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1.
ACS Biomater Sci Eng ; 10(4): 2442-2450, 2024 04 08.
Article in English | MEDLINE | ID: mdl-38530812

ABSTRACT

With the progression of regenerative medicine and cell therapy, the importance of cryopreservation techniques for cultured cells continues to rise. Traditional cryoprotectants, such as dimethyl sulfoxide and glycerol, are effective in cryopreserving suspended cells, but they do not demonstrate sufficient efficacy for two-dimensional (2D)-cultured cells. In the past decade, small molecules and polymers have been studied as cryoprotectants. Some L-amino acids have been reported to be natural and biocompatible cryoprotectants. However, the cryoprotective effects of D-amino acids have not been investigated for such organized cells. In the present study, the cryoprotective effects of D- and L-amino acids and previously reported cryoprotectants were assessed using HepG2 cells cultured on a microplate without suspending the cells. d-Proline had the highest cryoprotective effect on 2D-cultured cells. The composition of the cell-freezing solution and freezing conditions were then optimized. The d-proline-containing cell-freezing solution also effectively worked for other cell lines. To minimize the amount of animal-derived components, fetal bovine serum in the cell freezing solution was substituted with bovine serum albumin and StemFit (a commercial supplement for stem cell induction). Further investigations on the mechanism of cryopreservation suggested that d-proline protected enzymes essential for cell survival from freeze-induced damage. In conclusion, an effective and xeno-free cell-freezing solution was produced using d-proline combined with dimethyl sulfoxide and StemFit for 2D-cultured cells.


Subject(s)
Cryoprotective Agents , Dimethyl Sulfoxide , Animals , Humans , Cryoprotective Agents/pharmacology , Cryoprotective Agents/chemistry , Dimethyl Sulfoxide/pharmacology , Amino Acids/pharmacology , Cryopreservation/methods , Cell Line , Proline/pharmacology , Amines
2.
Ann Biomed Eng ; 52(5): 1213-1221, 2024 May.
Article in English | MEDLINE | ID: mdl-38324074

ABSTRACT

Cell's shape is dependent on the cytoskeleton mechanical properties. Hybrid models were developed that combine the discrete structure for the cytoskeleton and continuum parts for other cell organelles. Tensegrity-based structures that consist of tensile and compression elements are useful models to understand the cytoskeleton mechanical behavior. In this study, we are looking to examine the reaction of the cell to a variety of substrate stiffnesses and explain the relationship between cell behavior and substrate mechanical properties. However, which tensegrity structure is appropriate for modeling a living cell? Is the structure's complexity play a major role? We used two spherical tensegrities with different complexities to assess the impact of the structure on the cell's mechanical response versus substrate's stiffness. Six- and twelve-strut tensegrities together with membrane, cytoplasm, nucleoskeleton, and nucleus envelope were assembled in Abaqus package to create a hybrid cell model. A compressive load was applied to the cell model and the reaction forces versus deflection curves were analyzed for number of substrate stiffness values. By analyzing the difference due to two different tensegrities it became clear that the lower density structure is a better choice for modeling stiffer cells. It was also found that the six-strut tensegrity is sensitive to higher range of substrate stiffness.


Subject(s)
Cytoskeleton , Models, Biological , Microtubules , Stress, Mechanical
3.
Comput Biol Med ; 168: 107823, 2024 01.
Article in English | MEDLINE | ID: mdl-38061155

ABSTRACT

Transformer has shown excellent performance in various visual tasks, making its application in medicine an inevitable trend. Nevertheless, simply using transformer for small-scale cervical nuclei datasets will result in disastrous performance. Scarce nuclei pixels are not enough to compensate for the lack of CNNs-inherent intrinsic inductive biases, making transformer difficult to model local visual structures and deal with scale variations. Thus, we propose a Pixel Adaptive Transformer(PATrans) to improve the segmentation performance of nuclei edges on small datasets through adaptive pixel tuning. Specifically, to mitigate information loss resulting from mapping different patches into similar latent representations, Consecutive Pixel Patch (CPP) embeds rich multi-scale context into isolated image patches. In this way, it can provide intrinsic scale invariance for 1D input sequences to maintain semantic consistency, allowing the PATrans to establish long-range dependencies quickly. Futhermore, due to the existing handcrafted-attention is agnostic to the widely varying pixel distributions, the Pixel Adaptive Transformer Block (PATB) effectively models the relationships between different pixels across the entire feature map in a data-dependent manner, guided by the important regions. By collaboratively learning local features and global dependencies, PATrans can adaptively reduce the interference of irrelevant pixels. Extensive experiments demonstrate the superiority of our model on three datasets(Ours, ISBI, Herlev).


Subject(s)
Cell Nucleus , Medicine , Learning , Semantics , Image Processing, Computer-Assisted
4.
Front Cell Dev Biol ; 11: 1267822, 2023.
Article in English | MEDLINE | ID: mdl-37779894

ABSTRACT

Ventral actin stress fibers (SFs) are a subset of actin SFs that begin and terminate at focal adhesion (FA) complexes. Ventral SFs can transmit forces from and to the extracellular matrix and serve as a prominent mechanosensing and mechanotransduction machinery for cells. Therefore, quantitative analysis of ventral SFs can lead to deeper understanding of the dynamic mechanical interplay between cells and their extracellular matrix (mechanoreciprocity). However, the dynamic nature and organization of ventral SFs challenge their quantification, and current quantification tools mainly focus on all SFs present in cells and cannot discriminate between subsets. Here we present an image analysis-based computational toolbox, called SFAlab, to quantify the number of ventral SFs and the number of ventral SFs per FA, and provide spatial information about the locations of the identified ventral SFs. SFAlab is built as an all-in-one toolbox that besides analyzing ventral SFs also enables the identification and quantification of (the shape descriptors of) nuclei, cells, and FAs. We validated SFAlab for the quantification of ventral SFs in human fetal cardiac fibroblasts and demonstrated that SFAlab analysis i) yields accurate ventral SF detection in the presence of image imperfections often found in typical fluorescence microscopy images, and ii) is robust against user subjectivity and potential experimental artifacts. To demonstrate the usefulness of SFAlab in mechanobiology research, we modulated actin polymerization and showed that inhibition of Rho kinase led to a significant decrease in ventral SF formation and the number of ventral SFs per FA, shedding light on the importance of the RhoA pathway specifically in ventral SF formation. We present SFAlab as a powerful open source, easy to use image-based analytical tool to increase our understanding of mechanoreciprocity in adherent cells.

5.
Exp Biol Med (Maywood) ; 248(20): 1708-1717, 2023 10.
Article in English | MEDLINE | ID: mdl-37837381

ABSTRACT

Mechanical signals influence the morphology, function, differentiation, proliferation, and growth of cells. Due to the small size of cells, it is essential to analyze their mechanobiological responses with an in vitro mechanical loading device. Cells are cultured on an elastic silicone membrane substrate, and mechanical signals are transmitted to the cells by the substrate applying mechanical loads. However, large areas of non-uniform strain fields are generated on the elastic membrane, affecting the experiment's accuracy. In the study, finite-element analysis served as the basis of optimization, with uniform strain as the objective. The thickness of the basement membrane and loading constraints were parametrically adjusted. Through finite-element cycle iteration, the "M" profile basement membrane structure of the culture chamber was obtained to enhance the uniform strain field of the membrane. The optimized strain field of culture chamber was confirmed by three-dimensional digital image correlation (3D-DIC) technology. The results showed that the optimized chamber improved the strain uniformity factor. The uniform strain area proportion of the new chamber reached 90%, compared to approximately 70% of the current chambers. The new chamber further improved the uniformity and accuracy of the strain, demonstrating promising application prospects.


Subject(s)
Imaging, Three-Dimensional , Stress, Mechanical , Finite Element Analysis , Cell Differentiation
6.
Biosens Bioelectron ; 241: 115634, 2023 Dec 01.
Article in English | MEDLINE | ID: mdl-37696220

ABSTRACT

Spatially resolved transfection, intracellular delivery of proteins and nucleic acids, has the potential to drastically speed up the discovery of biologically active cargos, for instance for the development of cell therapies or new genome engineering tools. We recently demonstrated the use of a high-density microelectrode array for the targeted electrotransfection of cells grown on its surface, a process called High-Definition Electroporation (HD-EP). We also developed a framework based on Design of Experiments to quickly establish optimized electroporation conditions across five different electrical pulse parameters. Here, we used this framework to optimize the transfection efficiency of primary fibroblasts with a mCherry-encoding mRNA, resulting in 98% of the cells expressing the desired fluorescent protein without any sign of cell death. That transfection yield is the highest reported so far for electroporation. Moreover, varying the pulse number was shown to modulate the fluorescence intensity of cells, indicating the dosage-controlled delivery of mRNA and protein expression. Finally, exploiting the single-electrode addressability of the microelectrode array, we demonstrated spatially resolved, high efficiency, sequential transfection of cells with three distinct mRNAs. Since the chip can be easily redesigned to feature a much large number of electrodes, we anticipate that this methodology will enable the development of dedicated screening platforms for analysis of mRNA variants at scale.

7.
J Biochem ; 174(3): 273-278, 2023 Jul 31.
Article in English | MEDLINE | ID: mdl-37141918

ABSTRACT

Cryopreservation of mammalian cells is an important technology; however, freezing damage due to osmotic pressure differences and ice crystal formation is inevitable. In addition, cryopreserved cells cannot be used immediately after thawing in many cases. Therefore, in this study, we developed a method for supercooling and preserving adherent cells using a precision temperature-controlled CO2 incubator. The effects of the cooling rate from 37 to -4°C, the warming rate from -4 to 37°C and a preservation solution on cell viability after storage were examined. Human hepatocarcinoma-derived cell line HepG2 cells, preserved with HypoThermosol FRS at -4°C with a cooling rate of -0.028°C/min (24 h from 37°C to -4°C) and warming to 37°C at a rate of +1.0°C/min (40 min from -4 to 37°C), displayed high cell viability after 14 days of preservation. The superiority of supercooling preservation at -4°C was demonstrated by comparing the obtained results with that of refrigerated preservation at +4°C. Cells preserved for 14 days under optimal conditions showed no cell shape abnormalities and may be used for experiments immediately after thawing. The optimized supercooling preservation method determined in this study is suitable for the temporary preservation of adherent cultured cells.


Subject(s)
Cold Temperature , Cryopreservation , Humans , Cell Survival , Cells, Cultured , Cryopreservation/methods , Freezing , Temperature
8.
Biol Res ; 56(1): 18, 2023 Apr 21.
Article in English | MEDLINE | ID: mdl-37081568

ABSTRACT

BACKGROUND: Isolation of nuclei or nuclear proteins is a prerequisite for western blot, nuclear proteome profiling, and other evaluations of nuclear proteins. Here, we developed a simple method for in situ isolation of nuclei or nuclear proteins by in situ removing the extranuclear part of adherent cells via a classical nonionic detergent triton X-100. RESULTS: First, the feasibility of our method was confirmed by confocal microscopy, atomic force microscopy, scanning electron microscopy, dynamic light scattering, immunofluorescence imaging, and time-lapse dynamic observation. Next, the optimal concentration range (approximately 0.1-1% for ~ 10 min) of triton X-100 and the optimal treatment time (< 30 min) of 0.1-1% Triton X-100 for our method were determined via western blotting of eight extra-/intra-nuclear proteins. Subsequently, the effectiveness, sensitivity, and cytoplasmic contamination of our method were tested by investigating the levels of phosphorylated p65 (a NF-κB subunit) in the nuclei of endothelial or tumor cells treated with/without lipopolysaccharide (LPS) via western blotting and by comparing with a commercial nuclear protein extraction kit (a classical detergent-based method). The data show that compared with the commercial kit our method obtained a higher yield of total nuclear proteins, a higher pP65 level in both control and LPS groups, and much lower content of GAPDH (as a reference for cytoplasmic contamination) in nuclei. CONCLUSIONS: The in situ isolation of nuclei or nuclear proteins from adherent cells in this study is a simple, effective method with less cytoplasmic contamination. This method/strategy has the potential of improving the quality of downstream evaluations including western blotting and proteomic profiling.


Subject(s)
Lipopolysaccharides , Nuclear Proteins , Detergents/pharmacology , Octoxynol/pharmacology , Proteomics , NF-kappa B/metabolism
9.
Metabolites ; 13(3)2023 Feb 21.
Article in English | MEDLINE | ID: mdl-36984754

ABSTRACT

Dendritic cells (DCs) are essential immune cells for defense against external pathogens. Upon activation, DCs undergo profound metabolic alterations whose precise nature remains poorly studied at a large scale and is thus far from being fully understood. The goal of the present work was to develop a reliable and accurate untargeted metabolomics workflow to get a deeper insight into the metabolism of DCs when exposed to an infectious agent (lipopolysaccharide, LPS, was used to mimic bacterial infection). As DCs transition rapidly from a non-adherent to an adherent state upon LPS exposure, one of the leading analytical challenges was to implement a single protocol suitable for getting comparable metabolomic snapshots of those two cellular states. Thus, a thoroughly optimized and robust sample preparation method consisting of a one-pot solvent-assisted method for the simultaneous cell lysis/metabolism quenching and metabolite extraction was first implemented to measure intracellular DC metabolites in an unbiased manner. We also placed special emphasis on metabolome coverage and annotation by using a combination of hydrophilic interaction liquid chromatography and reverse phase columns coupled to high-resolution mass spectrometry in conjunction with an in-house developed spectral database to identify metabolites at a high confidence level. Overall, we were able to characterize up to 171 unique meaningful metabolites in DCs. We then preliminarily compared the metabolic profiles of DCs derived from monocytes of 12 healthy donors upon in vitro LPS activation in a time-course experiment. Interestingly, the resulting data revealed differential and time-dependent activation of some particular metabolic pathways, the most impacted being nucleotides, nucleotide sugars, polyamines pathways, the TCA cycle, and to a lesser extent, the arginine pathway.

10.
MethodsX ; 10: 102107, 2023.
Article in English | MEDLINE | ID: mdl-36970027

ABSTRACT

Microinjection is a method commonly used to deliver various substances into cells. The procedure is performed on a widefield microscope stage using fine glass needle to penetrate the cell membrane. Microinjection can be carried out using a manual or semi-automatic mode. For commercially available equipment currently reported microinjection success rate and cell viability are relatively low (around 50% for both indicators). Here, for the first time, we systematically show how the microinjection effectiveness and cell viability are influenced by needle diameter and chosen microinjection mode. We found that manual mode entailed a higher injection rate, reducing cell viability at the same time. The reduction in needle diameter caused a significant increase in cell survival rate (from 43 to 73% for manual mode and from 58% to 86% for semi-automatic mode) and did not affect significantly the success rate. Our findings will help optimize this method in the context of cell biology research.•This study shows how to improve microinjection parameters, such as procedure efficiency and cell survival rate, for commercially available equipment.•Manual mode, in comparison with semi-automatic mode, results in higher microinjection efficiency, but lower cell survival rate.•The increase in micropipette diameter causes lower cell viability and a higher microinjection success rate.

11.
Curr Stem Cell Res Ther ; 18(7): 937-946, 2023.
Article in English | MEDLINE | ID: mdl-36045541

ABSTRACT

Over 50 years have passed since discovering mesenchymal stromal cells (MSCs). Initially, despite gaps in the knowledge of the identity of these cells, their therapeutic aspects were recognized. Consequently, MSCs became candidates for treating a wide range of diseases. However, the therapeutic effects of MSCs are not stable in the long term, and there are inconsistent data on their clinical efficacy. Even though more than 1000 MSC-based clinical trials have been registered, and the safety of MSCbased cell therapies has been proven, data on the clinical efficacy of MSCs have not been enough to warrant FDA approval for clinical treatment and marketing purposes. The available information on MSCs still contains some controversies, perhaps owing to little progress in understanding their in vivo identity. MSCs have been used for therapeutic purposes despite poor knowledge of their in vivo origin or functions. Hence, perhaps we need to go back to the basics of MSCs and spend more time understanding the biology of these cells. An improved understanding of MSCs' location and function within tissues may improve their therapeutic efficacy and, consequently, their establishment as a cell therapy product.


Subject(s)
Mesenchymal Stem Cell Transplantation , Mesenchymal Stem Cells , Humans , Cell- and Tissue-Based Therapy
12.
Biol. Res ; 56: 18-18, 2023. ilus, graf
Article in English | LILACS | ID: biblio-1439485

ABSTRACT

BACKGROUND: Isolation of nuclei or nuclear proteins is a prerequisite for western blot, nuclear proteome profiling, and other evaluations of nuclear proteins. Here, we developed a simple method for in situ isolation of nuclei or nuclear proteins by in situ removing the extranuclear part of adherent cells via a classical nonionic detergent triton X-100. RESULTS: First, the feasibility of our method was confirmed by confocal microscopy, atomic force microscopy, scanning electron microscopy, dynamic light scattering, immunofluorescence imaging, and time-lapse dynamic observation. Next, the optimal concentration range (approximately 0.1-1% for ~ 10 min) of triton X-100 and the optimal treatment time (< 30 min) of 0.1-1% Triton X-100 for our method were determined via western blotting of eight extra-/ intra-nuclear proteins. Subsequently, the effectiveness, sensitivity, and cytoplasmic contamination of our method were tested by investigating the levels of phosphorylated p65 (a NF-κB subunit) in the nuclei of endothelial or tumor cells treated with/without lipopolysaccharide (LPS) via western blotting and by comparing with a commercial nuclear protein extraction kit (a classical detergent-based method). The data show that compared with the commercial kit our method obtained a higher yield of total nuclear proteins, a higher pP65 level in both control and LPS groups, and much lower content of GAPDH (as a reference for cytoplasmic contamination) in nuclei. CONCLUSIONS: The in situ isolation of nuclei or nuclear proteins from adherent cells in this study is a simple, effective method with less cytoplasmic contamination. This method/strategy has the potential of improving the quality of downstream evaluations including western blotting and proteomic profiling.


Subject(s)
Nuclear Proteins , Lipopolysaccharides , NF-kappa B/metabolism , Octoxynol/pharmacology , Proteomics , Detergents/pharmacology
13.
Biomedicines ; 10(11)2022 Oct 24.
Article in English | MEDLINE | ID: mdl-36359207

ABSTRACT

Non-adherent cells are difficult to transfect with chemical-mediated delivery methods. Electroporation is an attractive strategy to transfer the molecules of interest into suspension cells. Care must be taken with the viability of the transfected cells since parameters, which increase cell membrane permeability, subsequently increase transfection efficiency, leading to higher cell death indices. We intended to evaluate the distribution of hard-to-transfect UT-7 cells among different subpopulations: transfected/viable, untransfected/viable, transfected/dead, and untransfected/dead populations, for a better understanding of the relation between gene electrotransfer efficacy and cell death. The following electroporation parameters were tested: pulse strength, duration, plasmid DNA concentration, and ZnSO4 as DNase inhibitor. BTX T820 square-wave generator was used, and 48 h after electroporation, cells were observed for viability and fluorescence analysis. Increasing pulse strength correlated directly with an increased ratio of pEGFP-positive cells and inversely with cell viability. The best results, representing 21% pEGFP positive/viable cells, were obtained after EP with 1 HV 1400 V/cm pulse of 250 µs duration using 200 µg/mL plasmid concentration. Results demonstrated that plasmid concentration played the most significant role in pEGFP electrotransfer into UT-7 cells. These results can represent a relevant improvement of gene electrotransfer to obtain genetically modified suspension cells for further downstream experiments.

14.
Sheng Wu Yi Xue Gong Cheng Xue Za Zhi ; 39(5): 997-1004, 2022 Oct 25.
Article in Chinese | MEDLINE | ID: mdl-36310489

ABSTRACT

Based on the current study of the influence of mechanical factors on cell behavior which relies heavily on experiments in vivo, a culture chamber with a large uniform strain area containing a linear motor-powered, up-to-20-Hz cell stretch loading device was developed to exert mechanical effects on cells. In this paper, using the strain uniformity as the target and the substrate thickness as the variable, the substrate bottom of the conventional incubation chamber is optimized by using finite element technique, and finally a new three-dimensional model of the incubation chamber with "M" type structure in the section is constructed, and the distribution of strain and displacement fields are detected by 3D-DIC to verify the numerical simulation results. The experimental results showed that the new cell culture chamber increased the accuracy and homogeneous area of strain loading by 49.13% to 52.45% compared with that before optimization. In addition, the morphological changes of tongue squamous carcinoma cells under the same strain and different loading times were initially studied using this novel culture chamber. In conclusion, the novel cell culture chamber constructed in this paper combines the advantages of previous techniques to deliver uniform and accurate strains for a wide range of cell mechanobiology studies.


Subject(s)
Cell Culture Techniques , Stress, Mechanical , Computer Simulation , Finite Element Analysis
15.
Biotechnol Bioeng ; 119(6): 1498-1508, 2022 06.
Article in English | MEDLINE | ID: mdl-35319094

ABSTRACT

Rapid expansion of biopharmaceutical market calls for more efficient and reliable platforms to culture mammalian cells on a large scale. Stirred-tank bioreactors have been widely used for large-scale cell culture. However, it requires months of trials and errors to optimize culture conditions for each cell line. In this article, we extend our earlier studies on rolled scaffold (RS) bioreactors for high-density adherent cell culture and report two new implementations of RSs with greatly enhanced mass-manufacturability, termed as Mesh-RS and Fiber-RS. CHO-K1 cells were successfully expanded in Mesh-RS and Fiber-RS bioreactors with an average growth rate of 1.09 ± 0.04 1/day and 0.95 ± 0.07 1/day, which were higher than those reported in similar studies. Fiber-RS bioreactor exhibited a very high cell density of 72.8 × 106 cells/ml. Besides, a dialyzer was integrated into the RS bioreactor to remove cellular waste and to replenish nutrients without disturbing the cells. By collecting the dialyzed media separately, the dialysis efficiency was significantly improved. In conclusion, the developed RS bioreactor has a strong potential to provide a highly reliable and easily scalable platform for large-scale cell culture in the biopharmaceutical industry.


Subject(s)
Biological Products , Bioreactors , Animals , CHO Cells , Cell Culture Techniques , Cricetinae , Cricetulus
16.
Methods Mol Biol ; 2445: 127-137, 2022.
Article in English | MEDLINE | ID: mdl-34972990

ABSTRACT

The detection of autophagic vesicles in interphase cells is well characterized with markers such as LC3, SQSTM1 (also known as p62) and LAMP2, which are commonly used in immunofluorescence and biochemistry assays to evaluate the status of autophagy in adherent cells. During mitosis, cells undergo important morphological changes which alter the position of the central plane, therefore the imaging of dividing cells has to be specifically designed. Here, we describe a method to label and image autophagic vesicles in mitotic cells to systematically analyze their number, morphology and distribution.


Subject(s)
Autophagy , Mitosis , Fluorescent Antibody Technique , Sequestosome-1 Protein
17.
Membranes (Basel) ; 11(8)2021 Jul 22.
Article in English | MEDLINE | ID: mdl-34436313

ABSTRACT

Delivering extracellular materials into adherent cells presents several challenges. A homemade photoporation platform, mediated by gold nanoparticles (AuNPs), was constructed to find a suitable method for finding all adherent cells in this process with high delivery efficiency. The thermal dynamics of AuNPs could be monitored. Based on this system, 60 nm AuNPs were selected to be attached to cells for optimal photoporation. After irradiating the cells covered with AuNPs using a nanosecond pulse laser, fluorescein isothiocyanate-dextran in the medium were delivered into optoporated adherent HeLa (human cervical cell lines) cells. The delivery efficiency and cell viability of this process were evaluated using a fluorescence microscope and flow cytometry. The experimental results showed that targeting cells using antibodies, laser irradiation from the top of the cell culture well, and reducing the cell medium are important for improving the delivery efficiency. The optimal loading efficiency for adherent HeLa cells was 53.4%.

18.
Sensors (Basel) ; 21(16)2021 Aug 05.
Article in English | MEDLINE | ID: mdl-34450726

ABSTRACT

Measurement of cell surface coverage has become a common technique for the assessment of growth behavior of cells. As an indirect measurement method, this can be accomplished by monitoring changes in electrode impedance, which constitutes the basis of electric cell-substrate impedance sensing (ECIS). ECIS typically yields growth curves where impedance is plotted against time, and changes in single cell growth behavior or cell proliferation can be displayed without significantly impacting cell physiology. To provide better comparability of ECIS curves in different experimental settings, we developed a large toolset of R scripts for their transformation and quantification. They allow importing growth curves generated by ECIS systems, edit, transform, graph and analyze them while delivering quantitative data extracted from reference points on the curve. Quantification is implemented through three different curve fit algorithms (smoothing spline, logistic model, segmented regression). From the obtained models, curve reference points such as the first derivative maximum, segmentation knots and area under the curve are then extracted. The scripts were tested for general applicability in real-life cell culture experiments on partly anonymized cell lines, a calibration setup with a cell dilution series of impedance versus seeded cell number and finally IPEC-J2 cells treated with 1% and 5% ethanol.


Subject(s)
Biosensing Techniques , Cell Line , Cell Proliferation , Electric Impedance , Electrodes
19.
Methods Mol Biol ; 2305: 301-322, 2021.
Article in English | MEDLINE | ID: mdl-33950396

ABSTRACT

The advances in electron cryo-microscopy have enabled high-resolution structural studies of vitrified macromolecular complexes in situ by cryo-electron tomography (cryo-ET). Since utilization of cryo-ET is generally limited to the specimens with thickness < 500 nm, a complex sample preparation protocol to study larger samples such as single eukaryotic cells by cryo-ET was developed and optimized over the last decade. The workflow is based on the preparation of a thin cellular lamella by cryo-focused ion beam milling (cryo-FIBM) from the vitrified cells. The sample preparation protocol is a multi-step process which includes utilization of several high-end instruments and comprises sample manipulation prone to sample deterioration. Here, we present a workflow for preparation of three different model specimens that was optimized to provide high-quality lamellae for cryo-ET or electron diffraction tomography with high reproducibility. Preparation of lamellae from large adherent mammalian cells, small suspension eukaryotic cell line, and protein crystals of intermediate size is described which represents examples of the most frequently studied samples used for cryo-FIBM in life sciences.


Subject(s)
Cryoelectron Microscopy/methods , Macromolecular Substances/ultrastructure , Specimen Handling/methods , Animals , Cells/ultrastructure , Electron Microscope Tomography/methods , Ions , Molecular Biology/methods , Proteins/ultrastructure , Reproducibility of Results , Saccharomyces cerevisiae/ultrastructure , Workflow
20.
Mol Oncol ; 15(8): 2011-2025, 2021 08.
Article in English | MEDLINE | ID: mdl-33932101

ABSTRACT

Neuroblastoma (NB) is the most common extracranial solid tumour in children. NB is highly heterogeneous and is comprised of a mixture of neuroblastic cancer cells and stromal cells. We previously reported that N-type cells (neuroblastic cells) and S-type cells (substrate-adherent cells) in the SK-N-SH cell line shared almost identical genetic backgrounds. Sublines of N- and S-type cells were isolated from an early passage (P35) of SK-N-SH. Sequencing analysis revealed that all sublines harboured the anaplastic lymphoma kinase (ALK) F1174L mutation, indicating that they were tumour derived. Surprisingly, over 74% resembled S-type cells. In coculture experiments, S-type cells protected N-type cells from apoptosis induced by the oncogenic ALK inhibitor TAE684. Western blotting analyses showed that ALK, protein kinase A (AKT) and STAT3 signalling were stimulated in the cocultures. Furthermore, the conditioned medium from S-type cells activated these downstream signalling molecules in the N-type cells. The activation of STAT3 in the N-type cells was ALK-independent, while AKT was regulated by the ALK activation status. To identify the responsible soluble factors, we used a combination of transcriptomic and proteomic analysis and found that plasminogen activator inhibitor 1, secreted protein acidic and cysteine rich, periostin and galectin-1 were potential mediators of STAT3 signalling. The addition of recombinant proteins to the tumour cells treated with the ALK inhibitor partially enhanced cell viability. Overall, the tumour-derived S-type cells prevented apoptosis in the N-type cells via ALK-independent STAT3 activation triggered by secreted factors. The inhibition of these factors in combination with ALK inhibition could provide a new direction for targeted therapies to treat high-risk NB.


Subject(s)
Cell Adhesion , Cell Survival , Neuroblastoma/pathology , Anaplastic Lymphoma Kinase/antagonists & inhibitors , Anaplastic Lymphoma Kinase/genetics , Anaplastic Lymphoma Kinase/metabolism , Cell Proliferation , Coculture Techniques , Culture Media, Conditioned , Humans , Mass Spectrometry/methods , Mutation , Neuroblastoma/enzymology , Neuroblastoma/metabolism , Protein Kinase Inhibitors/pharmacology , Proteomics , Pyrimidines/pharmacology , STAT3 Transcription Factor/metabolism , Sequence Analysis, RNA/methods , Transcriptome
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