the fields of tissue engineering, drug screening, and pathological research.

MMP13 promotes the osteogenic potential of BMP9 by enhancing Wnt/β-catenin signaling via HIF-1α upregulation in mouse embryonic fibroblasts.

Bone morphogenetic protein 9 (BMP9) has been validated as one of the most potent osteoinduction factors, but its underlying mechanism remains unclear. As a member of the matrix metalloproteinase (MMP) family, MMP13 may be involved in regulating the lineage-specific differentiation of mouse embryonic fibroblasts (MEFs). The goal of this study was to determine whether MMP13 regulates the osteoinduction potential of BMP9 in MEFs, which are multipotent progenitor cells widely used for stem cell biology research. In vitro and in vivo experiments showed that BMP9-induced osteogenic markers and/or bone were enhanced by exogenous MMP13 in MEFs, but were reduced by MMP13 knockdown or inhibition. The expression of hypoxia inducible factor 1 alpha (HIF-1α) was induced by BMP9, which was enhanced by MMP13. The protein expression of β-catenin and phosphorylation level of glycogen synthase kinase-3 beta (GSK-3β) were increased by BMP9 in MEFs, as was the translocation of β-catenin from the cytoplasm to the nucleus; all these effects of BMP9 were enhanced by MMP13. Furthermore, the MMP13 effects of increasing BMP9-induced β-catenin protein expression and GSK-3β phosphorylation level were partially reversed by HIF-1α knockdown. These results suggest that MMP13 can enhance the osteoinduction potential of BMP9, which may be mediated, at least in part, through the HIF-1α/β-catenin axis. Our findings demonstrate a novel role of MMP13 in the lineage decision of progenitor cells and provide a promising strategy to speed up bone regeneration.

What Strengthens Protein-Protein Interactions: Analysis and Applications of Residue Correlation Networks

Identifying residues critical to protein–protein binding and efficient design of stable and specific protein binders are challenging tasks. Extending beyond the direct contacts in a protein–protein binding interface, our study employs computational modeling to reveal the essential network of residue interactions and dihedral angle correlations critical in protein–protein recognition. We hypothesized that mutating residues exhibiting highly correlated dynamic motion within the interaction network could efficiently optimize protein–protein interactions to create tight and selective protein binders. We tested this hypothesis using the ubiquitin (Ub) and MERS coronaviral papain-like protease (PLpro) complex, since Ub is a central player in multiple cellular functions and PLpro is an antiviral drug target. Our designed ubiquitin variant (UbV) hosting three mutated residues displayed a ∼3,500-fold increase in functional inhibition relative to wild-type Ub. Further optimization of two C-terminal residues within the Ub network resulted in a KD of 1.5 nM and IC50 of 9.7 nM for the five-point Ub mutant, eliciting 27,500-fold and 5,500-fold enhancements in affinity and potency, respectively, as well as improved selectivity, without destabilizing the UbV structure. Our study highlights residue correlation and interaction networks in protein–protein interactions, and introduces an effective approach to design high-affinity protein binders for cell biology research and future therapeutics.

FocA: A deep learning tool for reliable, near-real-time imaging focus analysis in automated cell assay pipelines.

The increasing use of automation in cellular assays and cell culture presents significant opportunities to enhance the scale and throughput of imaging assays, but to do so, reliable data quality and consistency are critical. Realizing the full potential of automation will thus require the design of robust analysis pipelines that span the entire workflow in question. Here we present FocA, a deep learning tool that, in near real-time, identifies in-focus and out-of-focus images generated on a fully automated cell biology research platform, the NYSCF Global Stem Cell Array®. The tool is trained on small patches of downsampled images to maximize computational efficiency without compromising accuracy, and optimized to make sure no sub-quality images are stored and used in downstream analyses. The tool automatically generates balanced and maximally diverse training sets to avoid bias. The resulting model correctly identifies 100% of out-of-focus and 98% of in-focus images in under 4s per 96-well plate, and achieves this result even in heavily downsampled data (∼30 times smaller than native resolution). Integrating the tool into automated workflows minimizes the need for human verification as well as the collection and usage of low-quality data. FocA thus offers a solution to ensure reliable image data hygiene and improve the efficiency of automated imaging workflows using minimal computational resources.

Culturing cells for life: innovative approaches in macroscopic and microfluidic cultures, with an emphasis on stem cells

In 2006, Whitesides, writing about microfluidics, said that microfluidics is in early adolescence and it is not yet clear how it will develop. Today, almost 20 years later, microfluidics became a fully developed, highly sophisticated, multidisciplinary field that had entirely honoured its early promise. Its strength stems from the knowledge and know-how, coming from multiple disciplines such as physics of fluids, engineering, and microfabrication in the beginning, followed, more recently, by cell biological research, in full bloom nowadays. In microfluidic devices, the environment of cells such as chemical and mechanical gradients can be reproduced, making biological studies even more compelling. The red thread of this review paper follows the new insights and discoveries in both traditional macro- and microfluidic cell culture brought into the cell biology field, especially in the culture of stem cells, filled with promise in the field of regenerative medicine. Microfluidic devices provide an environment that is much closer to that of in vivo cell culture than the conventional culture platforms, where large amounts of cells are cultured and the environment of individual cells cannot be distinguished. The convenience of live cell imaging, portability, and the integration of sensors to precisely, control various parameters, has expanded cell biologists’ arsenal In addition, microfluidic devices, integrated with different functionalities, that is, the automated cell culture systems, will be discussed as well.

Chondroitin sulfate modified calcium phosphate nanoparticles for efficient transfection via caveolin-mediated endocytosis

Efficient transfection remains a challenge for gene delivery in both cell biological scientific research and gene therapeutic fields. Existing transfection strategies rarely pay attention to altering the endocytosis pathway of nanocarriers for transfection efficiency improvement. In this work, we innovatively postulated that calcium phosphate nanoparticles coated with glycosaminoglycan could be internalized by cells mainly through caveolin-mediated endocytosis pathway allowing genes to bypass lysosome route, and hence enhance the transfection efficiency. To achieve this, we developed calcium phosphate nanoparticles (CP-ALN-CS) coated with chondroitin sulfate (CS) and alendronate (ALN) in a modular manner. The CP-ALN-CS had a hydrodynamic size of 131.0 ± 8.7 nm and exhibited favorable dispersity, stability, and resistance to nuclease degradation. Unlike conventional calcium phosphate and PEI-based transfection, CP-ALN-CS exhibited efficient cellular uptake with co-localization in Golgi apparatus and endoplasmic reticulum. Through bypassing the lysosome involved cellular uptake route, CP-ALN-CS can effectively protect genes from degradation and relieve cytotoxicity. After loading plasmid DNA, CP-ALN-CS showed extraordinary transfection efficiency in HEK 293T cells, outperforming the PEI which is considered as the gold standard. The current work provides a novel and facile approach to improve gene transfection efficiency and is valuable for the design of next-generation in vitro transfection reagents.

Xeno-free generation of new Yazd human embryonic stem cell lines (Yazd4-7) as a prior stage toward good manufacturing practice of clinical-grade raw materials from discarded embryos: A lab resources report.

Xeno-free generation of human embryonic stem cells (hESCs) is important to prevent potential animal contaminations in culture for advanced cell-based therapeutic applications. Xeno-free production of hESCs is the first step for manufacturing clinical-grade hESC lines. To produce new hESC lines in xeno-free condition. This lab resources report was conducted at Stem Cell Biology Research Center, Yazd, Iran from 2019-2022. 4 new hESC lines from 11 (10 fresh and 1 frozen) donated surplus discarded human embryos were established. In this study, we report the xeno-free derivation of new Yazd hESC lines (Yazd4-7), without using immunosurgery, by culturing intact zona-free blastocysts obtained from discarded embryos onto the YhFF#8 cells as a feeder layer in a microdrop culture system. The pluripotency gene expression profile of the cell lines was assessed by reverse transcription polymerase chain reaction and the expression of specific surface markers was detected using immunofluorescent staining. In vitro differentiation was induced using embryoid body formation and gene expression profile of 3 germ layers and germ cells. Reverse transcriptase polymerase chain reaction was investigated to prove their pluripotent capacity. In sum, we have been able to generate 4 new hESC lines (Yazd4-7) from 11 discarded embryos in xeno-free culture conditions using a micro drop culture system and YhFF#8 as a human source feeder layer. The outcome of this work can be the foundation for the future allogeneic cell-based therapeutic application using clinical grade good manufacturing practice-derived hESC derivatives.

The Use of Small-Molecule Compounds for Cell Adhesion and Migration in Regenerative Medicine.

Cell adhesion is essential for cell survival, communication, and regulation, and it is of fundamental importance in the development and maintenance of tissues. Cell adhesion has been widely explored due to its many important roles in the fields of tissue regenerative engineering and cell biology. This is because the mechanical interactions between a cell and its extracellular matrix (ECM) can influence and control cell behavior and function. Currently, biomaterials for regenerative medicine have been heavily investigated as substrates for promoting a cells' adhesive properties and subsequent proliferation, tissue differentiation, and maturation. Specifically, the manipulation of biomaterial surfaces using ECM coatings such as fibronectin extracted from animal-derived ECM have contributed significantly to tissue regenerative engineering as well as basic cell biology research. Additionally, synthetic and natural bioadhesive agents with pronounced abilities to enhance adhesion in numerous biological components and molecules have also been assessed in the field of tissue regeneration. Research into the use of facilitative bioadhesives has aimed to further optimize the biocompatibility, biodegradability, toxicity levels, and crosslinking duration of bioadhesive materials for improved targeted delivery and tissue repair. However, the restrictive drawbacks of some of these bioadhesive and animal-derived materials include the potential risk of disease transmission, immunogenicity, poor reproducibility, impurities, and instability. Therefore, it is necessary for alternative strategies to be sought out to improve the quality of cell adhesion to biomaterials. One promising strategy involves the use of cell-adhesive small molecules. Small molecules are relatively inexpensive, stable, and low-molecular-weight (<1000 Da) compounds with great potential to serve as efficient alternatives to conventional bioadhesives, ECM proteins, and other derived peptides. Over the past few years, a number of cell adhesive small molecules with the potential for tissue regeneration have been reported. In this review, we discuss the current progress using cell adhesive small molecules to regulate tissue regeneration.

The Reasoning Engine: A Satisfiability Modulo Theories-Based Framework for Reasoning About Discrete Biological Models.

We present a framework called the Reasoning Engine, which implements Satisfiability Modulo Theories (SMT)-based methods within a unified computational environment to address diverse biological analysis problems. The Reasoning Engine was used to reproduce results from key scientific studies, as well as supporting new research in stem cell biology. The framework utilizes an intermediate language for encoding partially specified discrete dynamical systems, which bridges the gap between high-level domain-specific languages and low-level SMT solvers. We provide this framework as open source together with various biological case studies, illustrating the synthesis, enumeration, optimization, and reasoning over models consistent with experimental observations to reveal novel biological insights.

Depicting a cellular space occupied by condensates.

Condensates have emerged as a new way to understand how cells are organized, and have been invoked to play crucial roles in essentially all cellular processes. In this view, the cell is occupied by numerous assemblies, each composed of member proteins and nucleic acids that preferentially interact with each other. However, available visual representations of condensates fail to communicate the growing body of knowledge about how condensates form and function. The resulting focus on only a subset of the potential implications of condensates can skew interpretations of results and hinder the generation of new hypotheses. Here we summarize the discussion from a workshop that brought together cell biologists, visualization and computation specialists, and other experts who specialize in thinking about space and ways to represent it. We place the recent advances in condensate research in a historical perspective that describes evolving views of the cell; highlight different attributes of condensates that are not well-served by current visual conventions; and survey potential approaches to overcome these challenges. An important theme of these discussions is that the new understanding on the roles of condensates exposes broader challenges in visual representations that apply to cell biological research more generally.