Intracellular ATP and total adenylate concentrations are critical predictors of reovirus productivity from Vero cells

Characterization of Carnosine Effect on Human Microglial Cells under Basal Conditions

The activity of microglia is fundamental for the regulation of numerous physiological processes including brain development, synaptic plasticity, and neurogenesis, and its deviation from homeostasis can lead to pathological conditions, including numerous neurodegenerative disorders. Carnosine is a naturally occurring molecule with well-characterized antioxidant and anti-inflammatory activities, able to modulate the response and polarization of immune cells and ameliorate their cellular energy metabolism. The better understanding of microglia characteristics under basal physiological conditions, as well as the possible modulation of the mechanisms related to its response to environmental challenges and/or pro-inflammatory/pro-oxidant stimuli, are of utmost importance for the development of therapeutic strategies. In the present study, we assessed the activity of carnosine on human HMC3 microglial cells, first investigating the effects of increasing concentrations of carnosine on cell viability. When used at a concentration of 20 mM, carnosine led to a decrease of cell viability, paralleled by gene expression increase and decrease, respectively, of interleukin 6 and heme oxygenase 1. When using the maximal non-toxic concentration (10 mM), carnosine decreased nitric oxide bioavailability, with no changes in the intracellular levels of superoxide ion. The characterization of energy metabolism of HMC3 microglial cells under basal conditions, never reported before, demonstrated that it is mainly based on mitochondrial oxidative metabolism, paralleled by a high rate of biosynthetic reactions. The exposure of HMC3 cells to carnosine seems to ameliorate microglia energy state, as indicated by the increase in the adenosine triphosphate/adenosine diphosphate (ATP/ADP) ratio and energy charge potential. The improvement of cell energy metabolism mediated by 10 mM carnosine could represent a useful protective weapon in the case of human microglia undergoing stressing conditions.

Vero cell upstream bioprocess development for the production of viral vectors and vaccines

The Vero cell line is considered the most used continuous cell line for the production of viral vectors and vaccines. Historically, it is the first cell line that was approved by the WHO for the production of human vaccines. Comprehensive experimental data on the production of many viruses using the Vero cell line can be found in the literature. However, the vast majority of these processes is relying on the microcarrier technology. While this system is established for the large-scale manufacturing of viral vaccine, it is still quite complex and labor intensive. Moreover, scale-up remains difficult and is limited by the surface area given by the carriers. To overcome these and other drawbacks and to establish more efficient manufacturing processes, it is a priority to further develop the Vero cell platform by applying novel bioprocess technologies. Especially in times like the current COVID-19 pandemic, advanced and scalable platform technologies could provide more efficient and cost-effective solutions to meet the global vaccine demand. Herein, we review the prevailing literature on Vero cell bioprocess development for the production of viral vectors and vaccines with the aim to assess the recent advances in bioprocess development. We critically underline the need for further research activities and describe bottlenecks to improve the Vero cell platform by taking advantage of recent developments in the cell culture engineering field.

Metabolic host response and therapeutic approaches to influenza infection

Based on available metabolomic studies, influenza infection affects a variety of cellular metabolic pathways to ensure an optimal environment for its replication and production of viral particles. Following infection, glucose uptake and aerobic glycolysis increase in infected cells continually, which results in higher glucose consumption. The pentose phosphate shunt, as another glucose-consuming pathway, is enhanced by influenza infection to help produce more nucleotides, especially ATP. Regarding lipid species, following infection, levels of triglycerides, phospholipids, and several lipid derivatives undergo perturbations, some of which are associated with inflammatory responses. Also, mitochondrial fatty acid β-oxidation decreases significantly simultaneously with an increase in biosynthesis of fatty acids and membrane lipids. Moreover, essential amino acids are demonstrated to decline in infected tissues due to the production of large amounts of viral and cellular proteins. Immune responses against influenza infection, on the other hand, could significantly affect metabolic pathways. Mainly, interferon (IFN) production following viral infection affects cell function via alteration in amino acid synthesis, membrane composition, and lipid metabolism. Understanding metabolic alterations required for influenza virus replication has revealed novel therapeutic methods based on targeted inhibition of these cellular metabolic pathways.

ATeam technology for detecting early signs of viral cytopathic effect

Adenosine 5’-triphosphate (ATP), the major energy currency of the cell, is involved in many cellular processes, including the viral life cycle, and can be used as an indicator of early signs of cytopathic effect (CPE). In this study, we demonstrated that CPE can be analyzed using an FRET-based ATP probe named ATP indicator based on Epsilon subunit for Analytical Measurements (ATeam). The results revealed that as early as 3 hr, the virus infected cells showed a significantly different Venus/cyan fluorescent protein (CFP) ratio compared to the mock-infected cells. The ATeam technology is therefore useful to determine the early signs of ATP-based CPE as early as 3 hr without morphology-based CPE by light microscopy, and enables high throughput determination of the presence of microorganisms in neglected samples stored in laboratories.

Antiviral activity of nobiletin against chikungunya virus in vitro

BACKGROUND

Chikungunya virus (CHIKV), a highly contagious re-emerging virus, is transmitted by infected mosquitoes. CHIKV is prevalent in tropical countries and is continuing to creep farther north into temperate areas. CHIKV is responsible for induction of chikungunya fever (CF) and severe joint stiffness with the capability of developing into bilateral and systemic arthralgia or even encephalitis. Despite the high morbidity rate, no approved antiviral drug is available. Therefore, an anti-CHIKV therapy is necessary to control this disease. In this study, we screened four flavonoids for anti-CHIKV activities: nobiletin, phlorizin, resveratrol and oxyresveratrol.

METHODS

We performed MTT, Viral ToxGlo^TM and lactate dehydrogenase (LDH) assays to assess the viability of CHIKV-infected host cells. Plaque assay and immunofluorescent assay were utilized to evaluate the levels of viral production in quantification and qualification, respectively.

RESULTS

We first confirmed that nobiletin can maintain the cellular survival of infected cells without inducing significant toxicity to host cells. Nobiletin suppressed virus-induced cell death and viral production. Also, the antiviral efficacy of nobiletin can last for at least 48 h during infection. More importantly, nobiletin inhibited CHIKV infection during the translation/replication stages and viral entry, making nobiletin a potential clinical antiviral agent in prophylaxis and post-exposure treatment.

CONCLUSIONS

In this study, our results provided a strategy to develop anti-chikungunya agents by utilizing natural compounds. Also, we believe that nobiletin can be a potential antiviral agent against CHIKV infection worthy of being further investigated as a remedial candidate in vivo.

Correlation-based iterative clustering methods for time course data: The identification of temporal gene response modules for influenza infection in humans

Many pragmatic clustering methods have been developed to group data vectors or objects into clusters so that the objects in one cluster are very similar and objects in different clusters are distinct based on some similarity measure. The availability of time course data has motivated researchers to develop methods, such as mixture and mixed-effects modelling approaches, that incorporate the temporal information contained in the shape of the trajectory of the data. However, there is still a need for the development of time-course clustering methods that can adequately deal with inhomogeneous clusters (some clusters are quite large and others are quite small). Here we propose two such methods, hierarchical clustering (IHC) and iterative pairwise-correlation clustering (IPC). We evaluate and compare the proposed methods to the Markov Cluster Algorithm (MCL) and the generalised mixed-effects model (GMM) using simulation studies and an application to a time course gene expression data set from a study containing human subjects who were challenged by a live influenza virus. We identify four types of temporal gene response modules to influenza infection in humans, i.e., single-gene modules (SGM), small-size modules (SSM), medium-size modules (MSM) and large-size modules (LSM). The LSM contain genes that perform various fundamental biological functions that are consistent across subjects. The SSM and SGM contain genes that perform either different or similar biological functions that have complex temporal responses to the virus and are unique to each subject. We show that the temporal response of the genes in the LSM have either simple patterns with a single peak or trough a consequence of the transient stimuli sustained or state-transitioning patterns pertaining to developmental cues and that these modules can differentiate the severity of disease outcomes. Additionally, the size of gene response modules follows a power-law distribution with a consistent exponent across all subjects, which reveals the presence of universality in the underlying biological principles that generated these modules.

Evaluation of Quenching and Extraction Methods for Nucleotide/Nucleotide Sugar Analysis

Nucleotide sugars are the donor substrates of glycosyltransferases and their availability is known to have an impact on the glycosylation of recombinant proteins including monoclonal antibodies. In addition, the intracellular concentration levels of these metabolites can provide information about the physiological/energetic state of the cell. Therefore, the ability to qualitatively and quantitatively determine the intracellular nucleotides and nucleotide sugars can give valuable insight into the metabolism associated with the glycosylation processes in cells. However, in order to be able to perform a consistent and reliable time specific analysis of these metabolites during a cell culture the metabolism of the cell needs to be stopped immediately at the point of sampling and an efficient extraction needs to be performed. Once the nucleotides and nucleotide sugars are extracted from the cell sample an efficient HPLC method is needed to separate all or most of the metabolites of interest to allow for their identification and quantification. Here, we describe an optimized method for the analysis of the intracellular nucleotide/nucleotide sugar pool in CHO suspension cells which includes protocols for quenching, extraction and HPLC analysis.

Low glucose depletes glycan precursors, reduces site occupancy and galactosylation of a monoclonal antibody in CHO cell culture

Controlled feeding of glucose has been employed previously to enhance the productivity of recombinant glycoproteins but there is a concern that low concentrations of glucose could limit the synthesis of precursors of glycosylation. Here we investigate the effect of glucose depletion on the metabolism, productivity and glycosylation of a chimeric human-llama monoclonal antibody secreted by CHO cells. The cells were inoculated into media containing varying concentrations of glucose. Glucose depletion occurred in cultures with an initial glucose ≤5.5 mM and seeded at low density (2.5 × 10(5) cells/mL) or at high cell inoculum (≥2.5 × 10(6) cells/mL) at higher glucose concentration (up to 25 mM). Glucose-depleted cultures produced non-glycosylated Mabs (up to 51%), lower galactosylation index (GI <0.43) and decreased sialylation (by 85%) as measured by mass spectrometry and HPLC. At low glucose a reduced intracellular pool of nucleotides (0.03-0.23 fmoles/cell) was measured as well as a low adenylate energy charge (<0.57). Low glucose also reduced GDP-sugars (by 77%) and UDP-hexosamines (by 90%). The data indicate that under glucose deprivation, low levels of intracellular nucleotides and nucleotide sugars reduced the availability of the immediate precursors of glycosylation. These results are important when applied to the design of fed-batch cultures.

The changing dielectric properties of CHO cells can be used to determine early apoptotic events in a bioprocess

To ensure maximum productivity of recombinant proteins it is desirable to prolong cell viability during a mammalian cell bioprocess, and therefore important to carefully monitor cell density and viability. In this study, five different and independent methods of monitoring were applied to Chinese hamster ovary (CHO) cells grown in a batch culture in a controlled bioreactor to determine cell density and/or cell viability. They included: a particle counter, trypan blue exclusion (Cedex), an in situ bulk capacitance probe, an off-line fluorescent flow cytometer, and a prototype dielectrophoretic (DEP) cytometer. These various techniques gave similar values during the exponential growth phase. However, beyond the exponential growth phase the viability measurements diverged. Fluorescent flow cytometry with a range of fluorescent markers was used to investigate this divergence and to establish the progress of cell apoptosis: the cell density estimates by the intermediate stage apoptosis assay agreed with those obtained by the bulk capacitance probe and the early stage apoptosis assay viability measurements correlated well with the DEP cytometer. The trypan blue assay showed higher estimates of viable cell density and viability compared to the capacitance probe or the DEP cytometer. The DEP cytometer measures the dielectric properties of individual cells and identified at least two populations of cells, each with a distinct polarizability. As verified by comparison with the Nexin assay, one population was associated with viable (non-apoptotic) cells and the other with apoptotic cells. From the end of the exponential through the stationary and decline stages there was a gradual shift of cell count from the viable into the apoptotic population. However, the two populations maintained their individual dielectric properties throughout this shift. This leads to the conclusion that changes in bulk dielectric properties of cultures might be better modeled as shifts in cells between different dielectric sub-populations, rather than assuming a homogeneous dielectric population. This shows that bulk dielectric probes are sensitive to the early apoptotic changes in cells. DEP cytometry offers a novel and unique technology for analyzing and characterizing mammalian cells based on their dielectric properties, and suggests a potential application of the device as a low-cost, label-free, electronic monitor of physiological changes in cells.

Development of quenching and washing protocols for quantitative intracellular metabolite analysis of uninfected and baculovirus-infected insect cells

Metabolomics refer to the global analysis of small molecule metabolites in a biological system, and can be a powerful tool to elucidate and optimize cellular processes, particularly when integrated into a systems biology framework. Determining the endometabolome in cultured animal cells is especially challenging, due to the conflicting demands for rapid quenching of metabolism and retention of membrane integrity, while cells are separated from the complex medium. The challenge is magnified in virus infected cells due to increased membrane fragility. This paper describes an effective methodology for quantitative intracellular metabolite analysis of the baculovirus-insect cell expression system, an important platform for the production of heterologous proteins and baculovirus-based biopesticides. These two applications were represented by Spodoptera frugiperda (Sf9) and Helicoverpa zea (HzAM1) cells infected with recombinant Autographa californica and wild-type Helicoverpa armigera nucleopolyhedroviruses (AcMNPV and HaSNPV), respectively. Specifically, an ice-cold quenching solution comprising 1.1% w/v NaCl and 0.2% w/v Pluronic® F-68 (NaCl+P) was found to be efficacious in preserving cell viability and minimizing cell leakage during quenching and centrifugation-based washing procedures (prior to extraction using cold 50% v/v acetonitrile). Good recoveries of intracellular adenosine triphosphate, total adenosine phosphates and amino acids were obtained after just one wash step, for both uninfected and infected insect cells. The ability to implement wash steps is critical, as insect cell media are metabolites-rich, while infected insect cells are much more fragile than their uninfected counterparts. Hence, a promising methodology has been developed to facilitate endometabolomic analysis of insect cell-baculovirus systems for bioprocess optimization.

The virus as metabolic engineer

Recent genome-wide screens of host genetic requirements for viral infection have reemphasized the critical role of host metabolism in enabling the production of viral particles. In this review, we highlight the metabolic aspects of viral infection found in these studies, and focus on the opportunities these requirements present for metabolic engineers. In particular, the objectives and approaches that metabolic engineers use are readily comparable to the behaviors exhibited by viruses during infection. As a result, metabolic engineers have a unique perspective that could lead to novel and effective methods to combat viral infection.

Metabolic effects of influenza virus infection in cultured animal cells: Intra- and extracellular metabolite profiling

BACKGROUND

Many details in cell culture-derived influenza vaccine production are still poorly understood and approaches for process optimization mainly remain empirical. More insights on mammalian cell metabolism after a viral infection could give hints on limitations and cell-specific virus production capacities. A detailed metabolic characterization of an influenza infected adherent cell line (MDCK) was carried out based on extracellular and intracellular measurements of metabolite concentrations.

RESULTS

For most metabolites the comparison of infected (human influenza A/PR/8/34) and mock-infected cells showed a very similar behavior during the first 10-12 h post infection (pi). Significant changes were observed after about 12 h pi: (1) uptake of extracellular glucose and lactate release into the cell culture supernatant were clearly increased in infected cells compared to mock-infected cells. At the same time (12 h pi) intracellular metabolite concentrations of the upper part of glycolysis were significantly increased. On the contrary, nucleoside triphosphate concentrations of infected cells dropped clearly after 12 h pi. This behaviour was observed for two different human influenza A/PR/8/34 strains at slightly different time points.

CONCLUSIONS

Comparing these results with literature values for the time course of infection with same influenza strains, underline the hypothesis that influenza infection only represents a minor additional burden for host cell metabolism. The metabolic changes observed after 12 h pi are most probably caused by the onset of apoptosis in infected cells. The comparison of experimental data from two variants of the A/PR/8/34 virus strain (RKI versus NIBSC) with different productivities and infection dynamics showed comparable metabolic patterns but a clearly different timely behavior. Thus, infection dynamics are obviously reflected in host cell metabolism.

Complex responses to culture conditions in Pseudomonas syringae pv. tomato DC3000 continuous cultures: the role of iron in cell growth and virulence factor induction

The growth of a model plant pathogen, Pseudomonas syringae pv. tomato DC3000, was investigated using a chemostat culture system to examine environmentally regulated responses. Using minimal medium with iron as the limiting nutrient, four different types of responses were obtained in a customized continuous culture system: (1) stable steady state, (2) damped oscillation, (3) normal washout due to high dilution rates exceeding the maximum growth rate, and (4) washout at low dilution rates due to negative growth rates. The type of response was determined by a combination of initial cell mass and dilution rate. Stable steady states were obtained with dilution rates ranging from 0.059 to 0.086 h(-1) with an initial cell mass of less than 0.6 OD(600). Damped oscillations and negative growth rates are unusual observations for bacterial systems. We have observed these responses at values of initial cell mass of 0.9 OD(600) or higher, or at low dilution rates (<0.05 h(-1)) irrespectively of initial cell mass. This response suggests complex dynamics including the possibility of multiple steady states.Iron, which was reported earlier as a growth limiting nutrient in a widely used minimal medium, enhances both growth and virulence factor induction in iron-supplemented cultures compared to unsupplemented controls. Intracellular iron concentration is correlated to the early induction (6 h) of virulence factors in both batch and chemostat cultures. A reduction in aconitase activity (a TCA cycle enzyme) and ATP levels in iron-limited chemostat cultures was observed compared to iron-supplemented chemostat cultures, indicating that iron affects central metabolic pathways. We conclude that DC3000 cultures are particularly dependent on the environment and iron is likely a key nutrient in determining physiology.

Na-butyrate sustains energetic states of metabolism and t-PA productivity of CHO cells

The effects of Na-butyrate on the physiological behaviour and on the specific productivity of recombinant tissue plasminogen activator (t-PA) Chinese Hamster Ovary (CHO) cells were characterized. Batch cultures were performed in a 3.5-L bioreactor. Na-butyrate was added either at the mid-exponential growth phase (48 h) or at the end of the exponential growth phase (74 h). The cultures with Na-butyrate showed higher net specific productivity of t-PA and lower final cell density and viability. Maximum specific productivity of t-PA for all cultures coincided with the early plateau phase (84 h). The cell's specific oxygen uptake rate (qO2) increased after the Na-butyrate addition and remained higher than that of the controlled culture. Triphosphate nucleotides, ADP, AMP and UDP-sugars all increased after 84 h in the cultures with Na-butyrate, showing different behaviours when Na-butyrate was added at 48 h or 74 h. Na-butyrate did not affect the cell's adenylate energy charge until the cell's viability started to decrease (156-168 h). The controlled culture and the culture with Na-butyrate addition, showed at 74 h, similar time trends as for purine and nucleotide ratios ((ATP+GTP)/(UTP+CTP) and UTP/ATP) with clear shifts in behaviour at 84 h and 168 h. However, the addition of Na-butyrate at 48 h resulted in damped variations of purine and nucleotide ratios in comparison to both the control culture and the culture with Na-butyrate addition at 74 h.

Cell density effect in the baculovirus-insect cells system: a quantitative analysis of energetic metabolism

The cell density effect (i.e., the drop in the specific productivity in the baculovirus-insect cells expression system when cells are infected at high cell densities) has been extensively described in the literature. In this article, a model for the central metabolism of serum-free suspension cultures of Spodoptera frugiperda Sf9 cells is proposed and used to investigate the metabolic basis for this phenomenon. The main metabolic pathways (glycolysis, pentose phosphate pathway, tricarboxylic acids cycle, glutaminolysis, and amino acids metabolism), cellular growth and energetics were considered. The analysis of the stoichiometric model allowed further understanding of the interplay of the consumption of carbon and nitrogen sources in insect cells. Moreover, metabolic flux analysis revealed that Sf9 cells undergo a progressive inhibition of central metabolism when grown to high cell densities, for which the incorporation of amino acids carbon backbones into the TCA cycle (mainly glutamine) and the down-regulation of glycolysis are partially responsible. Following infection by baculovirus and cellular division arrest, central energy metabolism depended on the infection strategy chosen (cell concentration at the moment of infection and multiplicity of infection), inhibition being observed at high cell densities. Interestingly, the energetic status of the culture correlated with the decrease in cellular production of baculovirus, meaning that there is room for process optimization through the application of metabolic engineering techniques.

Effect of perturbation of ATP level on the activity and regulation of nitrogenase in Rhodospirillum rubrum

Nitrogenase activity in Rhodospirillum rubrum and in some other photosynthetic bacteria is regulated in part by the availability of light. This regulation is through a posttranslational modification system that is itself regulated by P(II) homologs in the cell. P(II) is one of the most broadly distributed regulatory proteins in nature and directly or indirectly senses nitrogen and carbon signals in the cell. However, its possible role in responding to light availability remains unclear. Because P(II) binds ATP, we tested the hypothesis that removal of light would affect P(II) by changing intracellular ATP levels, and this in turn would affect the regulation of nitrogenase activity. This in vivo test involved a variety of different methods for the measurement of ATP, as well as the deliberate perturbation of intracellular ATP levels by chemical and genetic means. To our surprise, we found fairly normal levels of nitrogenase activity and posttranslational regulation of nitrogenase even under conditions of drastically reduced ATP levels. This indicates that low ATP levels have no more than a modest impact on the P(II)-mediated regulation of NifA activity and on the posttranslational regulation of nitrogenase activity. The relatively high nitrogenase activity also shows that the ATP-dependent electron flux from dinitrogenase reductase to dinitrogenase is also surprisingly insensitive to a depleted ATP level. These in vivo results disprove the simple model of ATP as the key energy signal to P(II) under these conditions. We currently suppose that the ratio of ADP/ATP might be the relevant signal, as suggested by a number of recent in vitro analyses.

Simultaneous extraction of several metabolites of energy metabolism and related substances in mammalian cells: optimization using experimental design

As a basis for the development of predictive mathematical models in systems biology and a quantitative understanding of cellular metabolism, reliable experimental data sets of intracellular metabolites are indispensable. A prerequisite for the acquisition of such data is the identification of a suitable sample preparation method. In this work, the extraction procedure for the simultaneous measurement of a wide range of intracellular metabolites from adherent mammalian cells in culture was optimized. A screening of several commonly used extraction protocols with Madin-Darby canine kidney (MDCK) cells found the methanol/chloroform (MeOH/CHCl(3)) and MeOH/Boil methods to be promising candidates for further analysis by anion-exchange chromatography. Both methods were optimized based on experimental design techniques with four response variables: Nucleotide Content, Energy Charge, Fructose 1,6-Bisphosphate content (F16bP), and Absorption at 280 nm. After data evaluation and with the help of desirability functions, an overall optimum for the extraction conditions was found. Using optimal settings, the extraction performances for MDCK and Vero cell cultivations of both methods were compared. Both methods extracted nearly the same absolute amounts of intracellular metabolites, suggesting that these methods are equal. However, recoveries for nucleotide diphosphates were significantly above 100% for both methods. This most likely was due to remaining nucleotide kinase activity during extraction. After combining individual steps of both methods, recoveries close to 100% for all metabolites could be reached. Absolute values of intracellular metabolites extracted with this modified method are comparable to the results of the two previously optimized methods, indicating a good extraction procedure according to the chosen response variables.