Use of real-time cellular analysis and Plackett-Burman design to develop the serum-free media for PC-3 prostate cancer cells

Designing optimal experiments in metabolomics

BACKGROUND

Metabolomics data is often complex due to the high number of metabolites, chemical diversity, and dependence on sample preparation. This makes it challenging to detect significant differences between factor levels and to obtain accurate and reliable data. To address these challenges, the use of Design of Experiments (DoE) techniques in the setup of metabolomic experiments is crucial. DoE techniques can be used to optimize the experimental design space, ensuring that the maximum amount of information is obtained from a limited sample space.

AIM OF REVIEW

This review aims at providing a baseline workflow for applying DoE when generating metabolomics data.

KEY SCIENTIFIC CONCEPTS OF REVIEW

The review provides insights into the theory of DoE. The review showcases the theory being put into practice by highlighting different examples DoE being applied in metabolomics throughout the literature, considering both targeted and untargeted metabolomic studies in which the data was acquired using both nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry techniques. In addition, the review presents DoE concepts not currently being applied in metabolomics, highlighting these as potential future prospects.

Development of a serum-free medium for myoblasts long-term expansion and 3D culture for cell-based meat

Cell-based meat technology provides an effective method to meet the demand for meat, while also posing a huge challenge to the expansion of myoblasts. It is difficult to develop serum-free medium suitable for long-term culture and large-scale expansion of myoblasts, which causes limited understanding of myoblasts expansion. Therefore, this study used C2C12 myoblasts as model cells and developed a serum-free medium for large-scale expansion of myoblasts in vitro using the Plackett-Burman design. The serum-free medium can support short-term proliferation and long-term passage of C2C12 myoblasts, while maintaining myogenic differentiation potential well, which is comparable to those of growth medium containing 10% fetal bovine serum. Based on the C2C12 myoblasts microcarriers serum-free culture system established in this study, the actual expansion folds of myoblasts can reach 43.55 folds after 7 days. Moreover, cell-based meat chunks were preliminarily prepared using glutamine transaminase and edible pigments. The research results provide reference for serum-free culture and large-scale expansion of myoblasts in vitro, laying the foundation for cell-based meat production. PRACTICAL APPLICATION: This study developed a serum-free medium suitable for long-term passage of myoblasts and established a microcarrier serum-free culture system for myoblasts, which is expected to solve the problem of serum-free culture and large-scale expansion of myoblasts in cell culture meat production.

Rational search of genetic design space for a heterologous terpene metabolic pathway in Streptomyces

Modern tools in DNA synthesis and assembly give genetic engineers control over the nucleotide-level design of complex, multi-gene systems. Systematic approaches to explore genetic design space and optimize the performance of genetic constructs are lacking. Here we explore the application of a five-level Plackett-Burman fractional factorial design to improve the titer of a heterologous terpene biosynthetic pathway in Streptomyces. A library of 125 engineered gene clusters encoding the production of diterpenoid ent-atiserenoic acid (eAA) via the methylerythritol phosphate pathway was constructed and introduced into Streptomyces albidoflavus J1047 for heterologous expression. The eAA production titer varied within the library by over two orders of magnitude and host strains showed unexpected and reproducible colony morphology phenotypes. Analysis of Plackett-Burman design identified expression of dxs, the gene encoding the first and the flux-controlling enzyme, having the strongest impact on eAA titer, but with a counter-intuitive negative correlation between dxs expression and eAA production. Finally, simulation modeling was performed to determine how several plausible sources of experimental error/noise and non-linearity impact the utility of Plackett-Burman analyses.

Adaptation process of engineered cell line FCHO/IL-24 stably secreted rhIL-24 in serum-free suspension culture

Interleukin-24 (IL-24) displays tumor cell-specific proliferation inhibition in vitro and in vivo. Recombinant human IL-24 (rhIL-24) has significantly higher activity, yet significantly lower expression level in mammalian cells than in bacteria. To further realize therapeutic potential of IL-24, we enhanced rhIL-24 expression in mammalian cell systems by adapting engineered Flp-In^TMCHO/IL-24 (FCHO/IL-24) cells (adherent cultured in Ham's F12 medium with 10% serum) to serum-free suspension culture. First, MTT assay showed that among four different media (F12, DMEM/F12, 1640 and DMEM), DMEM/F12 medium was the most suitable media for lower-serum adherent culture. Then, cells were adherently cultured in DMEM/F12 with serum concentration reduced from 10% to 0.5% in a gradient manner. Compared to cells in 10% serum, cells in 0.5% serum displayed significantly lower relative cell viability by 40%, increased G0/G1 phase arrest (8.5 ± 2.4%, p < 0.05), decreased supernatant rhIL-24 concentration by 73%, and altered metabolite profiles, such as glucose, lactate and ammonia concentration. Next, the cells were directly adapted to 0.5% serum suspension culture in 125 mL shake flask at 119 rpm with the optimal cell seeding density of 5 × 10⁵ cells/mL (3.3 times higher than that of adherent culture), under which the concentration of rhIL-24 in culture medium was stable at 3.5 ng/mL. Finally, cells adapted to 0.5% serum proliferated better in serum-free medium Eden™-B300S with higher rhIL-24 expression level compared to CDM4CHO. The successful adaptation of engineered cells FCHO/IL-24 laid foundation for adapting cells from adherent culture to suspension serum-free culture to mass produce rhIL-24 protein for therapeutic purposes.

Toxicity monitoring of solvents, hydrocarbons, and heavy metals using statistically optimized model of luminous Vibrio sp. 6HFE

Background

The utilization of bioluminescent bacteria in environmental monitoring of water contaminates considers being a vital and powerful approach. This study aimed to isolate, optimize, and apply luminescent bacteria for toxicity monitoring of various toxicants in wastewater.

Results

On the basis of light intensity, strain Vibrio sp. 6HFE was initially selected, physiologically/morphologically characterized, and identified using the 16SrDNA gene. The luminescence production was further optimized by employing statistical approaches (Plackett-Burman design and central composite design). The maximum bioluminescence intensity recorded 1.53 × 10⁶ CPS using optimized medium containing (g/L), yeast extract (0.2g), CaCl₂ (4.0), MgSO₄ (0.1), and K₂HPO₄ (0.1) by 2.3-fold increase within 1h. The harnessing of Vibrio sp. 6HFE as a bioluminescent reporter for toxicity of organic solvents was examined using a bioluminescence inhibition assay. According to IC₅₀ results, the toxicity order of such pollutants was chloroform > isoamyl > acetic acid > formamide > ethyl acetate > acetonitrile > DMSO > acetone > methanol. However, among eight heavy metals tested, the bioluminescence was most sensitive to Ag⁺ and Hg⁺ and least sensitive to Co²⁺ and Ni²⁺. Additionally, the bioluminescence was inhibited by benzene, catechol, phenol, and penta-chlorophenol at 443.1, 500, 535.1, and 537.4 ppm.

Conclusion

Vibrio sp. 6HFE succeeded in pollution detection at four different environmental and wastewater samples revealing its efficiency in ecotoxicity monitoring.

Clever Experimental Designs: Shortcuts for Better iPSC Differentiation

For practical use of pluripotent stem cells (PSCs) for disease modelling, drug screening, and regenerative medicine, the cell differentiation process needs to be properly refined to generate end products with consistent and high quality. To construct and optimize a robust cell-induction process, a myriad of cell culture conditions should be considered. In contrast to inefficient brute-force screening, statistical design of experiments (DOE) approaches, such as factorial design, orthogonal array design, response surface methodology (RSM), definitive screening design (DSD), and mixture design, enable efficient and strategic screening of conditions in smaller experimental runs through multifactorial screening and/or quantitative modeling. Although DOE has become routinely utilized in the bioengineering and pharmaceutical fields, the imminent need of more detailed cell-lineage specification, complex organoid construction, and a stable supply of qualified cell-derived material requires expedition of DOE utilization in stem cell bioprocessing. This review summarizes DOE-based cell culture optimizations of PSCs, mesenchymal stem cells (MSCs), hematopoietic stem cells (HSCs), and Chinese hamster ovary (CHO) cells, which guide effective research and development of PSC-derived materials for academic and industrial applications.

Transferosomes as nanocarriers for drugs across the skin: Quality by design from lab to industrial scale

Transferosomes, also known as transfersomes, are ultradeformable vesicles for transdermal applications consisting of a lipid bilayer with phospholipids and an edge activator and an ethanol/aqueous core. Depending on the lipophilicity of the active substance, it can be encapsulated within the core or amongst the lipid bilayer. Compared to liposomes, transferosomes are able to reach intact deeper regions of the skin after topical administration delivering higher concentrations of active substances making them a successful drug delivery carrier for transdermal applications. Most transferosomes contain phosphatidylcholine (C18) as it is the most abundant lipid component of the cell membrane, and hence, it is highly tolerated for the skin, decreasing the risk of undesirable effects, such as hypersensitive reactions. The most common edge activators are surfactants such as sodium deoxycholate, Tween® 80 and Span® 80. Their chain length is optimal for intercalation within the C18 phospholipid bilayer. A wide variety of drugs has been successfully encapsulated within transferosomes such as phytocompounds like sinomenine or apigenin for rheumatoid arthritis and leukaemia respectively, small hydrophobic drugs but also macromolecules like insulin. The main factors to develop optimal transferosomal formulations (with high drug loading and nanometric size) are the optimal ratio between the main components as well as the critical process parameters for their manufacture. Application of quality by design (QbD), specifically design of experiments (DoE), is crucial to understand the interplay among all these factors not only during the preparation at lab scale but also in the scale-up process. Clinical trials of a licensed topical ketoprofen transferosomal gel have shown promising results in the alleviation of symptons in orthreothritis with non-severe skin and subcutaneous tissue disorders. However, the product was withdrawn from the market which probably was related to the higher cost of the medicine linked to the expensive manufacturing process required in the production of transferosomes compared to other conventional gel formulations. This example brings out the need for a careful formulation design to exploit the best properties of this drug delivery system as well as the development of manufacturing processes easily scalable at industrial level.

A serum-free medium suitable for maintaining cell morphology and liver-specific function in induced human hepatocytes

hiHep is a new type of hepatocyte-like cell that is predicted to be a potential unlimited source of hepatocytes for a bioartificial liver. However, hiHep cannot currently be used in clinical settings because serum must be added during the culture process. Thus, a defined medium is required. Because serum is complex, an efficient statistical approach based on the Plackett-Burman design was used. In this manner, an original medium and several significant cell growth factors were identified. These factors include insulin, V_H, and V_E, and the original medium was optimized based on these significant factors. Additionally, hiHep liver-specific functions and metabolism in the optimized serum-free medium were measured. Results showed that hiHep functions, such as glycogen storage, albumin secretion, and urea production, were well maintained in our optimized serum-free medium. In summary, we created a chemically defined, serum-free medium in which cell growth, proliferation, metabolism, and function were well maintained. This medium has the potential to support the clinical use of hiHep.

Application of Mixture Design Response Surface Methodology for Combination Chemotherapy in PC-3 Human Prostate Cancer Cells

Combining chemotherapeutics to treat malignant tumors has been shown to be effective in preventing drug resistance, tumor recurrence, and reducing tumor size. We modeled combination drug therapy in PC-3 human prostate cancer cells using mixture design response surface methodology (MDRSM), a statistical technique designed to optimize compositions that we applied in a novel manner to design combinations of chemotherapeutics. Conventional chemotherapeutics (mitoxantrone, cabazitaxel, and docetaxel) and natural bioactive compounds (resveratrol, piperlongumine, and flavopiridol) were used in 12 different combinations containing three drugs at varying concentrations. Cell viability and cell cycle data were collected and used to plot response surfaces in MDRSM that identified the most effective concentrations of each drug in combination. MDRSM allows for extrapolation of data from three or more compounds in variable ratio combinations, unlike the Chou-Talalay method. MDRSM combinations were compared with combination index data from the Chou-Talalay method and were found to coincide. We propose MDRSM as an effective tool in devising combination treatments that can improve treatment effectiveness and increase treatment personalization, because MDRSM measures effectiveness rather than synergism, potentiation, or antagonism.