HEK293 Cell Culture Research Articles

Isoform-Level Interpretation of High-Throughput Proteomics Data Enabled by Deep Integration with RNA-seq.

Cellular control of gene expression is a complex process that is subject to multiple levels of regulation, but ultimately it is the protein produced that determines the biosynthetic state of the cell. One way that a cell can regulate the protein output from each gene is by expressing alternate isoforms with distinct amino acid sequences. These isoforms may exhibit differences in localization and binding interactions that can have profound functional implications. High-throughput liquid chromatography tandem mass spectrometry proteomics (LC-MS/MS) relies on enzymatic digestion and has lower coverage and sensitivity than transcriptomic profiling methods such as RNA-seq. Digestion resultsin predictable fragmentation of a protein, which can limit the generation of peptides capable of distinguishing between isoforms. Here we exploit transcript-level expression from RNA-seq to set prior likelihoods and enable protein isoform abundances to be directly estimated from LC-MS/MS, an approach derived from the principle that most genes appear to be expressed as a single dominant isoform in a given cell type or tissue. Through this deep integration of RNA-seq and LC-MS/MS data from the same sample, we show that a principal isoform can be identified in >80% of gene products in homogeneous HEK293 cell culture and >70% of proteins detected in complex human brain tissue. We demonstrate that the incorporation of translatome data from ribosome profiling further refines this process. Defining isoforms in experiments with matched RNA-seq/translatome and proteomic data increases the functional relevance of such data sets and will further broaden our understanding of multilevel control of gene expression.

Catalytic cyclometallation in steroid chemistry VI: Targeted synthesis of hybrid molecules based on steroids and tetradeca-5Z,9Z-diene-1,14-dicarboxylic acid and study of their antitumor activity

Hybrid molecules based on a number of steroids (cholesterol, pregnenolone, androsterone) and 1,14-tetradeca-5Z,9Z-dienedicarboxylic acid linked via mono- and diethylene glycol spacers were synthesized for the first time and studied for antitumor activity in vitro. The acid was prepared using catalytic cyclomagnesiation of oxygenated 1,2-dienes with Grignard reagent in the presence of Cp2TiCl2 as the key synthetic step. Using flow cytometry, the new molecules were shown for the first time to be efficient apoptosis inducers in the HeLa, Hek293, U937, Jurkat, and K562 cell cultures and to have dose-dependent effect on the S and G2 phases of the cell cycle.

Process optimization for the rapid production of adenoviral vectors for clinical trials in a disposable bioreactor system.

Recombinant adenoviral (Ad) vectors are highly efficient gene transfer vectors widely used in vaccine development and immunotherapy. To promote the industrial application of Ad vectors, studies focusing on reducing the cost of manufacturing, shortening the preclinical research period, and improving the quality of products are needed. Here, we describe a highly efficient and economical process for producing Ad vector in a novel, single-use bioreactor system suitable for clinical trials. A mini-bioreactor was used for parameter optimization and development of medium replacement protocols for Ad5-GFP production before scale-up. HEK293 cell culture and virus infection were monitored in a disposable AmProtein Current Perfusion Bioreactor and Bioflo310 bioreactor using optimized parameters and medium replacement protocols. The total cell number increased from 2.0 × 109 to 3.2 × 1010 after 6days of culture. The total number of viral particles obtained in a single batch was 1.2 × 1015. These results demonstrate the efficiency and suitability of this system for Ad vector production for research and GMP applications.

Changes in gene expression in chronic allergy mouse model exposed to natural environmental PM2.5-rich ambient air pollution

Particulate matter (PM) air pollution has been associated with an increase in the incidence of chronic allergic diseases; however, the mechanisms underlying the effect of exposure to natural ambient air pollution in chronic allergic diseases have not been fully elucidated. In the present study, we aimed to investigate the cellular responses induced by exposure to natural ambient air pollution, employing a mouse model of chronic allergy. The results indicated that exposure to ambient air pollution significantly increased the number of eosinophils in the nasal mucosa. The modulation of gene expression profile identified a set of regulated genes, and the Triggering Receptor Expressed on Myeloid cells1(TREM1) signaling canonical pathway was increased after exposure to ambient air pollution. In vitro, PM2.5 increased Nucleotide-binding oligomerization domain-containing protein 1 (Nod1) and nuclear factor (NF)-κB signaling pathway activation in A549 and HEK293 cell cultures. These results suggest a novel mechanism by which, PM2.5 in ambient air pollution may stimulate the innate immune system through the PM2.5-Nod1-NF-κB axis in chronic allergic disease.

Photoacoustic imaging of voltage responses beyond the optical diffusion limit

Non-invasive optical imaging of neuronal voltage response signals in live brains is constrained in depth by the optical diffusion limit, which is due primarily to optical scattering by brain tissues. Although photoacoustic tomography breaks this limit by exciting the targets with diffused photons and detecting the resulting acoustic responses, it has not been demonstrated as a modality for imaging voltage responses. In this communication, we report the first demonstration of photoacoustic voltage response imaging in both in vitro HEK-293 cell cultures and in vivo mouse brain surfaces. Using spectroscopic photoacoustic tomography at isosbestic wavelengths, we can separate voltage response signals and hemodynamic signals on live brain surfaces. By imaging HEK-293 cell clusters through 4.5 mm thick ex vivo rat brain tissue, we demonstrate photoacoustic tomography of cell membrane voltage responses beyond the optical diffusion limit. Although the current voltage dye does not immediately allow in vivo deep brain voltage response imaging, we believe our method opens up a feasible technical path for deep brain studies in the future.

Accelerated mass production of influenza virus seed stocks in HEK-293 suspension cell cultures by reverse genetics

Despite major advances in developing capacities and alternative technologies to egg-based production of influenza vaccines, responsiveness to an influenza pandemic threat is limited by the time it takes to generate a Candidate Vaccine Virus (CVV) as reported by the 2015 WHO Informal Consultation report titled “Influenza Vaccine Response during the Start of a Pandemic”.In previous work, we have shown that HEK-293 cell culture in suspension and serum free medium is an efficient production platform for cell culture manufacturing of influenza candidate vaccines. This report, took advantage of, recombinant DNA technology using Reverse Genetics of influenza strains, and advances in the large-scale transfection of suspension cultured HEK-293 cells. We demonstrate the efficient generation of H1N1 with the PR8 backbone reassortant under controlled bioreactor conditions in two sequential steps (transfection/rescue and infection/production). This approach could deliver a CVV for influenza vaccine manufacturing within two-weeks, starting from HA and NA pandemic sequences. Furthermore, the scalability of the transfection technology combined with the HEK-293 platform has been extensively demonstrated at >100L scale for several biologics, including recombinant viruses.Thus, this innovative approach is better suited to rationally engineer and mass produce influenza CVV within significantly shorter timelines to enable an effective global response in pandemic situations.

Low-basicity 5-HT7 Receptor Agonists Synthesized Using the van Leusen Multicomponent Protocol

A series of 5-aryl-1-alkylimidazole derivatives was synthesized using the van Leusen multicomponent reaction. The chemotype is the first example of low-basicity scaffolds exhibiting high affinity for 5-HT7 receptor together with agonist function. The chosen lead compounds 3-(1-ethyl-1H-imidazol-5-yl)-5-iodo-1H-indole (AGH-107, 1o, Ki 5-HT7 = 6 nM, EC50 = 19 nM, 176-fold selectivity over 5-HT1AR) and 1e (5-methoxy analogue, Ki 5-HT7 = 30 nM, EC50 = 60 nM) exhibited high selectivity over related CNS targets, high metabolic stability and low toxicity in HEK-293 and HepG2 cell cultures. A rapid absorption to the blood, high blood-brain barrier permeation and a very high peak concentration in the brain (Cmax = 2723 ng/g) were found for 1o after i.p. (5 mg/kg) administration in mice. The compound was found active in novel object recognition test in mice, at 0.5, 1 and 5 mg/kg. Docking to 5-HT7R homology models indicated a plausible binding mode which explain the unusually high selectivity over the related CNS targets. Halogen bond formation between the most potent derivatives and the receptor is consistent with both the docking results and SAR. 5-Chlorine, bromine and iodine substitution resulted in a 13, 27 and 89-fold increase in binding affinities, respectively, and in enhanced 5-HT1AR selectivity.

Critical phases of viral production processes monitored by capacitance

Over the last decade industrial manufacturing of viral vaccines and viral vectors for prophylactic and therapeutic applications is experiencing a remarkable growth. Currently, the quality attributes of viral derived products are assessed only at the end-point of the production process, essentially because in-process monitoring tools are not available or not implemented at industrial scale. However, to demonstrate process reproducibility and robustness, manufacturers are strongly advised by regulatory agencies to adopt more on-line process monitoring and control. Dielectric spectroscopy has been successfully used as an excellent indicator of the cell culture state in mammalian and yeast cell systems. We previously reported the use of this technique for monitoring influenza and lentiviral productions in HEK293 cell cultures. For both viruses, multi-frequency capacitance measurements allowed not only the on-line monitoring of the production kinetics, but also the identification of the viral release time from the cells. The present study demonstrates that the same approach can be successfully exploited for the on-line monitoring of different enveloped and non-enveloped virus production kinetics in cell culture processes. The on-line monitoring multi-frequency capacitance method was assessed in human HEK293 and Sf9 insect cells expression systems, with viral productions initiated by either infection or transfection. The comparative analyses of all the data acquired indicate that the characteristic capacitance signals were highly correlated with the occurrence of viral replication phases. Furthermore the evolution of the cell dielectric properties (intracellular conductivity and membrane capacitance) were indicative of each main replication steps. In conclusion, multi-frequency capacitance has a great potential for on-line monitoring, supervision and control of viral vector production in cell culture processes.

Relief of Oxidative Stress Using Curcumin and Glutathione Functionalized ZnO Nanoparticles in HEK-293 Cell Line.

To elucidate the effect of zinc oxide nanoparticles (ZnO-NPs) with different surface modifications in relieving the oxidative stress in cultured human embryonic kidney cells (HEK-293) following investigation was performed. Oxidative stress was artificially induced by hydrogen peroxide in HEK-293 cell culture and its management was studied. Alkyl amines modified ZnO-NPs with curcumin and reduced glutathione (GSH) functionalization was used in managing oxidative stress and had shown promising results. ZnO-NPs used in this study were synthesized via non-aqueous sol-gel method and FESEM characterisation showed them of spherical shape of about 20-50 nm size with amine, curcumin and GSH functionalization. UV-visible and FTIR spectroscopic characterizations confirmed functionalization of ZnO-NPs. Decrease in oxidative stress was found with the dose-dependent culture of HEK-293 cells with these functionalized ZnO-NPs. Cell viability and morphology, as observed using AFM and inverted microscope, was retained with the prescribed dosages of the functionalized nanoparticles while at higher dosages they caused cytotoxicity and death. Diethylamine (DEA) modified ZnO-NPs and their functionalization with GSH and curcumin were found more effective in managing oxidative stress in cells. Present study could help in designing economical and bio-compatible functionalized non-toxic nanoparticles designed for managing oxidative stress leading to possible therapeutical and medicinal uses.

Lactate and glucose concomitant consumption as a self-regulated pH detoxification mechanism in HEK293 cell cultures.

One of the most important limitations of mammalian cell-based processes is the secretion and accumulation of lactate as a by-product of their metabolism. Among the cell lines commonly used in industrial bioprocesses, HEK293 has been gaining importance over the last years. Up recently, HEK293 cells were known to consume lactate in late stages of cell culture usually when glucose and/or glutamine were depleted from media. Remarkably, in both scenarios, no significant cell growth was reported. However, we have observed a different metabolic behavior regarding lactate production and consumption in HEK293 cultures. HEK293 cells were able to co-metabolize glucose and lactate simultaneously, even in exponentially growing cell cultures. Our deep study of the effects of environmental conditions on lactate metabolism revealed that pH was the key to trigger the metabolic shift from lactate production to lactate and glucose concomitant consumption. Remarkably, this shift could be triggered at will when pH was set at 6.8. Even more interesting was the fact that lowering pH to 6.6 and supplementing media with exogenous lactate resulted in co-consumption of glucose and lactate from the beginning of cell culture, without affecting cell growth or protein productivity. On the contrary, cell growth was clearly hampered at this low pH if extracellular lactate was lacking. From our results, we hypothesize that HEK293 cells metabolize extracellular lactate as a strategy for pH detoxification, by means of co-transporting extracellular protons together with lactate into the cytosol. This novel hypothesis for unraveling lactate metabolism in HEK293 cells could open a door to re-direct genetic engineering strategies in order to obtain more efficient cell lines and also to further develop animal cell technology applications.

Antiviral activity of 1-(1-arylimidazolidine-2-ylidene)-3-(4-chlorobenzyl)urea derivatives

The aim of the study was evaluation of the biological activity of 1-(1-arylimidazolidine-2-ylidene)-3-(4-chlorobenzyl)urea derivatives (I – IV) against the Coxsackievirus B3 (CVB3). The cytotoxic activity was tested in HEK293 cell culture. Cells were incubated for 72 hours at 37° C in a 5% CO2 atmosphere. Cytotoxicity of substances was measured by the MTT test. After determining the highest non-toxic concentration of substances their activity against the Coxsackievirus B3 from the Picornaviridae family was estimated. In order to check the antiviral activity of the compounds, a virus suspension was added to the cell culture and incubated for 1 hour at 37 °C. The virus was then removed from the culture and the tested compounds were added. The cell culture was incubated at 37° C in a 5% CO2 atmosphere until the cytophatic effect in the virus control was achieved, and then the virus was titrated. The virus titre was calculated by the Reed-Muench method. EC50 values of compounds I – IV were contained within the range of 211.4 – 359.7 μg/ml. The research demonstrated that only compound II slightly influenced the CVB3 replication by reducing the virus replication level by 0.77 log, which resulted in reducing the titre by 12.8%.

MicroRNAs in bovine milk are bioavailable in healthy adults and downregulate reporter gene activity in human kidney HEK‐293 cell cultures (271.4)

MicroRNAs (miRNA) repress gene expression at the level of transcription and translation. MiRNA are stable and evolutionary conserved. We tested the novel hypothesis that dietary miRNA in bovine milk are bioavailable and affect human gene expression. Milk and miR‐29b were chosen as models because of the large amounts of milk consumed in the U.S., the abundance of miR‐29b in milk, and the role of miR‐29b in bone health. We tested our hypothesis in milk feeding studies in adults using a randomized crossover design, and a reporter gene assay in HEK‐293 cell cultures. Plasma levels of miR‐29b peaked 3 h after milk consumption to 247% above baseline levels (as per qRT‐PCR; P=0.03; n=6; t‐test), consistent with absorption occurring in the upper small intestine. Levels of miR‐200c and miR‐150 (neg. control) in milk are 800% and <1%, respectively, that of miR‐29b. The peak plasma level of miR‐200c increased 383% above baseline, whereas miR‐150 levels did not change, consistent with a dose‐response relationship and assay specificity. Culturing HEK‐293 cells with miRNA from milk decreased the activity of a miR‐200c reporter gene by 24% compared with vehicle controls. We conclude that milk‐borne miRNA alter the expression of human genes, creating a pattern conducive to bone health. Our findings are significant in infant nutrition (miRNA content in formulas vs. breast milk) and the nutrition of postmenopausal women (osteoporosis).Grant Funding Source: Supported by ARD Hatch and NIH.

Type 1 metabotropic glutamate receptors (m G lu1) trigger the gating of G lu D 2 delta glutamate receptors

The orphan GluD2 receptor belongs to the ionotropic glutamate receptor family but does not bind glutamate. Ligand-gated GluD2 currents have never been evidenced, and whether GluD2 operates as an ion channel has been a long-standing question. Here, we show that GluD2 gating is triggered by type 1 metabotropic glutamate receptors, both in a heterologous expression system and in Purkinje cells. Thus, GluD2 is not only an adhesion molecule at synapses but also works as a channel. This gating mechanism reveals new properties of glutamate receptors that emerge from their interaction and opens unexpected perspectives regarding synaptic transmission and plasticity.

HEK293 cell culture media study: increasing cell density for different bioprocess applications

Background The increasing demand for biopharmaceuticals produced in mammalian cells has lead industries to enhance bioprocess volumetric productivity through different strategies. Among them, media development is of major interest [1]. According to the increasing constraints regarding the use of animal derived components on industrial bioprocesses but also the drawbacks of its depletion from cell culture [2], the main goal of the present work was to provide different cell culture platforms which are suitable for a wide range of applications depending on the type and the final use of the product obtained.

HEK293 cell culture media study towards bioprocess optimization: Animal derived component free and animal derived component containing platforms

The increasing demand for biopharmaceuticals produced in mammalian cells has lead industries to enhance bioprocess volumetric productivity through different strategies. Among those strategies, cell culture media development is of major interest. In the present work, several commercially available culture media for Human Embryonic Kidney cells (HEK293) were evaluated in terms of maximal specific growth rate and maximal viable cell concentration supported. The main objective was to provide different cell culture platforms which are suitable for a wide range of applications depending on the type and the final use of the product obtained. Performing simple media supplementations with and without animal derived components, an enhancement of cell concentration from 2 × 10(6) cell/mL to 17 × 10(6) cell/mL was achieved in batch mode operation. Additionally, the media were evaluated for adenovirus production as a specific application case of HEK293 cells. None of the supplements interfered significantly with the adenovirus infection although some differences were encountered in viral productivity. To the best of our knowledge, the high cell density achieved in the work presented has never been reported before in HEK293 batch cell cultures and thus, our results are greatly promising to further study cell culture strategies in bioreactor towards bioprocess optimization.

Analysis of Proteolytic Processes and Enzymatic Activities in the Generation of Huntingtin N-Terminal Fragments in an HEK293 Cell Model

BackgroundN-terminal fragments of mutant huntingtin (htt) that terminate between residues 90–115, termed cleavage product A or 1 (cp-A/1), form intracellular and intranuclear inclusion bodies in the brains of patients with Huntington's disease (HD). These fragments appear to be proteolytic products of the full-length protein. Here, we use an HEK293 cell culture model to investigate huntingtin proteolytic processing; previous studies of these cells have demonstrated cleavage of htt to cp-A/1 like htt fragments.ResultsRecombinant N-terminal htt fragments, terminating at residue 171 (also referred to as cp-B/2 like), were efficiently cleaved to produce cp-A/1 whereas fragments representing endogenous caspase, calpain, and metalloproteinase cleavage products, terminating between residues 400–600, were inefficiently cleaved. Using cysteine-labeling techniques and antibody binding mapping, we localized the C-terminus of the cp-A/1 fragments produced by HEK293 cells to sequences minimally limited by cysteine 105 and an antibody epitope composed of residues 115–124. A combination of genetic and pharmacologic approaches to inhibit potential proteases, including γ-secretase and calpain, proved ineffective in preventing production of cp-A/1.ConclusionsOur findings indicate that HEK293 cells express a protease that is capable of efficiently cleaving cp-B/2 like fragments of htt with normal or expanded glutamine repeats. For reasons that remain unclear, this protease cleaves longer htt fragments, with normal or expanded glutamine expansions, much less efficiently. The protease in HEK293 cells that is capable of generating a cp-A/1 like htt fragment may be a novel protease with a high preference for a cp-B/2-like htt fragment as substrate.

Real‐time monitoring of influenza virus production kinetics in HEK293 cell cultures

There is an increased interest from the vaccine industry to use mammalian cell cultures for influenza vaccine manufacturing. Therefore, it became important to study the influenza infection mechanism, the viral-host interaction, and the replication kinetics from a bioprocessing stand point to maximize the influenza viral production yield in cell culture. In the present work, influenza replication kinetics was studied in HEK293 cells. Two infection conditions were evaluated, a low (0.01) and a high multiplicity of infection (1.0). Critical time points of the viral production cycle (infection, protein synthesis, viral assembly and budding, viral release, and host-cell death) were identified in small-scale cell cultures. Additionally, cell growth, viability, and viral titers were monitored in the viral production process. The infection state of the cultivated cell population was assessed by influenza immunolabeling throughout the culture period. Influenza virus production kinetics were also on-line monitored by dielectric spectroscopy and successfully correlated to real-time capacitance measures. Overall, this work provided insights into the mechanisms associated with the infection of human HEK293 cell line by the influenza virus and demonstrated, once again, the usefulness of multifrequency scanning permittivity for in-line monitoring and supervision of cell-based viral production processes.

High level over-expression of different NCX isoforms in HEK293 cell lines and primary neuronal cultures is protective following oxygen glucose deprivation

In this study we have assessed sodium–calcium exchanger (NCX) protein over-expression on cell viability in primary rat cortical neuronal and HEK293 cell cultures when subjected to oxygen–glucose deprivation (OGD). In cortical neuronal cultures, NCX2 and NCX3 over-expression was achieved using adenoviral vectors, and following OGD increased neuronal survival from ≈20% for control vector treated cultures to ≈80% for both NCX isoforms. In addition, we demonstrated that NCX2 and NCX3 over-expression in cortical neuronal cultures enables neurons to maintain intracellular calcium at significantly lower levels than control vector treated cultures when exposed to high (9mM) extracellular calcium challenge. Further assessment of NCX activity during OGD was performed using HEK293 cell lines generated to over-express NCX1, NCX2 or NCX3 isoforms. While it was shown that NCX isoform expression differed considerably in the different HEK293 cell lines, high levels of NCX over-expression was associated with increased resistance to OGD. Taken together, our findings show that high levels of NCX over-expression increases neuronal and HEK293 cell survival following OGD, improves calcium management in neuronal cultures and provides additional support for NCX as a therapeutic target to reduce ischemic brain injury.

Comparative Effects of New Generation Oxazaphosphorines on the Size and Viability of Human Acute Myeloblastic Leukemia Cells

Mafosfamide cyclohexylamine salt (D-17272), 4-hydro-peroxy-cyclophosphamide (D-18864), and beta-D-glucose-isophosphoramide mustard (D-19575, glufosfamide) are three new generation oxazaphosphorine agents. The aim of the present study was to compare the cell response to the action of these three oxazaphosphorines. The experiments were performed in vitro on human acute myeloblastic leukemia ML-1 cells. After exposure of ML-1 cells to the oxazaphosphorines, the size, viability and count of these cells were determined. The research was conducted using the spectrophotometric MTT assay and the electronic Beckman Coulter method. The temporary changes in the ML-1 cell size, viability and count, were dependent on the oxazaphosphorine agent tested, its dose, and the time intervals after its application. Among the three oxazaphosphorine agents, D-18864 proved to be the most cytotoxic, and D-19575 was characterized by the lowest cytotoxicity. The results suggest the possibility of using the electronic sizing and counting method and the MTT assay as a rapid in vitro test for assessing leukemic cell sensitivity to the action of new potential chemotherapeutic agents.

Modulation of Porcine Endogenous Retroviruses (PERVs) expression in vitro by shRNA in the presence of cyclosporine A and dexamethasone

Despite the fact that the risk of Porcine Endogenous Retroviruses (PERV) infection and propagation in human recipients is extremely low, such an event cannot be completely ruled out, especially in immunosuppressed patients. Therefore, the aim of this study was to analyze the expression of PERVs in vitro in the presence of immunosuppression agents: cyclosporine A (CsA), and dexamethasone (DEX). We investigated the possible interactions between immunosuppression drugs, CsA and DEX, and the efficiency of anti-PERV RNAi. Plasmid-based vectors expressing shRNAs against all PERV genes were constructed and analyzed. PERVs expression in cultures transfected with anti-PERV RNAi constructions and treated with CsA or DEX was analyzed by Real-Time RT-PCR, Western blot, and by the measurement of RT activity. Both CsA and DEX inhibited PERVs expression in cell cultures in vitro. RNAi constructions efficiently knocked down PERV expression in Circe, and de novo PERV-infected HeLa and HEK-293 cell cultures. Pretreatment of Circe cultures with CsA or DEX increased PERVs knockdown by RNAi, but no specific interaction between the drugs and transfection efficiency was observed. Our results demonstrate that cyclosporine A and dexamethasone decrease expression of PERVs in vitro. We also proved that these drugs did not synergize or antagonize RNAi-mediated knockdown of PERVs. These observations may be beneficial in immunosuppressed xenograft recipients; however, due to the controversial literature data concerning influence of immune suppression on graft recipients, our results should be further analyzed.