细胞生物学

Epithelial tissues form barriers to the flow of ions, nutrients, waste products, bacteria, and viruses. The conventional electrophysiology measurement of transepithelial resistance (TEER/TER) can quantify epithelial barrier integrity, but does not capture all the electrical behavior of the tissue or provide insight into membrane-specific properties. Electrochemical impedance spectroscopy, in addition to measurement of TER, enables measurement of transepithelial capacitance (TEC) and a ratio of electrical time constants for the tissue, which we term the membrane ratio. This protocol describes how to perform galvanostatic electrochemical impedance spectroscopy on epithelia using commercially available cell culture inserts and chambers, detailing the apparatus, electrical signal, fitting technique, and error quantification. The measurement can be performed in under 1 min on commercially available cell culture inserts and electrophysiology chambers using instrumentation capable of galvanostatic sinusoidal signal processing (4 μA amplitude, 2 Hz to 50 kHz). All fits to the model have less than 10 Ω mean absolute error, revealing repeatable values distinct for each cell type. On representative retinal pigment (n = 3) and bronchiolar epithelial samples (n = 4), TER measurements were 500–667 Ω·cm² and 955–1,034 Ω·cm² (within the expected range), TEC measurements were 3.65–4.10 μF/cm² and 1.07–1.10 μF/cm², and membrane ratio measurements were 18–22 and 1.9–2.2, respectively.

Human intestinal barrier function is crucial for health. Beneficial microbes, such as commensal gut bacteria and probiotics, are known to contribute to the regulation of this barrier function. Interactions between bacteria and human intestinal cells can be analyzed by co-culturing bacteria with mammalian cells in vitro. Here, we describe a method to assess the effect of individual bacterial strains on intestinal barrier function using automated transepithelial electrical resistance (TEER) measurements. Caco-2 cells are used as a model of the intestinal epithelium, as these cells spontaneously differentiate into small intestinal epithelial-like cells characterized by tight junctions between adjacent cells. These cells are seeded on polyester filter inserts and cultured for 17 days to form a differentiated monolayer prior to the co-culture experiment. Bacteria are grown on agar, and a single colony is used to prepare a liquid culture in bacterial broth appropriate for the bacteria of interest. On the day of the co-culture experiment, the bacterial culture is resuspended in cell culture medium at the desired concentration. Inserts are transferred to cellZscope cell modules to enable automated TEER measurements, and the medium in the insert is replaced with cell culture medium containing the bacteria of interest. This method allows for intestinal tight junction barrier function to be assessed non-invasively and in real-time in response to probiotics. The use of the automated cellZscope system eliminates the need for labor-intensive manual TEER measurements, which reduces the variability in data that results from human handling and temperature changes that occur when cells are removed from the incubator.

The Seahorse 96 XF Analyzer (Agilent Technologies, Santa Clara, CA, USA) has been an effective tool in non-invasively measuring mitochondrial function for the past decade. It is a high-throughput respirometer that is considered the “gold standard” for quantifying mitochondrial function and bioenergetics in cells. Peripheral blood mononuclear cells (PBMCs) play a selective role in immune system responses and are key components of human immunity. Recent studies have suggested that these cell populations provide an overview of systemic changes within the body and therefore provide a source of sensitive biomarkers. Assessing mitochondrial function in PBMCs has been shown to provide an indication of metabolic stress associated with diseases such as diabetes and neurodegenerative conditions such as Alzheimer’s disease. In this protocol, we use two adhesive compounds, Poly-D-Lysine (PDL) and Poly-L-Lysine (PLL), at 50 μg/mL each per well, to immobilize PBMCs to a specialized Seahorse microplate to perform mitochondrial stress assay using the Seahorse Analyzer. We compared six cell densities of PBMCs to identify the optimal cell density for use in Seahorse Mito Stress analysis. This protocol includes the immobilization of freshly isolated PBM cells into a Seahorse microplate, hydration and calibration of the sensor cartridge, cell seeding, running the Seahorse Analyzer for the Mito Stress test, and simple data analysis to compare the effectiveness of PLL and PDL as the coating agent for PBMCs. The data analysis indicates that there is no statistical difference between PLL and PDL.

Plastic pollution presents a looming danger to the environment and virtually all life on planet Earth. Especially pernicious are nanoplastics (NPs), which are plastic fragments with dimensions ≤1 μm. Conventional detection methods are ineffective for NPs, while their high specific surface area renders them efficient carriers of toxic substances; additionally, they may even be inherently toxic. Although NP waste chiefly arises from environmental weathering of larger plastic fragments, most published studies employed manufactured pristine NPs of uniform size and shape. Furthermore, almost all NP effects were studied using polystyrene (PS) as a convenient model material, despite PS accounting for <6% of all plastic pollution. There is thus an urgent need to expand investigations of environmental NP pollution and effects on biota. The present work provides a comprehensive roadmap for studying the effects of “real-world” NP pollution on living systems, using, for example, lung alveolar epithelial cells on which such NPs deposit by breathing ambient air. Herein, we describe detailed in-house methods to fabricate various NPs that are weathered with UV light and O₃ gas exposure to more closely mimic real environmental NPs. We also illustrate a simple and straightforward bioelectrical method for assessing passive and active ion transport properties of primary rat lung alveolar epithelial cell monolayers as a model for the distal mammalian lung exposed to one of the generated NPs. This protocol allows researchers to rapidly and more accurately assess the biological impact of various simulated environmental NPs on a vulnerable air–blood barrier in the lung.

In vitro lymphocyte proliferation assays are essential for assessing immune responses and antiproliferative drug efficacy. Such assays rely on antigen presentation or mitogen stimulation, with performance determined by reagent concentration and incubation time. Although splenocytes are often used, peripheral blood mononuclear cells (PBMCs) offer more accessible and practical sampling. However, a streamlined protocol for porcine PBMCs proliferation with robust batch analysis has been lacking. We therefore developed a detailed workflow for inducing proliferation in cryopreserved porcine PBMCs using 5 μg/mL concanavalin A (ConA). The protocol covers cell isolation, cryopreservation, ConA stimulation, CD4+ T-cell staining, flow cytometry acquisition and gating on an Attune NxT instrument, and batch analysis with FCS Express^TM 7.18. This approach yielded 78.9% viable cells, of which 33.8% were CD4+ lymphocytes. Moreover, 93.9% (n = 216) of cells proliferated, yielding up to nine cell generations. Batch analysis in FCS Express^TM enhanced the accuracy and interpretation of proliferation metrics. This validated protocol provides a reliable framework for generating consistent proliferation data in porcine immunology studies.

In response to DNA-damaging physical or chemical agents, the DNA damage repair (DDR) pathway is activated in eukaryotic cells. In the radiobiology field, it is important to assess the DNA damage effect of a certain irradiation regime on cancer cells and compare it to the effect on non-transformed cells exposed to identical conditions. The first step in the DNA repair mechanism consists of the attachment of proteins such as the phosphorylated histone γ-H2AX (p-γ-H2AX) to DNA double-strand breaks (DSB) in the nucleus, which leads to the formation of repairing foci. Therefore, imaging methods were established to evaluate the presence of foci inside the nucleus after exposure to DNA-damaging agents. This approach is superior in sensitivity to other methods, such as the comet assay or the pulsed-field gel electrophoresis (PFGE), that allow direct detection of cleaved DNA fragments. These electrophoresis-based methods require high ionizing radiation dosages and are difficult to reproduce compared to imaging-based assays. Conventionally, the number of foci is determined visually, with limited accuracy and throughput. Here, by exploring the effect of laser-plasma accelerated electrons FLASH irradiation on cancer cells, we describe an image cytometry protocol for the quantification of foci with increased throughput, upon large areas, with increased precision and sample-to-sample consistency. It consists of the automatic scanning of fluorescently labeled cells and using a gating strategy similar to flow cytometry to discriminate cells in co-culture based on nuclei elongation properties, followed by automatic quantification of foci number and statistical analysis. The protocol can be used to monitor the kinetics of DNA repair by quantification of p-γ-H2AX at different time points post-exposure or by quantification of other DNA repair proteins that form foci at the DNA DSB sites. Also, the protocol can be used for quantifying the response to chemical agents targeting DNA. This protocol can be performed on any type of cancer cells, and our gating strategy to discriminate cells in co-culture can also be used in other research applications.

Microglial cells are crucial patrolling immune cells in the brain and pivotal contributors to neuroinflammation during pathogenic or degenerative stress. Microglia exhibit a heterogeneous "dendrite-like" dense morphology that is subject to change depending on inflammatory status. Understanding the association between microglial morphology, reactivity, and neuropathology is key to informing treatment design in diverse neurodegenerative conditions from inherited encephalopathies to traumatic brain injuries. However, existing protocols for microglial morphology analyses lack standardization and are too complex and time-consuming for widescale adoption. Here, we describe a customized pipeline to quantitatively assess intricate microglial architecture in three dimensions under various conditions. This user-friendly workflow, comprising standard immunofluorescence staining, built-in functions of standard microscopy image analysis software, and custom Python scripts for data analysis, allows the measurement of important morphological parameters such as soma and dendrite volumes and branching levels for users of all skill levels. Overall, this protocol aims to simplify the quantification of the continuum of microglial pathogenic morphologies in biological and pharmacological studies, toward standardization of microglial morphometrics and improved inter-study comparability.

Macrophages are known for engulfing and digesting pathogens and dead cells through a specialized form of endocytosis called phagocytosis. Unfortunately, many macrophage cell lines are refractory to most reagents used for transient transfections. Alternative transient approaches, such as electroporation or transduction with lentiviral vectors, typically cause cell death (electroporation) or can be time-consuming to generate numerous lentivirus when using different genes of interest. Therefore, we use the Sleeping Beauty system to generate stably transfected cells. The system uses a “resurrected” transposase gene named Sleeping Beauty found in salmonid fish. Experimentally, the system introduces two plasmids: one carrying the Sleeping Beauty transposase and the other with an integration cassette carrying the gene of interest, a reverse-doxycycline controlled repressor gene, and an antibiotic resistance gene. The construct used in this protocol provides puromycin resistance. Stable integrations are selected by culturing the cells in the presence of puromycin, and further enrichment can be obtained using fluorescence-activated cell sorting (FACS). In this protocol, we use the Sleeping Beauty transposon system to generate RAW264.7 cells with doxycycline-inducible inositol polyphosphate 4-phosphatase B containing a C-terminal CaaX motif (INPP4B-CaaX). INPP4B-CaaX dephosphorylates the D-4 position of phosphatidylinositol 3,4-bisphosphate and inhibits phagocytosis. One benefit is that generating stable cell lines is substantially faster than selecting for random integrations. Without FACS, the method typically gives ~50% of the cells that are transfected; with sorting, this approaches 100%. This makes phagocytosis experiments easier since more cells can be analyzed per experiment, allowing for population-based measurements where a ~10% transient transfection rate is insufficient. Finally, using the doxycycline-promoter allows for low near endogenous expression of proteins or robust overexpression.

Cell viability and cytotoxicity assays are commonly used to investigate protein function and to evaluate drug efficacy in cancer and other disease models. Cytotoxicity is the measure of dead or damaged cells and is often quantified using assays based on cellular characteristics such as membrane integrity or mitochondrial metabolism. However, these assays are typically limited to endpoint analysis and lack emulation of physiological conditions. The IncuCyte Live and Dead Cell assay described here leverages common cell permeability methodologies but uses fluorescence microscopy channels to image both live and dead cells over time and phase microscopy channels to measure confluency. Cytotox green reagent is a cell membrane–impermeable dye that can only be taken up by cells with poor cell membrane integrity. NucLight rapid red dye is a cell membrane–permeable nuclear dye that can be taken up by all cells. Based on dye uptake and fluorescence intensity, the IncuCyte software can be used to analyze images for live and dead cell detection and quantification. Phase microscopy is used to determine confluency and can be further quantified using the IncuCyte software. We provide an application of this assay, using it to calculate IC₅₀ and EC₅₀ values for the assessment of drug efficacy.

Protein synthesis is by far the most energetically costly cellular process in rapidly dividing cells. Quantifying translating ribosomes in individual cells and their average mRNA transit rate is arduous. Quantitating assembled ribosomes in individual cells requires electron microscopy and does not indicate ribosome translation status. Measurement of average transit rates entails in vitro pulse-chase radiolabeling of isolated cells or ribosome profiling after ribosome runoff, which is expensive and extremely demanding technically. Here, we detail protocols based on ribosome-mediated nascent chain puromycylation, harringtonine to stall initiating ribosomes while allowing ribosome elongation to continue normally, and cycloheximide to freeze translating ribosomes in place. Each compound is delivered intravenously to mice in the appropriate order, and after ex vivo cell fixation and permeabilization, translating ribosome numbers and transit rates are measured by flow cytometry using a directly conjugated puromycin-specific antibody.