Extracellular vesicles concentration is a promising and important parameter for industrial bioprocess monitoring

Extracellular vesicles (EVs) are membrane vesicles that are produced by cells to be released into their microenvironment. In this study, we present the EV concentration as a new factor for optimization of industrial bioprocess control. The release of EVs depends on many cell properties, including cell activation and stress status, and cell death. Therefore, the EV concentration might provide a readout for identification of the cell state and the conditions during a bioprocess. Our data show that the EV concentration increased during the bioprocess, which indicated deteriorating conditions in the bioreactor. This increase in EV concentration in the fermentation broth was the consequence of two different processes: cell activation, and cell death. However, the release of EVs from activated living cells had a much weaker impact on EV concentration in the bioreactor than those released during cell death. EVs and cells in the bioprocess environment were quantified by flow cytometry. The most accurate data were obtained directly from unprocessed samples, making the monitoring of the EV concentration a rapid, easy, and cheap method. These EV concentrations reflect the conditions in the bioreactor and provide new information regarding the state of the bioprocess. Therefore, we suggest EV concentration as a new and important parameter for the monitoring of industrial bioprocesses.     

Metabolic engineering of apoptosis in cultured animal cells: implications for the biotechnology industry

Animal cells have been widely used to obtain a wide range of products for human and animal healthcare applications. However, the extreme sensitivity of these cells in respect to changes experienced in their environment is evidenced by the activation of a gene-encoded program known as apoptosis, resulting in their death and destruction. From the bioprocess angle, losses in cell viability bring lower productivities and higher risks of product degradation. Consequently, many research efforts have been devoted to the development of apoptosis protective mechanisms, including the metabolic engineering of apoptosis pathways, that has proven effective in diminishing programmed cell death in a variety of biotechnological relevant cell lines. This review is focused especially in the encouraging initial results obtained with the over-expression of cloned anti-apoptosis genes, from both endogenous and viral origin interfering at mitochondrial and initiator caspases levels.     

Estimating environmental impacts of early-stage bioprocesses

The use of bioprocesses in industrial production promises resource- and energy-efficient processes starting from renewable, nonfossil feedstocks. Thus, the environmental benefits must be demonstrated, ideally in the early development phase with standardized methods such as life cycle assessment (LCA). Herein we discuss selected LCA studies of early-stage bioprocesses, highlighting their potential and contribution to estimating environmental impacts and decision support in bioprocess development. However, LCAs are rarely performed among bioprocess engineers due to challenges such as data availability and process uncertainties. To address this issue, recommendations are provided for conducting LCAs of early-stage bioprocesses. Opportunities are identified to facilitate future applicability, for example, by establishing dedicated bioprocess databases that could enable the use of LCAs as standard tools for bioprocess engineers.     

‘Omics driven discoveries of gene targets for apoptosis attenuation in CHO cells

Chinese hamster ovary (CHO) cells are widely used in biopharmaceutical production. Improvements to cell lines and bioprocesses are constantly being explored. One of the major limitations of CHO cell culture is that the cells undergo apoptosis, leading to rapid cell death, which impedes reaching high recombinant protein titres. While several genetic engineering strategies have been successfully employed to reduce apoptosis, there is still room to further enhance CHO cell lines performance. ‘Omics analysis is a powerful tool to better understand different phenotypes and for the identification of gene targets for engineering. Here, we present a comprehensive review of previous CHO 'omics studies that revealed changes in the expression of apoptosis‐related genes. We highlight targets for genetic engineering that have reduced, or have the potential to reduce, apoptosis or to increase cell proliferation in CHO cells, with the final aim of increasing productivity.     

Plasmid DNA fermentation strategies: influence on plasmid stability and cell physiology

In order to provide sufficient pharmaceutical-grade plasmid DNA material, it is essential to gain a comprehensive knowledge of the bioprocesses involved; so, the development of protocols and techniques that allow a fast monitoring of process performance is a valuable tool for bioprocess design. Regarding plasmid DNA production, the metabolic stress of the host strain as well as plasmid stability have been identified as two of the key parameters that greatly influence plasmid DNA yields. The present work describes the impact of batch and fed-batch fermentations using different C/N ratios and different feeding profiles on cell physiology and plasmid stability, investigating the potential of these two monitoring techniques as valuable tools for bioprocess development and design. The results obtained in batch fermentations showed that plasmid copy number values suffered a pronounced increase at the end of almost all fermentation conditions tested. Regarding fed-batch fermentations, the strategies with exponential feeding profiles, in contrast with those with constant feeding, showed higher biomass and plasmid yields, the maximum values obtained for these two parameters being 95.64 OD₆₀₀ and 344.3 mg plasmid DNA (pDNA)/L, respectively, when using an exponential feed rate of 0.2 h⁻¹. Despite the results obtained, cell physiology and plasmid stability monitoring revealed that, although higher pDNA overall yields were obtained, this fermentation exhibited lower plasmid stability and percentage of viable cells. In conclusion, this study allowed clarifying the bioprocess performance based on cell physiology and plasmid stability assessment, allowing improvement of the overall process and not only plasmid DNA yield and cell growth.     

A systematic strain selection approach for halotolerant and halophilic bioprocess development: a review

Halotolerant and halophilic microorganisms have potential applications in a number of very relevant environmental and industrial bioprocesses, from wastewater treatment to production of value-added chemicals. While numerous microbial strains have been identified and studied in the literature, the number of those successfully used in industrial applications is comparatively small. Literature is abundant in terms of characterisation of specific strains under a microbiology perspective; however, there is a need for studies tackling the selection of strains for bioprocess applications. This review presents a database of over 200 halophilic and halotolerant prokaryote strains compiled from taxonomic microbiological resources and classified by trophic groups as well as by their salinity, pH and temperature tolerance and optimum ranges, all under a process development perspective. In addition to this database, complementary systematic approaches for the selection of suitable strains for a given trophic activity and environmental conditions are also presented. Both the database and the proposed selection approaches together constitute a general tool for process development that allows researchers to systematically search for strains capable of specific substrate degradations under specific conditions (pH, T, salinity). Many exiting established halotolerant and halophilic environmental and industrial bioprocesses appear to have been developed following strategies in line with the systematic approaches proposed here.     

Analyzing and understanding the robustness of bioprocesses

The robustness of bioprocesses is becoming increasingly important. The main driving forces of this development are, in particular, increasing demands on product purities as well as economic aspects. In general, bioprocesses exhibit extremely high complexity and variability. Biological systems often have a much higher intrinsic variability compared with chemical processes, which makes the development and characterization of robust processes tedious task. To predict and control robustness, a clear understanding of interactions between input and output variables is necessary. Robust bioprocesses can be realized, for example, by using advanced control strategies for the different unit operations. In this review, we discuss the different biological, technical, and mathematical tools for the analysis and control of bioprocess robustness.     

Attenuating apoptosis in Chinese hamster ovary cells for improved biopharmaceutical production

Chinese hamster ovary (CHO) cells are the predominant host cell line for the production of biopharmaceuticals, a growing industry currently worth more than $188 billion USD in global sales. CHO cells undergo programmed cell death (apoptosis) following different stresses encountered in cell culture, such as substrate limitation, accumulation of toxic by-products, and mechanical shear, hindering production. Genetic engineering strategies to reduce apoptosis in CHO cells have been investigated with mixed results. In this review, a contemporary understanding of the real complexity of apoptotic mechanisms and signaling pathways is described; followed by an overview of antiapoptotic cell line engineering strategies tested so far in CHO cells.     

Production of hepatitis B surface antigen (preS2 + S) by high-cell density cultivations of a recombinant yeast.

A high-cell density bioprocess has been developed for the production of hepatitis B surface protein (preS2 + S) by recombinant yeast. This fed-batch process utilizes a growth medium containing yeast extract, soy peptone and glucose which was fed at a constant rate to maintain cells in a respiratory state. Cell densities of up to 60 g l-1 dry weight were achieved, which represented a 6-fold increase over those from batch bioprocesses. This increase in cell mass was attained without compromising specific activity; therefore, volumetric productivities of six times those of batch bioprocesses were achieved.     

TRAIL and vitamins: opting for keys to castle of cancer proteome instead of open sesame

ABSTRACT: Cancer is a multifaceted molecular disorder that is modulated by a combination of genetic, metabolic and signal transduction aberrations, which severely impair the normal homeostasis of cell growth and death. Accumulating findings highlight the fact that different genetic alterations, such as mutations in tumor suppressor genes, might be related to distinct and differential sensitivity to targeted therapies. It is becoming increasingly apparent that a multipronged approach that addresses genetic milieu (alterations in upstream and/or parallel pathways) eventually determines the response of individual tumors to therapy. Cancerous cells often acquire the ability to evade death by attenuating cell death pathways that normally function to eliminate damaged and harmful cells. Therefore impaired cell death nanomachinery and withdrawal of death receptors from cell surface are some of major determinants for the development of chemotherapeutic resistance encountered during treatment. It is therefore essential to emphasize underlying factors which predispose cells to refractoriness against TRAIL mediated cell death pathway and the relevant regulatory components involved. We bring to limelight the strategies to re-sensitize TRAIL resistant cells via vitamins to induce apoptosis.     

Aqueous two-phase systems strategies to establish novel bioprocesses for stem cells recovery

Abstract

During the past decade, stem cell transplantation has emerged as a novel therapeutic alternative for several diseases. Nevertheless, numerous challenges regarding the recovery and purification steps must be addressed to supply the number of cells required and in the degree of purity needed for clinical treatments. Currently, there is a wide range of methodologies available for stem cells isolation. Nevertheless, there is not a golden standard method that accomplishes all requirements. A desirable recovery method for stem cells has to guarantee high purity and should be sensitive, rapid, quantitative, scalable, non- or minimally invasive to preserve viability and differentiation capacity of the purified cells. In this context, aqueous two-phase systems (ATPS) represent a promising alternative to fulfill the mentioned requirements, promoting the use of stem cell-based therapies for incurable diseases. This practical review focuses on presenting the bases for the development of a novel and scalable bioprocess for the purification of stem cells, with a case scenario of CD133⁺ cells. The bioengineering strategies include the application of immunoaffinity ATPS in its multiple variants, including antibody-polymer conjugation, antibody addition and antibody immobilization. Conclusions are drawn in the light of the potential generic implementation of these strategies as an initial step in the establishment of bioprocesses for the purification of stem cells.     

The bioprocess TEA calculator: An online technoeconomic analysis tool to evaluate the commercial competitiveness of potential bioprocesses

Techno-economic analysis connects R&D, engineering, and business. By linking process parameters to financial metrics, it allows researchers to understand the factors controlling the potential success of their technologies. In particular, metabolic and bioprocess engineering, as disciplines, are aimed at engineering cells to synthesize products with an ultimate goal of commercial deployment. As a result it is critical to be able to understand the potential impact of strain engineering strategies and lab scale results on commercial potential. To date, while numerous techno-economic models have been developed for a wide variety of bioprocesses, they have either required process engineering expertise to adapt and/or use or do not directly connect financial outcomes to potential strain engineering results. Despite the clear value of techno-economic analysis, these challenges have made it inaccessible to many researchers. I have developed this online calculator (https://bioprocesstea.com OR http://bioprocess-tea-calculator.herokuapp.com/) to make the basic capabilities of early-stage techno-economic analysis of bioprocesses readily accessible. The tool, currently focused on aerobic fermentation processes, can be used to understand the impact of fermentation level metrics on the commercial potential of a bioprocess for the production of a wide variety of organic molecules. Using the calculator, I review the commercially relevant targets for an aerobic bioprocess for the production of diethyl malonate.     

Enhancement of survivability of mammalian cells by overexpression of the apoptosis-suppressor gene bcl-2

Cell lines derived from the hemopoetic lineages are widely used as hosts for the production of biologicals. These cell lines have been demonstrated to undergo high levels of the active death program commonly referred to as apoptosis. The effects of overexpression of the apoptosis suppressor gene bcl-2 on the properties of a Burkitt lymphoma were compared with the control cell line (transfected with a negative control plasmid) under a variety of conditions relevant to cell culture production technology. In stationary batch cultures, there was a clear reduction in both the rate of total cell death and the level of apoptosis during the decline phase of the bcl-2 transfected cell cultures as compared with that of the control cell cultures. Nutrient analysis revealed that the onset of death during the control cell cultures occurred following complete exhaustion of glutamine. However, the bcl-2 transfected cell cultures continued to grow even though glutamine had been exhausted, and a significant decline in viability only occurred when glucose had also been completely exhausted.When cells were cultured in suspension without prior adaptation, the bcl-2 transfected cells grew significantly better, suggesting that the bcl-2 gene protected the cells from apoptosis triggered by either the lack of substrate or the hydrodynamic environment. Fluorescence microscopy revealed that death of the control cells was almost entirely by apoptosis, whereas death was almost exclusively by necrosis in the delayed decline phase of the transfected cell cultures. In both instances, death occurred before total exhaustion of glucose and glutamine.The induction of apoptosis following growth arrest is a major impediment to the development of culture strategies that optimize specific productivity by reducing the growth rate. Results presented here suggest that suppression of apoptosis by bcl-2 under the condition of excess thymidine allows the maintenance of cells in a growth-arrested state for much longer than would otherwise be possible.When cells were transferred to a range of commercial serum-free media, cell growth was, in all cases, much better for the bcl-2 transfected cell line. Moreover, when cells were cultivated in glutamine-free medium, the control cells exhibited a decrease in viable cell number within the first 24 h whereas, for the bcl-2 transfected cell cultures, viable cell number did not exhibit any clear decrease until after 75 h. Clearly, these results indicate that the metabolic engineering approach can be used to alter advantageously the survival and proliferative capacity of cells in cell culture environments. (c) 1996 John Wiley & Sons, Inc.     

Combinatorial impact of Sec signal peptides from Bacillus subtilis and bioprocess conditions on heterologous cutinase secretion by Corynebacterium glutamicum

The impact of Sec signal peptides (SPs) from Bacillus subtilis in combination with isopropyl-β- d -1-thiogalactopyranoside concentration and feeding profile was investigated for heterologous protein secretion performance by Corynebacterium glutamicum using cutinase as model enzyme. Based on a comprehensive data set of about 150 bench-scale bioreactor cultivations in fed-batch mode and choosing the cutinase yield as objective, it was shown that relative secretion performance for bioprocesses remains very similar, irrespective of the applied SP enabling Sec-mediated cutinase secretion. However, to achieve the maximal absolute cutinase yield, careful adjustment of bioprocess conditions was found to be necessary. A model-based, two-step multiple regression approach resembled the collected data in a comprehensive way. The corresponding results suggest that the choice of the heterologous Sec SP and its interaction with the adjusted exponential feeding profile is highly relevant to maximize absolute cutinase yield in this study. For example, the impact of Sec SP is high at low growth rates and low at high growth rates. However, promising Sec SPs could be inferred from less complex batch cultivations. The extensive data were also evaluated in terms of cutinase productivity, highlighting the well-known trade-off between yield and productivity in bioprocess development in detail. Conclusively, only the right combination of target protein, Sec SP, and bioprocess conditions is the key to success.     

Physiological state-specific models in estimation of recombinant Escherichia coli fermentation performance

Implementation of advanced control strategies in bioprocesses is often hindered by the lack of on-line measurements reflecting the physiological state of the culture. Although a number of techniques have been used to estimate key variables from data monitored on-line, these often do not explicitly take into account changes in physiological state and information on many aspects of physiological state that may not be present in on-line data. Here we demonstrate that data obtained from chemical fingerprinting methods, such as pyrolysis mass spectrometry, can be used to identify changes in the physiological state during cultivation. This information can be utilized for the estimation of the physiological state and can enable physiological state-specific-model development for on-line bioprocess control.     

Autophagy can be a killer even in apoptosis-competent cells

Despite abundant evidence for autophagic cell death as a morphological type, the notion that autophagy can actually contribute mechanistically to the cell's death is controversial. In cells capable of apoptosis, autophagic cell death has been dismissed by some authors as a morphologically unusual form of apoptosis. But strong recent evidence for autophagy-mediated death of cells rendered incapable of apoptosis has been criticized on the grounds that this cell death is too artificial to be relevant to normal cells. We here argue from our own and other recent evidence that autophagy can mediate the death even of apoptosis-competent cells.     

Life and death in mammalian cell culture: strategies for apoptosis inhibition

Mammalian cell culture is widely used to produce valuable biotherapeutics including monoclonal antibodies, vaccines and growth factors. Industrial cell lines such as Chinese hamster ovary (CHO), mouse myeloma (NS0), baby hamster kidney (BHK) and human embryonic kidney (HEK)-293 retain many molecular components of the apoptosis cascade. Consequently, these cells often undergo programmed cell death upon exposure to stresses encountered in bioreactors. The implementation of strategies to control apoptosis and enhance culture productivities represents a major goal of biotechnologists. Fortunately, previous research has uncovered many intracellular proteins involved in activating and inhibiting apoptosis. Here, we summarize three apoptotic pathways and discuss different environmental and genetic methodologies implemented to limit cell death for biotechnology applications.     

Apoptosis and its control in cell culture systems

Apoptosis is a form of programmed cell death which exhibits highly distinctive morphology. Research activity in this area has increased substantially in recent years, primarily due to the realisation that disregulation of apoptosis is involved in the development of a number of pathological conditions, including cancer and AIDS. However, it is now clear that apoptosis also represents the dominant form of cell death during the culture of industrially important cell lines. This review focuses on the induction of apoptosis during industrial cell cultures as well as the effects of the apoptosis suppresser gene bcl-2 on cell survival in conditions relevant to bioreaction environments. We also present new data which demonstrates that bcl-2 can protect cells from apoptosis induced by oxygen deprivation, a finding which has important implications for large scale and intensive cultivation of cells. We also describe experiments which suggest that bcl-2 can reduce the specific nutrient consumption rate of cells.     

Coupled metabolic-hydrodynamic modeling enabling rational scale-up of industrial bioprocesses

Metabolomics aims to address what and how regulatory mechanisms are coordinated to achieve flux optimality, different metabolic objectives as well as appropriate adaptations to dynamic nutrient availability. Recent decades have witnessed that the integration of metabolomics and fluxomics within the goal of synthetic biology has arrived at generating the desired bioproducts with improved bioconversion efficiency. Absolute metabolite quantification by isotope dilution mass spectrometry represents a functional readout of cellular biochemistry and contributes to the establishment of metabolic (structured) models required in systems metabolic engineering. In industrial practices, population heterogeneity arising from fluctuating nutrient availability frequently leads to performance losses, that is reduced commercial metrics (titer, rate, and yield). Hence, the development of more stable producers and more predictable bioprocesses can benefit from a quantitative understanding of spatial and temporal cell-to-cell heterogeneity within industrial bioprocesses. Quantitative metabolomics analysis and metabolic modeling applied in computational fluid dynamics (CFD)-assisted scale-down simulators that mimic industrial heterogeneity such as fluctuations in nutrients, dissolved gases, and other stresses can procure informative clues for coping with issues during bioprocessing scale-up. In previous studies, only limited insights into the hydrodynamic conditions inside the industrial-scale bioreactor have been obtained, which makes case-by-case scale-up far from straightforward. Tracking the flow paths of cells circulating in large-scale bioreactors is a highly valuable tool for evaluating cellular performance in production tanks. The “lifelines” or “trajectories” of cells in industrial-scale bioreactors can be captured using Euler-Lagrange CFD simulation. This novel methodology can be further coupled with metabolic (structured) models to provide not only a statistical analysis of cell lifelines triggered by the environmental fluctuations but also a global assessment of the metabolic response to heterogeneity inside an industrial bioreactor. For the future, the industrial design should be dependent on the computational framework, and this integration work will allow bioprocess scale-up to the industrial scale with an end in mind.