Disulfide bond reduction has been a challenging issue in antibody manufacturing, as it leads to reduced product purity, failed product specifications and more importantly, impacting drug safety and efficacy. Scientists across industry have been examining the root causes and developing mitigation strategies to address the challenge. In recent years, with the development of high-titer mammalian cell culture processes to meet the rapidly growing demand for antibody biopharmaceuticals, disulfide bond reduction has been observed more frequently. Thus, it is necessary to continue evolving the disulfide reduction mitigation strategy and development of novel approaches to achieve high product quality. Additionally, in recent years as more complex molecules emerge such as bispecific and trispecific antibodies, the molecular heterogeneity due to incomplete formation of the interchain disulfide bonds becomes a more imperative issue. Given the disulfide reduction challenges that our industry are facing, in this review, we provide a comprehensive contemporary scientific insight into the root cause analysis of disulfide reduction during process development of antibody therapeutics, mitigation strategies and recovery based on our expertise in commercial and clinical manufacturing of biologics. First, this paper intended to highlight different aspects of the root cause for disulfide reduction. Secondly, to provide a broader understanding of the disulfide bond reduction in downstream process, this paper discussed disulfide bond reduction impact to product stability and process performance, analytical methods for detection and characterization, process control strategies and their manufacturing implementation. In addition, brief perspectives on development of future mitigation strategies will also be reviewed, including platform alignment, mitigation strategy application for bi- and tri-specific antibodies and using machine learning to identify molecule susceptibility of disulfide bond reduction. The data in this review are originated from both the published papers and our internal development work.

Frontal chromatography has seen increased interest for protein purification, in particular as a polishing step in downstream processes for therapeutic proteins production, as for example the purification of monoclonal antibodies (mAbs) from high molecular weight impurities, e.g., aggregates, using cation exchange resins. In this work we introduce a new two-column continuous process implementing frontal chromatography. The design procedure and its performance, compared to classical batch technology, are discussed. This represents an additional option in the realisation of optimised continuous downstream processing of therapeutic proteins.

The field of optogenetics is rapidly growing in relevance and number of developed tools. Amongst other things, the optogenetic repertoire includes light-responsive ion channels and methods for gene regulation. This review will be confined to the optogenetic control of gene expression in mammalian cells as suitable models for clinical applications. Here optogenetic gene regulation might offer an excellent method for spatially and timely regulated gene and protein expression in cell therapeutic approaches. Well-known systems for gene regulation, such as the LOV-, CRY2/CIB-, PhyB/PIF-systems, as well as other, in mammalian cells not yet fully established systems will be described. Advantages and disadvantages with regard to clinical applications are outlined in detail. Among the many unanswered questions concerning the application of optogenetics, we discuss items such as the use of exogenous chromophores and their effects on the biology of the cells and methods for a gentle, but effective gene transfection method for optogenetic tools for in vivo applications.

Exposure of Chinese hamster ovary cells (CHO) to highly concentrated feed solution during fed-batch cultivation is known to result in an unphysiological osmolality increase (>300 mOsm/kg), affecting cell physiology and morphology. Extending previous observation on osmotic adaptation, the present study investigates for the first time potential effects of hyperosmolality on CHO cells on both population and single-cell level. We intentionally exposed CHO cells to hyperosmolality of up to 545 mOsm/kg during fed-batch cultivation. Contrarily to an expected osmosis effect promoting cell shrinkage, hyperosmolality-exposed CHO cells showed a nearly triplicated volume accompanied by ablation of proliferation. On the molecular level, we observed a strong hyperosmolality-dependent increase in mitochondrial activity in CHO cells compared to control. The companion article “Hyperosmolality in CHO Culture: Effects on Proteome” provides a proteome-based insight into the effects of hyperosmolality on mitochondria. In contrast to mitochondrial activity, hyperosmolality-dependent proliferation arrest of CHO cells was not accompanied by DNA accumulation or caspase-3/7-mediated apoptosis. Notably, we demonstrate for the first time a formation of up to eight multiple, small nuclei in single hyperosmolality-stressed CHO cells. The here presented observations reveal unknown hyperosmolality-dependent morphological changes and support existing data on the osmotic response in mammalian cells.

Cancer is a disease of somatic mutations. These cellular mutations compete to dominate their microenvironment and dictate the disease outcome. While a therapeutic approach to target specific driver mutations helps to manage the disease, subsequent molecular evolution of tumor cells threatens to overtake therapeutic progress. There is need for rapid, high-throughput, unbiased in-vitro discovery screening platforms that capture the native complexities of the tumor and rapidly identifiy mutations that confer chemotherapeutic drug resistance.Taking the example of CDK4/6 inhibitor (CDK4/6i) class of drugs, we show that the pooled in-vitro CRISPR screening platform enables rapid discovery of drug resistance mutations in a 3D setting. Gene edited cancer cell clones assembled into an organotypic multicellular tumor spheroid (MCTS), exposed to CDK4/6i caused selection and enrichment of the most drug resistant phenotype in a 3D setting, detectable by next gen sequencing after a span of 28 days. The platform was sufficiently sensitive to enrich for even a single drug resistant cell within a large, 2500-cell, drug-responsive complex 3D tumor spheroid. The genome-wide 3D CRISPR-mediated knockout screen (>18,000 genes) identified several genes whose disruptions conferred resistance to CDK4/6i. Further, multiple novel candidate genes were identified as top hits only in the microphysiological 3D enrichment assay platform and not the conventional 2D assays. Taken together, these findings suggest that including phenotypic 3D resistance profiling in decision trees could improve discovery and reconfirmation of drug resistance mechanisms and afford a platform for exploring non-cell autonomous interactions, selection pressures, and clonal competition.

The United States produces more than 10 million tons of waste oils and fats each year. This paper aims to establish a new biomanufacturing platform that convert waste oils or fats into a series of value-added products. Our research employs the oleaginous yeast Yarrowia lipolytica as a case study for citrate production from waste oils. First, we conducted the CFD simulation of the bioreactor system and identified that the extracellular mixing and mass transfer is the first limiting factor of an oil fermentation process due to the insolubility of oil in water. Based on the CFD simulation results, bioreactor design and operating conditions were optimized and successfully enhanced oil uptake and bioconversion in fed-batch fermentation experiments. After that, we investigated the impacts of cell morphology on oil uptake, intracellular lipid accumulation, and citrate formation by overexpressing and deleting the MHY1 gene in the wild type Y. lipolytica. Fairly good correlations were achieved between cell morphology and productivities of biomass, lipid, and citrate. Finally, fermentation kinetics with both glucose and oil substrates were compared and the oil fermentation process was carefully evaluated. Our research results suggest that waste oils or fats can be economical feedstocks for biomanufacturing of many high-value products.

SARS-CoV-2 is an RNA coronavirus that causes severe acute pneumonia, also known as COVID 19 disease. The World Health Organization declared the COVID-19 outbreak in January 2020 and a pandemic 2 months later. Serological assays are valuable tools to study virus spread among the population and, importantly, to identify individuals that were already infected and would be potentially immune to a virus re-infection. SARS-CoV-2 Spike protein and its Receptor Binding Domain (RBD) are the antigens with higher potential to develop SARS-CoV-2 serological assays. Moreover, structural studies of these antigens are key to understand the molecular basis for Spike interaction with angiotensin converting enzyme 2 receptor, hopefully enabling the discovery and development of COVID-19 therapeutics. Thus, it is urgent that significant amounts of this protein became available at the highest quality. In this work we evaluated the impact of different and scalable bioprocessing approaches on Spike and RBD production yields and, more importantly, in these antigens’ quality attributes. Using negative and positive sera collected from human donors, we show an excellent performance of the produced antigens, assessed in serologic ELISA tests, as denoted by the high specificity and sensitivity of the test. We have shown that, despite of the human cell host and the cell culture strategy used, for production scales ranging from 1 L to up to 30 L, final yields of approx. 2 mg and 90 mg per liter of purified bulk for Spike and RBD, respectively, could be obtained. To the best of our knowledge these are the highest yields for RBD production reported to date. An in-depth characterization of SARS CoV-2 Spike and RBD proteins was also performed, namely the antigens oligomeric state, glycosylation profiles and thermal stability during storage. The correlation of these quality attributes with ELISA performance show equivalent reactivity to SARS CoV 2 positive serum, for all Spike and RBD produced, and for all the storage conditions tested. Overall, we provide herein straightforward protocols to produce high-quality SARS CoV-2 Spike and RBD antigens, that can be easily adapted to both academic and industrial settings; and integrate, for the first time, studies on the impact of bioprocess with an in-deep characterization of these proteins, correlating antigens glycosylation and biophysical attributes to performance of COVID-19 serologic tests. We strongly believe that our work will contribute to advance the current and recent knowledge on SARS-CoV-2 proteins and support the scientific society that is persistently searching for solutions for COVID-19 pandemics.

Concerns about climate change and the search for renewable energy sources together with the goal of attaining sustainable product manufacturing have boosted the use of microbial platforms to produce fuels and high-value chemicals. In this regard, Y. lipolytica has been known as a promising yeast with potentials in diverse array of biotechnological applications such as being a host for different oleochemicals, organic acid and recombinant protein production. Having a rapidly increasing number of molecular and genetic tools available, Y. lipolytica has been well studied amongst oleaginous yeasts and metabolic engineering has been used to explore its potentials. More recently, with the advancement in systems biotechnology and the implementation of mathematical modeling and high throughput omics data-driven approaches, in-depth understanding of cellular mechanisms of cell factories have been made possible resulting in enhanced rational strain design. In case of Y. lipolytica, these systems-level studies and the related cutting-edge technologies have recently been initiated which is expected to result in enabling the biotechnology sector to rationally engineer Y. lipolytica-based cell factories with favorable production metrics. In this regard, here, we highlight the current status of systems metabolic engineering research and assess the potential of this yeast for future cell factory design development.

Host cell proteins (HCPs) are process-related impurities that may co-purify with biopharmaceutical drug products. Within this class of impurities there are some that are more problematic. These problematic HCPs can be considered high-risk and can include those that are immunogenic, biologically active, or enzymatically active with the potential to degrade either product molecules or excipients used in formulation, and often are difficult-to-purify. Why should the biopharmaceutical industry worry about these high-risk host cell proteins? What approach could be taken to understand the origin of this co-purification and to deal with these high-risk HCPs? To answer these questions, the BioPhorum Development Group (BPDG) HCP Workstream initiated a collaboration among its 26-company team with the goal of industry alignment around high-risk HCPs. A sub team was formed, in which the members performed literature searches and discussed the information available around this topic. A survey to the BPDG HCP Workstream team members led to team discussions and insights into a list of frequently seen problematic HCPs. These HCPs were further classified based on their potential impact into different risk categories that could be beneficial to the biopharmaceutical industry for targeted monitoring of those HCP impurities in CHO-produced biologics to minimize risk to product quality, safety, and efficacy.

Retroviral gene delivery is widely used in T cell therapies for hematological cancers. However, viral vectors are expensive to manufacture, they integrate genes in semi-random patterns, and their transduction efficiency is highly variable. In this study, several non-viral gene delivery vehicles, promoters, and additional variables were compared to optimize non-viral transgene delivery and expression in both Jurkat and primary T cells. Overall, transfecting Jurkat cells in X-VIVOTM 15 media with Lipofectamine LTX provided a high transfection efficiency (63.0±10.9% EGFP+). However, the same method yielded a much lower transfection efficiency in primary T cells (8.1±0.8% EGFP+). Subsequent confocal microscopy revealed that a majority of the lipoplexes did not enter the primary T cells, which might be due to relatively low expression levels of heparan sulfate proteoglycans (HSPGs) detected via mRNA-sequencing. PYHIN DNA sensors (e.g., AIM2, IFI16) were also expressed at high levels in Primary T cells, which can induce apoptosis when bound to cytoplasmic DNA. Therefore, transfection of primary T cells appears to be limited at the level of cellular uptake and/or DNA sensing in the cytoplasm, so both of these factors should be considered in the development of future viral and non-viral T cell gene delivery methods.

Monoclonal antibodies are high value agents used for disease therapy (‘biologic drugs’) or as diagnostic tools which are widely used in the health care sector. They are generally manufactured in mammalian cells, in particular Chinese hamster ovary (CHO) cells cultured in defined media, and are harvested from the medium. Rheb is a small GTPase which, when bound to GTP, activates mechanistic target of rapamycin complex 1 (mTORC1), a protein kinase that drives anabolic processes including protein synthesis and ribosome biogenesis. Here we show that certain constitutively-active mutants of Rheb drive faster protein synthesis in CHO cells and increase the expression of proteins involved in the processing of secreted proteins via the endoplasmic reticulum, which expands in response to expression of Rheb. Active Rheb mutants, in particular Rheb[T23M], drive increased cell number under serum-free conditions similar to those used in the biotechnology industry. Rheb[T23M] also enhances the expression of the reporter protein luciferase and, especially strongly, the secreted Gaussia luciferase. Moreover, Rheb[T23M] markedly (2-3 fold) enhances the amount of this luciferase and of a model immunoglobulin into the medium. Our data clearly demonstrate that expressing Rheb[T23M] in CHO cells provides a simple approach to promoting cell growth in defined medium and the production of secreted proteins of high commercial value

Yellow fever (YF) is a life-threatening viral disease endemic in large areas of Africa and Latin America. Although there is a very efficacious vaccine since the 1930s, YF still causes 29,000-60,000 annual deaths. During recent YF outbreaks there were issues of vaccine shortage due to limited supply of the current egg-derived vaccine; rare but fatal vaccine adverse effects occurred; and cases were imported to Asia, where the mosquito vector circulates and where local transmission could potentially start. In this work, we investigated the production of YF virus-like particles (VLPs) using suspension-adapted stably-transfected HEK293 cells. In order to develop an intensified process, we combined two strategies: the use of sequential FACS rounds to enrich the stable cell pool in terms of high producers, and the use of perfusion processes. At first, shaken tube experiments revealed that FACS enrichment of the cell pool allowed doubling VLP production, and that in pseudoperfusion cultures (with daily medium exchange) lasting 14 days VLP production increased by 8.3 fold as compared to batch cultures lasting 11 days. When true perfusion cultures were carried out in bioreactors, the use of an inclined cell settler as cell retention device showed operational advantages as compared to an ATF system.

The mechanical properties of biofilms can be used to predict biofilm deformation, for example under fluid flow. We used magnetic tweezers to spatially map the compliance of Pseudomonas aeruginosa biofilms at the micron scale, then used modeling to assess its effects on biofilm deformation. Biofilms were grown in capillary flow cells with Reynolds numbers (Re) ranging 0.28 to 13.9, bulk dissolved oxygen (DO) concentrations from 1 mg/L to 8 mg/L, and bulk calcium ion (Ca2+) concentrations of 0 and 100 mg CaCl2/L. Higher Re numbers resulted in more uniform biofilm morphologies. The biofilm was stiffer at the center of the flow cell than near the walls. Lower bulk DO led to more stratified biofilms. Higher Ca2+ led to increased stiffness and more uniform mechanical properties. Using the experimental mechanical properties, fluid-structure interaction models predicted up to 64% greater deformations for heterogeneous biofilms, compared to a homogeneous biofilms with the same average properties. However, the error depended on the biofilm morphology and flow regime. Our results show significant spatial mechanical variability exists at the micron scale, and that this variability can potentially affect biofilm deformation. The average mechanical properties, provided in many studies, should be used with caution when predicting biofilm deformation.

The serious drawbacks of conventional pancreatic ductal adenocarcinoma (PDAC) therapy like nonspecific toxicity and high resistance to chemo and radiation therapy, prompted the development and application of countless siRNA-based therapeutics. Significant technological success has been achieved in this area; however, the major challenges to siRNA-based therapeutics becoming a new paradigm in the pancreatic cancer therapy stem from enzymatic digestion, off-target effects, difficulty to enter cells, induction of innate immune responses, and renal clearance. Recent advances in drug delivery systems hold great promise for improving siRNA-based therapeutics and developing a new class of drugs, nano-siRNA drugs. However, a number of fundamental questions, regarding toxicity, immunostimulation, and poor knowledge of nano-bio interactions, need to be addressed before clinical translation. In this review, we provide recent achievements in designing and development of various non-viral delivery vehicles for pancreatic cancer therapy. More importantly, co-delivery of conventional anticancer drugs with siRNA as a new revolutionary pancreatic cancer combinational therapy is completely discussed.

pH is an important factor affecting the growth and production of microorganisms; especially, it is effective on the efficiency of ethanologenic microorganisms. It can change the ionization state of metabolites via the change in the charge of their functional groups that may lead to metabolic alteration. Here, we estimated the ionization state of metabolites and balanced the charge of reactions in genome-scale metabolic models of Saccharomyces cerevisiae, Escherichia coli, and Zymomonas mobilis at pH levels 5, 6, and 7. The robustness analysis was first implemented to anticipate the effect of proton exchange flux on growth rates for the constructed metabolic models at various pH. In accordance with previous experimental reports, the models predict that Z. mobilis is more sensitive to pH rather than S. cerevisiae and the yeast is more regulated by pH rather than E. coli. Then, a systemic approach was proposed to predict the pH effect on metabolic change and to find effective reactions on ethanol production in S. cerevisiae. The correlated reactions with ethanol production at predicted optimal pH in a range of proton exchange rates determined by robustness analysis were identified using the Pearson correlation coefficient. Then, fluxes of these reactions were applied to cluster the various pHs by principal component analysis and to identify the role of these reactions on metabolic differentiation because of pH change. Finally, 12 reactions were selected for up and down-regulation to improve ethanol production. Enzyme Regulators of the selected reactions were identified using the Brenda database and 11 selected regulators were screened and optimized via Plackett-Burman and 2-level full factorial designs, respectively. The proposed approach has enhanced yields of ethanol from 0.18 to 0.36 mol/mol carbon. Hence, not only a comprehensive approach for understanding the effect of pH on metabolism was proposed in this work, but also it successfully introduced key manipulations for ethanol overproduction.

We evaluated filtration behavior and virus removal capability for a mAb and plasma IgG under constant flow rate directly following flow-through column chromatography in an integrated process. For mAb solution with quantified host cell protein (HCP) content processed in flow-through mode on in-series mixed-mode AEX and modified CEX columns connected to the Planova BioEX filter (pool-less), HCP logarithmic reduction value (LRV) of 2.3 and 93.9% protein recovery were achieved for the process. Filtration behavior for 5 to 15 mg/mL plasma IgG run at flux of 10 to 100 LMH to 100 L/m2 throughput on Planova BioEX filters showed similar behavior across the protein concentrations tested although filtration pressure increased with throughput at 50 LMH and above, indicating the suitability of lower flux processes for continuous processing. Comparing both plasma IgG and mAb filtration behavior to four clogging models showed little difference in fit among the models, but with slightly better fit to the cake filtration model. Viral clearance tested by in-line spiking X-MuLV or MVM into purified plasma IgG showed robust removal at low flux. Integrating the Planova BioEX filter into continuous processes with column chromatography can achieve efficient downstream processing with reduced footprint and process time.

The heavy metals pollution represents one of the important issues in the environmental field since they are involved in many pathologies from cancer, neurodegenerative and metabolic diseases. We propose an innovative portable biosensor for the determination of traces of trivalent Arsenic (AsIII) and bivalent mercury (HgII) in water. The system implements a strategy combining two advanced sensing modules consisting in (a) a whole cell based on engineered Escherichia coli as selective sensing element towards the metals and (b) an electrochemical miniaturised silicon device with three microelectrodes and a portable reading system. The sensing mechanism relies on the selective recognition from the bacterium of given metals producing the 4-aminophenol (PAP) redox active mediator detected through a cyclic voltammetry analysis. The miniaturized biosensor is able to operate a portable, robust and high-sensitivity detection of AsIII with a sensitivity of 0.122 µA ppb-1, LoD of 1.5 ppb and a LoQ of 5 ppb. The LoD value is one order of magnitude below of the value indicated to WHO to be dangerous (10 μg/L). The system was proved to be fully versatile being effective in the detection of Hg(II) as well. A first study on Hg(II) showed sensitivity value of 2.11 µA/ppb a LOD value of 0.1 ppb and LoQ value of 0.34 ppb. Also in this case, the detected LOD was ten time lower than that indicated by WHO (1 ppb). These results pave the way for advanced sensing strategies suitable for the environmental monitoring and the public safety.

A bone regeneration scaffold is typically designed as a platform to effectively heal a bone defect while preventing soft tissue infiltration. Despite the wide variety of scaffold materials currently available, such as collagen, critical problems in achieving bone regeneration remain, including a rapid absorption period and low tensile strength as well as high costs. Inspired by extracellular matrix protein and topographical cues, we developed a polycaprolactone-based scaffold for bone regeneration using a soluble eggshell membrane protein (SEP) coating and a nanotopography structure for enhancing the physical properties and bioactivity. The scaffold exhibited adequate flexibility and mechanical strength as a biomedical platform for bone regeneration. The highly aligned nanostructures and SEP coating were found to regulate and enhance cell morphology, adhesion, proliferation, and differentiation in vitro. In a calvarial bone defect mouse model, the scaffolds coated with SEP applied to the defect site promoted bone regeneration along the direction of the nanotopography in vivo. These findings demonstrate that bone-inspired nanostructures and SEP coatings have high potential to be applicable in the design and manipulation of scaffolds for bone regeneration.