Optimization of chemically defined cell culture media--replacing fetal bovine serum in mammalian in vitro methods

Exploring the biological impact of bacteria-derived indole compounds on human cell health: Cytotoxicity and cell proliferation across six cell lines

Over the past two decades, research has increasingly focused on the interactions between diet, gut microbiota, and host organisms. Recent evidence suggests that tryptophan, an essential amino acid, can be metabolized by gut microbiota into indoles, which have significant biological effects. However, most research is limited to indole and its liver metabolite, indoxyl sulfate. This study examines the cytotoxic effects of five indole derivatives - indole-3-carboxylic acid (I3CA), indole-3-aldehyde (I3A), indole-3-acetic acid (IAA), indole-3-propionic acid (IPA), and 3-methylindole (skatole, 3-MI) - on six human cell lines: adipose-derived mesenchymal stem cells (MSC), hepatocellular carcinoma (HepG2), liver progenitor cells (HepaRG), colorectal carcinoma cells (Caco-2), breast cancer cells (T47D), and lung fibroblast (MRC-5). Results show no sensitivity to indole itself across cell lines. MRC-5 was sensitive to all other compounds (EC50 0.52-49.8 µM). MSCs responded to IPA, I3CA, I3A, and 3-MI (EC50 0.33-1.87 µM), while HepaRG cells were affected by IAA, I3CA, I3A, and 3-MI (EC50 1.98-66.4 µM). T47D cells were sensitive to IPA and IAA, and Caco-2 cells only to IAA (EC50 2.02, 1.68, 0.52 µM, respectively). HepG2 cells showed no change in viability. AhR activation in HepG2-AhR-Lucia cells was triggered by all derivatives, particularly I3A, IPA, and I3CA. Growth experiments revealed I3CA decreased Caco-2 proliferation while increasing T47D proliferation. The findings suggest indole derivatives are generally non-cytotoxic to carcinomas but may adversely affect stem cells, with effects varying across cell lines.

Fetal bovine serum substitution efficacy of mealworm (Tenebrio molitor) protein hydrolysates and its physicochemical properties

Fetal bovine serum (FBS) is widely used in cell culture media but raises ethical, cost, and environmental concerns. This study hypothesized that mealworm protein hydrolysates (TAH), rich in essential amino acids and known for their protective effects against oxidative stress, could serve as an FBS substitute. Short- and long-term cultivation experiments replacing 70 % of FBS with TAH in various adherent (HaCaT, C2C12, L6, H460, Panc-1) and suspension (HL-60, Jurkat) cell lines revealed no significant differences in cell growth or morphology compared to controls. Transcriptomic analysis in HaCaT cells further confirmed a high level of equivalence between TAH and FBS. Additionally, TAH demonstrated excellent thermal stability and favorable physicochemical properties, including high zeta potential and small particle size within the typical pH range for cell culture media. These results suggest TAH's broad applicability as an FBS substitute, addressing ethical, environmental, safety, and cost concerns.

Allergenicity in cultured meat: assessment and strategic management

As global population and demand for meat products rise, traditional livestock production faces major challenges in economic efficiency and environmental sustainability. Cultured meat, produced through in vitro cultivation of animal cells, has emerged as a promising alternative, offering notable environmental and public health benefits. However, safety concerns persist owing to differences in technology and materials compared with conventional food production. Additionally, a comprehensive evaluation of newly expressed proteins for allergenic potential is essential. This review examines cultured meat production processes and explores allergenicity assessment methods used for genetically modified organisms, aiming to propose an approach tailored to cultured meat. Prioritizing allergenicity assessment of cultured meat is crucial for ensuring genomic and proteomic equivalence with conventionally produced foods. It is also necessary to assess the presence of allergenic proteins and the potential for novel sensitization through integrated proteomic analysis. The allergenicity assessment framework proposed in this study will support the development of regulatory systems for cultured meat, preventing consumer safety incidents associated with these novel food products.

Modulating fatty acid metabolism and composition of CHO cells by feeding high levels of fatty acids complexed using methyl-β-cyclodextrin

Chinese Hamster Ovary (CHO) cells are widely used in the pharmaceutical industry to produce therapeutic proteins. Increasing the productivity of CHO cells through media development and genetic engineering is a significant industry objective. Past research demonstrated the benefits of modulating fatty acid composition of CHO cells through genetic engineering. In this study, we describe an alternative approach to modulate fatty acid composition by directly feeding high levels of fatty acids in CHO cell culture. To accomplish this, we developed and optimized a pharmaceutically relevant feeding strategy using methyl-β-cyclodextrin (MBCD) to solubilize fatty acids. To quantify fatty acid composition of CHO cells, a new GC-MS protocol was developed and validated. In fed batch cultures, we found that the degree of saturation of fatty acids in CHO cell mass, i.e. the relative abundances of saturated, monounsaturated and polyunsaturated fatty acids, can be controlled by the choice of fatty acid supplement and feeding strategy. Feeding unsaturated fatty acids such as palmitoleic acid, oleic acid, and linoleic acid had the greatest impact the fatty acid composition of CHO cells, increasing their respective abundances in cell mass by upwards of 25x, 1.5x, and 50x, respectively. 13C-Tracing further revealed that the supplemented fatty acids were involved in a range of elongation, desaturation, and β-oxidation reactions to yield both common and uncommon fatty acids such as vaccenic acid and hypogeic acid. Finally, we show that CHO-K1 and CHO-GS cells take up fatty acids solubilized with MBCD at rates comparable to delivery using bovine serum albumin. Taken together, this work paves the way for new feed media formulations containing fatty acids to optimize CHO cell physiology in industrial cell cultures.

Serum-free medium for recombinant protein expression in insect cells

The baculovirus expression vector system (BEVS) has been widely used to produce recombinant proteins because of several advantages, such as eukaryotic post-translational modifications similar to those in mammalian cells, high expression levels and safety, and large gene capacity. Usually, insect cell culture requires 5%‒10% fetal bovine serum, which has many adverse effects, including high cost, heterogeneity between batches, complex composition, and pollution risks. Therefore, serum-free medium (SFM) is indispensable for the production of recombinant proteins in insect cell culture. Here, the most commonly used insect cell lines and three insect cell media, namely basic medium, SFM, and chemically defined medium, are summarized. The basic components of insect cell SFM are similar to those of other cells but contain special components. The components, functions, and issues of different SFM used for insect cell culture are reviewed. In recent years, some special additives have been demonstrated to increase recombinant protein expression yield and quality in BEVS, and the functions and possible mechanisms of small-molecule additives are reviewed herein. Finally, future perspectives of SFM used in BEVS for recombinant protein production are discussed.

Advancing humanized 3D tumor modeling using an open access xeno-free medium

Despite limitations like poor mimicry of the human cell microenvironment, contamination risks, and batch-to-batch variation, cell culture media with animal-derived components such as fetal bovine serum (FBS) have been used in vitro for decades. Moreover, a few reports have used animal-product-free media in advanced high throughput three-dimensional (3D) models that closely mimic in vivo conditions. To address these challenges, we combined a high throughput 3D model with an open access, FBS-free chemically-defined medium, Oredsson Universal Replacement (OUR) medium, to create a more realistic 3D in vitro drug screening system. To reach this goal, we report the gradual adaptation procedure of three cell lines: human HeLa cervical cancer cells, human MCF-7 breast cancer cells, and cancer-associated fibroblasts (CAFs) from FBS-supplemented medium to OUR medium, while closely monitoring cell attachment, proliferation, and morphology. Our data based on cell morphology studies with phase contrast and real-time live imaging demonstrates a successful adaptation of cells to proliferate in OUR medium showing sustained growth kinetics and maintaining population doubling time. The morphological analysis demonstrates that HeLa and MCF-7 cells displayed altered cell morphology, with a more spread-out cytoplasm and significantly lower circularity index, while CAFs remained unaffected when grown in OUR medium. 3D fiber scaffolds facilitated efficient cell distribution and ingrowth when grown in OUR medium, where cells expand and infiltrate into the depths of 3D scaffolds. Drug toxicity evaluation of the widely used anti-cancer drug paclitaxel (PTX) revealed that cells grown in 3D cultures with OUR medium showed significantly lower sensitivity to PTX, which was consistent with the FBS-supplemented medium. We believe this study opens the way and encourages the scientific community to use animal product-free cell culture medium formulations for research and toxicity testing.

Alteration of primary cilia and intraflagellar transport 20 (IFT20) expression in oral squamous cell carcinoma (OSCC) cell lines

Background

Aberrations in primary cilia expression and intraflagellar transport (IFT) protein function have been implicated in tumourigenesis. This study explores the relationship between the alteration of primary cilia and tumourigenesis by investigating primary cilia expression and the role of IFT20 in regulating matrix metalloproteinase 9 (MMP-9) expression in oral squamous cell carcinoma (OSCC) cell lines.

Methods

The frequency and length of primary cilia were determined in OKF6-TERT2 cells, HSC-2 cells, and HSC-3 cells using immunofluorescence. Additionally, primary cilia presence in non-proliferating OSCC cells was examined. OSCC cells were treated with either small interfering RNA (siRNA) negative control or siRNA targeting IFT20 for functional analysis. mRNA expression levels of IFT20 and MMP-9 were quantified using quantitative reverse transcription polymerase chain reaction (qRT-PCR).

Results

Results showed that HSC-2 cells exhibit abundant primary cilia when cultured in low serum media (2% serum) for 48 h, followed by serum starvation for over 72 h. No significant changes in cilia expression were observed in HSC-3 cells compared to OKF6-TERT2 cells. Ciliated cells were found in non-proliferating HSC-2 and HSC-3 cells. OSCC cells showed longer cilia than OKF6-TERT2 cells, indicating ciliary abnormalities. Changes in ciliation and cilium length of OSCC cells were accompanied by increased expression of IFT20, an intraflagellar transport protein crucial for the primary cilia assembly. However, IFT20 knockdown did not affect MMP-9 at the mRNA level in these cells.

Conclusions

This study reveals the differences in primary cilia expression among OSCC cells. Furthermore, the increased abundance and elongation of primary cilia in OSCC cells are accompanied by elevated expression of IFT20. Nonetheless, IFT20 did not affect MMP-9 mRNA expression in OSCC cells.

Animal origins free products in cell culture media: a new frontier

Despite the importance of finding replacements for fetal bovine serum (FBS), very few studies have focused on this subject. Historically, the use of animals and their derivatives in growth, reproduction, and physiological studies has raised several concerns. The supplementation of culture media with FBS, also known as fetal calf serum, continues to be widespread, despite its limitations in quality, reproducibility, and implications for animal welfare. Moreover, the presence of counterfeit and illegal products can adversely affect cell cultures and treatments, prompting the search for alternative solutions. To reduce reliance on FBS, various substitutes have been introduced, such as plant-derived proteins, bovine eye fluid, sericin protein, human platelet lysate, and inactivated coelomic fluid, which can provide roles similar to that of FBS. Therefore, it is essential to develop serum-free and animal supplement-free environments suitable for therapeutic and clinical applications, tailored to the specific needs of different cell types. Among the alternatives, plant-based options have gained attention as sustainable and ethical solutions. These include plant-derived peptones from sources like soy and wheat, which are rich in amino acids and peptides essential for mammalian cell growth, as well as plant protein hydrolysates from beans and peas that serve as sources of amino acids and growth factors. Plant extracts, especially from soy and various seeds, contain necessary proteins and growth factors, while phytohormones such as cytokinins and plant polysaccharides can help regulate cell growth. While these alternatives offer benefits like reduced costs and lower risks of disease transmission, further research is necessary to refine and align them with the specific requirements of diverse cell types.

Graphical abstract

Systemic regulation of retinal medium-chain fatty acid oxidation repletes TCA cycle flux in oxygen-induced retinopathy

Activation of anaplerosis takes away glutamine from the biosynthetic pathways to the energy-producing TCA cycle. Especially, induction of hyperoxia driven anaplerosis in neurovascular tissues such as the retina during early stages of development could deplete biosynthetic precursors from newly proliferating endothelial cells impeding physiological angiogenesis and leading to vasoobliteration. Using an oxygen-induced retinopathy (OIR) mouse model, we investigated the metabolic differences between OIR-resistant BALB/cByJ and OIR susceptible C57BL/6J strains at system levels to understand the molecular underpinnings that potentially contribute to hyperoxia-induced vascular abnormalities in the neural retina. Our systems level in vivo RNA-seq, proteomics, and lipidomic profiling and ex-vivo retinal explant studies show that the medium-chain fatty acids serves as an alternative source to feed the TCA cycle. Our findings strongly implicate that medium-chain fatty acids could suppress glutamine-fueled anaplerosis and ameliorate hyperoxia-induced vascular abnormalities in conditions such as retinopathy of prematurity.

A Streamlined High-Throughput LC-MS Assay for Quantifying Peptide Degradation in Cell Culture

Peptides are widely used in biomaterials due to their ease of synthesis, ability to signal cells, and modify the properties of biomaterials. A key benefit of using peptides is that they are natural substrates for cell-secreted enzymes, which creates the possibility of utilizing cell-secreted enzymes for tuning cell-material interactions. However, these enzymes can also induce unwanted degradation of bioactive peptides in biomaterials, or in peptide therapies. Liquid chromatography-mass spectrometry (LC-MS) is a widely used, powerful methodology that can separate complex mixtures of molecules and quantify numerous analytes within a single run. There are several challenges in using LC-MS for the multiplexed quantification of cell-induced peptide degradation, including the need for nondegradable internal standards and the identification of optimal sample storage conditions. Another problem is that cell culture media and biological samples typically contain both proteins and lipids that can accumulate on chromatography columns and degrade their performance. Removing these constituents can be expensive, time-consuming, and increases sample variability. However, loading unpurified samples onto the column without removing lipids and proteins will foul the column. Here, we show that directly injecting complex, unpurified samples onto the LC-MS without any purification enables rapid and accurate quantification of peptide concentration and that hundreds of LC-MS runs can be done on a single column without significantly diminishing the ability to quantify the degradation of peptide libraries. To understand how repeated injections degrade column performance, a model library was injected into the LC-MS hundreds of times. It was then determined that column failure is evident when hydrophilic peptides are no longer retained on the column and that failure can be easily identified by using standard peptide mixtures for column benchmarking. In total, this work introduces a simple and effective method for simultaneously quantifying the degradation of dozens of peptides in cell culture. By providing a streamlined and cost-effective method for the direct quantification of peptide degradation in complex biological samples, this work enables more efficient assessment of peptide stability and functionality, facilitating the development of advanced biomaterials and peptide-based therapies.

Cellular milk production: Proteins and minerals in secretomes from cultivated bovine milk-derived mammary cells

This study explores the feasibility of utilizing in vitro cultivated milk-derived bovine mammary epithelial cells (bMECs) for the production of milk constituents. BMECs were isolated from milk and treated with various lactogenic agents in 3D transwell systems. By proteomics, >900 proteins were identified and quantified in the secretomes, including >100 milk-related proteins such as caseins and enzymes. Despite limited secretion of total proteins and major milk proteins, 110 proteins were found phosphorylated, including 27 involved in metal- or calcium-binding. Mineral analysis confirmed that 6-9 % of minerals in secretomes were associated with proteins. Notably, six proteins, including prolactin, were secreted into the basolateral side of bMECs without lactogenic treatment, suggesting their local de novo synthesis. This research advances our understanding of bMECs biology, as well as the compositional and functional features of their secretomes, highlighting their potential for sustainable production of functional milk proteins, meanwhile emphasizing the need for further optimization.

In vitro and in vivo assessment of a non-animal sourced chitosan scaffold loaded with xeno-free umbilical cord mesenchymal stromal cells cultured under macromolecular crowding conditions

There is an increasing demand to not only accelerate the development of advanced therapy tissue engineered medicines, but to also eliminate xenogeneic materials from their development cycle. With these in mind, herein we first assessed the influence of carrageenan as macromolecular crowding agent to enhance and accelerate extracellular matrix deposition in xeno-free human umbilical cord mesenchymal stromal cell cultures and we developed and characterised a non-animal sourced chitosan scaffold. Following appropriate in vitro experimentation, a splinted nude mouse wound healing model was used to assess wound closure and scar size of non-treated control, non-animal sourced chitosan scaffold, non-animal sourced chitosan scaffold loaded with xeno-free human umbilical cord mesenchymal stromal cells and non-animal sourced chitosan scaffold loaded with xeno-free human umbilical cord mesenchymal stromal cells cultured under macromolecular crowding conditions groups. Across all three donors, carrageenan supplementation significantly increased collagen deposition at day 5, day 8 and day 11 without affecting cell morphology, viability, DNA concentration and metabolic activity. Through freeze drying, a non-animal sourced chitosan sponge was developed with appropriate structural and mechanical properties for wound healing applications. In vitro biological analysis made apparent that neither the scaffold nor macromolecular crowding negatively impacted xeno-free human umbilical cord mesenchymal stromal cell metabolic activity and proliferation. In vivo biological analysis revealed no significant differences between the groups in wound closure and scar size, raising question about the suitability of the model. In any case, this work sets the foundations for the development of completely xeno-free tissue engineered medicines.

Single cell-inductively coupled plasma-mass spectrometry (SC-ICP-MS) reveals metallic heterogeneity in a macrophage model of infectious diseases

Single cell-inductively coupled plasma-mass spectrometry (SC-ICP-MS) offers an attractive option for rapidly measuring trace metal heterogeneity at the single cell level. Chemical fixation has been previously applied to mammalian cells prior to sample introduction so that they can be resuspended in a solution suitable for SC-ICP-MS. However, the effect of fixation on the elemental composition of suspended cells is unknown, and robust methodologies are urgently needed so that the community can measure the effects of intracellular pathogens on elemental composition of their host cells. We demonstrate that different fixatives impact measured cell elemental composition. We have compared suspensions treated using different fixatives (methanol 60-100% in H2O and 4% paraformaldehyde in phosphate-buffered saline solution), and the number of distinguishable single cell events, keeping a constant particle number concentration. Significantly more single cell events (n = 3, P ≤ 0.05) were observed for Ca and Mg when cells were fixed in 4% paraformaldehyde than for the methanol-based fixatives, confirming the hypothesis that methanol fixatives cause leaching of these elements from the cells. The impact of fixation on Mn and Zn was less pronounced. Microbial and viral infection of eukaryotic cells can have profound effects on their elemental composition, but chemical fixation is necessary to render infected cells safe before analysis. We have successfully applied our methodology to a macrophage model of tuberculosis demonstrating utility in understanding metal homeostasis during microbial infection of mammalian cells.

Increasing sustainability and reproducibility of in vitro toxicology applications: serum-free cultivation of HepG2 cells

Fetal Bovine Serum (FBS) is an important ingredient in cell culture media and the current standard for most cells in vitro. However, the use of FBS is controversial for several reasons, including ethical concerns, political, and societal pressure, as well as scientific problems due to the undefined and variable nature of FBS. Nevertheless, scientists hesitate to change the paradigm without solid data de-risking the switch of their assays to alternatives. In this study, HepG2 cells, a human hepatoblastoma cell line commonly used to study drug hepatotoxicity, were adapted to serum-free conditions by using different commercially available media and FBS replacements. After transition to these new culture conditions, the success of adaptation was determined based on cell morphology and growth characteristics. Long-term culturing capacity for each medium was defined as the number of passages HepG2 cells could be cultured without any alterations in morphology or growth behavior. Two media (Advanced DMEM/F12 from ThermoFisher and TCM® Serum Replacement from MP Biomedicals) showed a long-term cultivation capacity comparable to media containing FBS and were selected for further analysis. Both media can be characterized as serum-free, however still contain animal-derived components: bovine serum albumin (both media) and bovine transferrin (only TCM® serum replacement). To assess the functionality of the cells cultivated in either of the two media, HepG2 cells were treated with reference compounds, specifically selected for their known hepatotoxicity characteristics in man. Different toxicological assays focusing on viability, mitochondrial toxicity, oxidative stress, and intracellular drug response were performed. Throughout the different assays, response to reference compounds was comparable, with a slightly higher sensitivity of serum-free cultivated HepG2 cells when assessing viability/cell death and a lower sensitivity towards oxidative stress. Taken together, the two selected media were shown to support growth, morphology, and function of serum-free cultivated HepG2 cells in the early preclinical safety space. Therefore, these results can serve as a starting point to further optimize culture conditions with the goal to remove any remaining animal-derived components.

Chemical-Specific T Cell Tests Aim to Bridge a Gap in Skin Sensitization Evaluation

T cell activation is the final key event (KE4) in the adverse outcome pathway (AOP) of skin sensitization. However, validated new approach methodologies (NAMs) for evaluating this step are missing. Accordingly, chemicals that activate an unusually high frequency of T cells, as does the most prevalent metal allergen nickel, are not yet identified in a regulatory context. T cell reactivity to chemical sensitizers might be especially relevant in real-life scenarios, where skin injury, co-exposure to irritants in chemical mixtures, or infections may trigger the heterologous innate immune stimulation necessary to induce adaptive T cell responses. Additionally, cross-reactivity, which underlies cross-allergies, can only be assessed by T cell tests. To date, several experimental T cell tests are available that use primary naïve and memory CD4+ and CD8+ T cells from human blood. These include priming and lymphocyte proliferation tests and, most recently, activation-induced marker (AIM) assays. All approaches are challenged by chemical-mediated toxicity, inefficient or unknown generation of T cell epitopes, and a low throughput. Here, we summarize solutions and strategies to confirm in vitro T cell signals. Broader application and standardization are necessary to possibly define chemical applicability domains and to strengthen the role of T cell tests in regulatory risk assessment.

Hepatocellular-Carcinoma-Derived Organoids: Innovation in Cancer Research

Hepatocellular carcinomas (HCCs) are highly heterogeneous malignancies. They are characterized by a peculiar tumor microenvironment and dense vascularization. The importance of signaling between immune cells, endothelial cells, and tumor cells leads to the difficult recapitulation of a reliable in vitro HCC model using the conventional two-dimensional cell cultures. The advent of three-dimensional organoid tumor technology has revolutionized our understanding of the pathogenesis and progression of several malignancies by faithfully replicating the original cancer genomic, epigenomic, and microenvironmental landscape. Organoids more closely mimic the in vivo environment and cell interactions, replicating factors such as the spatial organization of cell surface receptors and gene expression, and will probably become an important tool in the choice of therapies and the evaluation of tumor response to treatments. This review aimed to describe the ongoing and potential applications of organoids as an in vitro model for the study of HCC development, its interaction with the host's immunity, the analysis of drug sensitivity tests, and the current limits in this field.

detectCilia: An R Package for Automated Detection and Length Measurement of Primary Cilia

Background and objective

The primary cilium is a small protrusion found on most mammalian cells. It acts as a cellular antenna, being involved in various cell signaling pathways. The length of the primary cilium affects its function. To study the impact of physical or chemical stimuli on cilia, their lengths must be determined easily and reproducibly.

Methods

We have developed and evaluated an open-source R package called detectCilia to detect and measure primary cilia automatically. As a case study to demonstrate the capability of our tool, we compared the influence of 4 different cell culture media compositions on the lengths of primary cilia in human chondrocytes. These media compositions include (1) insulin-transferrin-selenium (ITS); (2) ITS and dexamethasone (Dexa); (3) ITS, Dexa, insulin-like growth factor 1 (IGF-1), and transforming growth factor beta 1 (TGF-β1); and (4) fetal bovine serum (FBS).

Results

The assessment of detectCilia included a comparison with 2 similar tools: ACDC (Automated Cilia Detection in Cells) and CiliaQ. Several differences and advantages of our package make it a valuable addition to these tools. In the case study, we have observed variations in the ciliary lengths associated with using different media compositions.

Conclusions

We conclude that detectCilia can automatically and reproducibly detect and measure primary cilia in confocal microscopy images with low false-positive rates without requiring extensive user interaction.

A Streamlined High-Throughput LC-MS Assay for Quantifying Peptide Degradation in Cell Culture

Peptides are widely used in biomaterials due to their easy of synthesis, ability to signal cells, and modify the properties of biomaterials. A key benefit of using peptides is that they are natural substrates for cell-secreted enzymes, which creates the possibility of utilizing cell-secreted enzymes for tuning cell-material interactions. However, these enzymes can also induce unwanted degradation of bioactive peptides in biomaterials, or in peptide therapies. Liquid chromatography-mass spectrometry (LC-MS) is a widely used, powerful methodology that can separate complex mixtures of molecules and quantify numerous analytes within a single run. There are several challenges in using LC-MS for the multiplexed quantification of cell-induced peptide degradation, including the need for non-degradable internal standards and the identification of optimal sample storage conditions. Another problem is that cell culture media and biological samples typically contain both proteins and lipids that can accumulate on chromatography columns and degrade their performance. However, removing these constituents can be expensive, time consuming, and increases sample variability. Here we show that directly injecting samples onto the LC-MS without any purification enables rapid and accurate quantification of peptide concentration, and that hundreds of LC-MS runs can be done on a single column without a significantly diminish the ability to quantify the degradation of peptide libraries. We also show that column failure is evident when hydrophilic peptides fail to be retained on the column, and this can be easily identified using standard peptide mixtures for column benchmarking. In total, this work introduces a simple and effective method for simultaneously quantifying the degradation of dozens of peptides in cell culture. By providing a streamlined and cost-effective method for the direct quantification of peptide degradation in complex biological samples, this work enables more efficient assessment of peptide stability and functionality, facilitating the development of advanced biomaterials and peptide-based therapies.

An autonucleolytic suspension HEK293F host cell line for high-titer serum-free AAV5 and AAV9 production with reduced levels of DNA impurity

We sought to engineer mammalian cells to secrete nuclease activity as a step toward removing the need to purchase commercial nucleases as process additions in bioprocessing of AAV5 and AAV9 as gene therapy vectors. Engineering HeLa cells with a serratial nuclease transgene did not bring about nuclease activity in surrounding media whereas engineering serum-free, suspension-adapted HEK293F cells with a staphylococcal nuclease transgene did result in detectable nuclease activity in surrounding media of the resultant stable transfectant cell line, "NuPro-1S." When cultivated in serum-free media, NuPro-1S cells yielded 3.06 × 1010 AAV5 viral genomes (vg)/mL via transient transfection, compared with 3.85 × 109 vg/mL from the parental HEK293F cell line. AAV9 production, followed by purification by ultracentrifugation, yielded 1.8 × 1013 vg/mL from NuPro-1S cells compared with 7.35 × 1012 vg/mL from HEK293F cells. AAV9 from both HEK293F and NuPro-1S showed almost identical ability to transduce cells embedded in a scaffold tissue mimic or cells of mouse neonate brain tissue in vivo. Comparison of agarose gel data indicated that the DNA content of AAV5 and AAV9 process streams from NuPro-1S cells was reduced by approximately 60% compared with HEK293F cells. A similar reduction in HEK293F cells was only achievable with a 50 U/mL Benzonase treatment.

Biomodulatory Effects of Molecular Delivery in Human T Cells Using 3D-Printed Acoustofluidic Devices

OBJECTIVE

Cell-based therapies have shown significant promise for treating many diseases, including cancer. Current cell therapy manufacturing processes primarily utilize viral transduction to insert genomic material into cells, which has limitations, including variable transduction efficiency and extended processing times. Non-viral transfection techniques are also limited by high variability or reduced molecular delivery efficiency. Novel 3D-printed acoustofluidic devices are in development to address these challenges by delivering biomolecules into cells within seconds via sonoporation.

METHODS

In this study, we assessed biological parameters that influence the ultrasound-mediated delivery of fluorescent molecules (i.e., calcein and 150 kDa FITC-Dextran) to human T cells using flow cytometry and confocal imaging.

RESULTS

Low cell plating densities (100,000 cells/mL) enhanced molecular delivery compared to higher cell plating densities (p < 0.001), even though cells were resuspended at equal concentrations for acoustofluidic processing. Additionally, cells in the S phase of the cell cycle had enhanced intracellular delivery compared to cells in the G2/M phase (p < 0.001) and G0/G1 phase (p < 0.01), while also maintaining higher viability compared to G0/G1 phase (p < 0.001). Furthermore, the calcium chelator (EGTA) decreased overall molecular delivery levels. Confocal imaging indicated that the actin cytoskeleton had important implications on plasma membrane recovery dynamics after sonoporation. In addition, confocal imaging indicates that acoustofluidic treatment can permeabilize the nuclear membrane, which could enable rapid intranuclear delivery of nucleic acids.

CONCLUSIONS

The results of this study demonstrate that a 3D-printed acoustofluidic device can enhance molecular delivery to human T cells, which may enable improved techniques for non-viral processing of cell therapies.

Development of a defined medium for the heterotrophic cultivation of Metallosphaera sedula

The heterotrophic cultivation of extremophilic archaea still heavily relies on complex media. However, complex media are associated with unknown composition, high batch-to-batch variability, potential inhibiting and interfering components, as well as regulatory challenges, hampering advancements of extremophilic archaea in genetic engineering and bioprocessing. For Metallosphaera sedula, a widely studied organism for biomining and bioremediation and a potential production host for archaeal ether lipids, efforts to find defined cultivation conditions have still been unsuccessful. This study describes the development of a novel chemically defined growth medium for M. sedula. Initial experiments with commonly used complex casein-derived media sources deciphered Casamino Acids as the most suitable foundation for further development. The imitation of the amino acid composition of Casamino Acids in basal Brock medium delivered the first chemically defined medium. We could further simplify the medium to 5 amino acids based on the respective specific substrate uptake rates. This first defined cultivation medium for M. sedula allows advanced genetic engineering and more controlled bioprocess development approaches for this highly interesting archaeon.

Non-animal protein hydrolysates from agro-industrial wastes: A prospect of alternative inputs for cultured meat

In light of the growing demand for alternative protein sources, laboratory-grown meat has been proposed as a potential solution to the challenges posed by conventional meat production. Cultured meat does not require animal slaughter and uses sustainable production methods, contributing to animal welfare, human health, and environmental sustainability. However, some challenges still need to be addressed in cultured meat production, such as the use of fetal bovine serum for medium supplementation. This ingredient has limited availability, increases production costs, and raises ethical concerns. This review explores the potential of non-animal protein hydrolysates derived from agro-industrial wastes as substitutes for critical components of fetal bovine serum in cultured meat production. Despite the lack of standardization of hydrolysate composition, the potential benefits of this alternative protein source may outweigh its disadvantages. Future research holds promise for increasing the accessibility of cultured meat.

Advances in serum-free media for CHO cells: From traditional serum substitutes to microbial-derived substances

The Chinese hamster ovary (CHO) cell is an epithelial-like cell that produces proteins with post-translational modifications similar to human glycosylation. It is widely used in the production of recombinant therapeutic proteins and monoclonal antibodies. Culturing CHO cells typically requires the addition of a certain proportion of fetal bovine serum (FBS) to maintain cell proliferation and passaging. However, serum is characterized by its complex composition, batch-to-batch variability, high cost, and potential risk of exogenous contaminants such as mycoplasma and viruses, which impact the purity and safety of the synthesized proteins. Therefore, search for serum alternatives and development of serum-free media for CHO-based protein biomanufacturing are of great significance. This review systematically summarizes the application advantages of CHO cells and strategies for high-density expression. It highlights the developmental trends of serum substitutes from human platelet lysates to animal-free extracts and microbial-derived substances and elucidates the mechanisms by which these substitutes enhance CHO cell culture performance and recombinant protein production, aiming to provide theoretical guidance for exploring novel serum alternatives and developing serum-free media for CHO cells.

The addition of mammalian cell culture medium impacts nanoparticle toxicity in zebrafish

Engineered nanomaterials (ENMs) are ubiquitous in contemporary applications, yet their environmental and human health impacts remain inadequately understood. This study addresses the challenge of identifying potential risks associated with ENM exposure by highlighting the significant variability in existing research methodologies. Without a systematic collection of toxicological data that encompasses standardized materials, relevant platforms, and assays, the task of identifying potential risks linked to ENM exposure becomes an intricate challenge. In vitro assessments often use media rich in ionic species, such as RPMI and fetal bovine serum (FBS). Zebrafish embryos, known to develop normally in low-ionic environments, were exposed to Cerium Oxide, Zinc Oxide, and Graphene Oxides in different media at varying concentrations. Here, we discovered that zebrafish embryos tolerated a mix of 80 % RPMI, 2 % FBS, and 1 % antibiotic cocktail. The results revealed that adverse effects observed in zebrafish with certain nanomaterials in Ultra-Pure (UP) water were mitigated in cell culture medium, emphasizing the importance of revisiting previously considered non-toxic materials in vitro. The zebrafish results underscore the importance of utilizing a multidimensional in vivo platform to gauge the biological activity of nanomaterials accurately.

The influence of xeno-free culture conditions on the angiogenic and adipogenic differentiation properties of adipose tissue-derived stem cells

Introduction

Before performing cell therapy clinical trials, it is important to understand how cells are influenced by different growth conditions and to find optimal xeno-free medium formulations. In this study we have investigated the properties of adipose tissue-derived stem cells (ASCs) cultured under xeno-free conditions.

Methods

Human lipoaspirate samples were digested to yield the stromal vascular fraction cells which were then seeded in i) Minimum Essential Medium-α (MEM-α) supplemented with 10 % (v/v) fetal bovine serum (FBS), ii) MEM-α supplemented with 2 % (v/v) human platelet lysate (PLT) or iii) PRIME-XV MSC expansion XSFM xeno-free, serum free medium (XV). Flow cytometry for ASCs markers CD73, CD90 and CD105 together with the putative pericyte marker CD146 was performed. Growth rates were monitored over multiple passages and adipogenic differentiation performed at early and expanded passage culture. Growth factor gene expression was analyzed and an in vitro angiogenesis assay performed.

Results

Cells in FBS and PLT grew at similar rates whereas the cells cultured in XV medium proliferated significantly faster up to 60 days in culture. All cultures were >98 % positive for CD73, CD90 and CD105, whereas CD146 expression was significantly higher in XV cells. Adipogenic differentiation was most pronounced in cells which had been cultured in XV medium whilst cells grown in PLT were inferior compared with cells from the FBS cultures. IGF1 gene expression was highest in cells cultured in PLT whilst cells grown in XV medium showed 10-fold lower expression compared with FBS cells. In contrast, HGF gene expression was 90-fold greater in cells cultured in XV medium compared with those cultured in FBS. Conditioned medium from XV cultured cells showed the most angiogenic activity, inducing the greatest endothelial cell network formation and maturation.

Conclusion

Culture under different conditions alters the ASCs characteristics. Since cells cultured in XV medium showed the best adipogenic and angiogenic profile this might be a preferred medium formulation for preparing cells required for reconstructive surgical applications such as cell-assisted fat grafting.

Development of a chemically disclosed serum-free medium for mouse pluripotent stem cells

Mouse embryonic stem cells (mESCs) have been widely used as a model system to study the basic biology of pluripotency and to develop cell-based therapies. Traditionally, mESCs have been cultured in a medium supplemented with fetal bovine serum (FBS). However, serum with its inconsistent chemical composition has been problematic for reproducibility and for studying the role of specific components. While some serum-free media have been reported, these media contain commercial additives whose detailed components have not been disclosed. Recently, we developed a serum-free medium, DA-X medium, which can maintain a wide variety of adherent cancer lines. In this study, we modified the DA-X medium and established a novel serum-free condition for both naïve mESCs in which all components are chemically defined and disclosed (DA-X-modified medium for robust growth of pluripotent stem cells: DARP medium). The DARP medium fully supports the normal transcriptome and differentiation potential in teratoma and the establishment of mESCs from blastocysts that retain the developmental potential in all three germ layers, including germ cells in chimeric embryos. Utility of chemically defined DA-X medium for primed mouse epiblast stem cells (mEpiSCs) revealed that an optimal amount of cholesterol is required for the robust growth of naïve-state mESCs, but is dispensable for the maintenance of primed-state mEpiSCs. Thus, this study provides reliable and reproducible culture methods to investigate the role of specific components regulating self-renewal and pluripotency in a wide range of pluripotent states.

Brain organoids engineered to give rise to glia and neural networks after 90 days in culture exhibit human-specific proteoforms

Human brain organoids are emerging as translationally relevant models for the study of human brain health and disease. However, it remains to be shown whether human-specific protein processing is conserved in human brain organoids. Herein, we demonstrate that cell fate and composition of unguided brain organoids are dictated by culture conditions during embryoid body formation, and that culture conditions at this stage can be optimized to result in the presence of glia-associated proteins and neural network activity as early as three-months in vitro. Under these optimized conditions, unguided brain organoids generated from induced pluripotent stem cells (iPSCs) derived from male-female siblings are similar in growth rate, size, and total protein content, and exhibit minimal batch-to-batch variability in cell composition and metabolism. A comparison of neuronal, microglial, and macroglial (astrocyte and oligodendrocyte) markers reveals that profiles in these brain organoids are more similar to autopsied human cortical and cerebellar profiles than to those in mouse cortical samples, providing the first demonstration that human-specific protein processing is largely conserved in unguided brain organoids. Thus, our organoid protocol provides four major cell types that appear to process proteins in a manner very similar to the human brain, and they do so in half the time required by other protocols. This unique copy of the human brain and basic characteristics lay the foundation for future studies aiming to investigate human brain-specific protein patterning (e.g., isoforms, splice variants) as well as modulate glial and neuronal processes in an in situ-like environment.

Sources of biases in the in vitro testing of nanomaterials: the role of the biomolecular corona

The biological fate of nanomaterials (NMs) is driven by specific interactions through which biomolecules, naturally adhering onto their surface, engage with cell membrane receptors and intracellular organelles. The molecular composition of this layer, called the biomolecular corona (BMC), depends on both the physical-chemical features of the NMs and the biological media in which the NMs are dispersed and cells grow. In this work, we demonstrate that the widespread use of 10% fetal bovine serum in an in vitro assay cannot recapitulate the complexity of in vivo systemic administration, with NMs being transported by the blood. For this purpose, we undertook a comparative journey involving proteomics, lipidomics, high throughput multiparametric in vitro screening, and single molecular feature analysis to investigate the molecular details behind this in vivo/in vitro bias. Our work indirectly highlights the need to introduce novel, more physiological-like media closer in composition to human plasma to produce realistic in vitro screening data for NMs. We also aim to set the basis to reduce this in vitro-in vivo mismatch, which currently limits the formulation of NMs for clinical settings.

Selection of Fermentation Supernatant from Probiotic Strains Exhibiting Intestinal Epithelial Barrier Protective Ability and Evaluation of Their Effects on Colitis Mouse and Weaned Piglet Models

The intestinal epithelial barrier can prevent the invasion of pathogenic microorganisms and food antigens to maintain a consistent intestinal homeostasis. However, an imbalance in this barrier can result in various diseases, such as inflammatory bowel disease, malnutrition, and metabolic disease. Thus, the aim of this study was to select probiotic strains with epithelial barrier-enhancing ability in cell-based model and further investigate them for their improving effects on colitis mouse and weaned piglet models. The results showed that selected specific cell-free fermentation supernatants (CFSs) from Ligilactobacillus salivarius P1, Lactobacillus gasseri P12, and Limosilactobacillus reuteri G7 promoted intestinal epithelial cell growth and proliferation, strengthening the intestinal barrier in an intestinal epithelial cell line Caco-2 model. Further, the administration of CFSs of L. salivarius P1, L. gasseri P12, and L. reuteri G7 were found to ameliorate DSS-induced colitis in mice. Additionally, spray-dried powders of CFS from the three strains were examined in a weaned piglet model, only CFS powder of L. reuteri G7 could ameliorate the feed/gain ratio and serum levels of D-lactate and endotoxin. In conclusion, a new potential probiotic strain, L. reuteri G7, was selected and showed ameliorating effects in both colitis mouse and weaned piglet models.

Protective role of fetal bovine serum on PLHC-1 spheroids exposed to a mixture of plastic additives: A lipidomic perspective

The use of fetal bovine serum (FBS) in cell culture is being questioned for scientific and ethical reasons, prompting the exploration of alternative approaches. Nevertheless, the influence of FBS on cell functioning, especially in fish cells, has not been comprehensively examined. This study aims to evaluate the impact of FBS on the lipidome of PLHC-1 spheroids and investigate cellular and molecular responses to plastic additives in the presence/absence of FBS. Lipidomic analyses were conducted on PLHC-1 cell spheroids using liquid chromatography coupled with a high-resolution quadrupole time-of-flight mass spectrometer (HRMS-QToF). The removal of FBS from the culture medium for 24 h significantly changed the lipid profile of spheroids, resulting in a depletion of cholesterol esters (CEs), phosphatidylcholines (PCs) and lyso-phosphatidylcholines (LPCs), while ceramides and certain glycerophospholipids slightly increased. Additionally, the exclusion of FBS from the medium led to increased cytotoxicity caused by a mixture of plastic additives and increased lipidomic alterations, including an elevation of ceramides. This study emphasizes the protective role of serum components in fish liver spheroids against a mixture of plastic additives and underscores the importance of considering exposure conditions when studying metabolomic and lipidomic responses to toxicants.

Bovine mammary epithelial cells can grow and express milk protein synthesis genes at reduced fetal bovine serum concentration

Milk proteins produced by lactating cells isolated from bovine mammary tissue can offer a sustainable solution to the high protein demand of a global growing population. Serum is commonly added to culture systems to provide compounds necessary for optimal growth and function of the cells. However, in a cellular agricultural context, its usage is desired to be decreased. This study aims at examining the minimum level of fetal bovine serum (FBS) required for the growth and functionality of bovine mammary epithelial cells (MECs). The cells were isolated from dairy cows in early and mid-lactation and cultured in reduced concentrations of FBS (10%, 5%, 1.25%, and 0%). Real-time cell analysis showed a significant effect of lactation stage on growth rate and 5% FBS resulted in similar growth rate as 10% while 0% resulted in the lowest. The effect of reducing FBS on cell functionality was examined by studying the expressions of selected marker genes involved in milk protein and fat synthesis, following differentiation. The gene expressions were not affected by the level of FBS. A reduction of FBS in the culture system of MEC, at least down to 5%, does not assert any negative effect on the growth and expression levels of studied genes. As the first attempt in developing an in-vitro model for milk component production using MEC, our results demonstrate the potential of MEC to endure FBS-reduced conditions.

Improving Bioprocess Conditions for the Production of Prodigiosin Using a Marine Serratia rubidaea Strain

The enormous potential attributed to prodigiosin regarding its applicability as a natural pigment and pharmaceutical agent justifies the development of sound bioprocesses for its production. Using a Serratia rubidaea strain isolated from a shallow-water hydrothermal vent, optimization of the growth medium composition was carried out. After medium development, the bacterium temperature, light and oxygen needs were studied, as was growth inhibition by product concentration. The implemented changes led to a 13-fold increase in prodigiosin production in a shake flask, reaching 19.7 mg/L. The conditions allowing the highest bacterial cell growth and prodigiosin production were also tested with another marine strain: S. marcescens isolated from a tide rock pool was able to produce 15.8 mg/L of prodigiosin. The bioprocess with S. rubidaea was scaled up from 0.1 L shake flasks to 2 L bioreactors using the maintenance of the oxygen mass transfer coefficient (kLa) as the scale-up criterion. The implemented parameters in the bioreactor led to an 8-fold increase in product per biomass yield and to a final concentration of 293.1 mg/L of prodigiosin in 24 h.

Toward reproducible tumor organoid culture: focusing on primary liver cancer

Organoids present substantial potential for pushing forward preclinical research and personalized medicine by accurately recapitulating tissue and tumor heterogeneity in vitro. However, the lack of standardized protocols for cancer organoid culture has hindered reproducibility. This paper comprehensively reviews the current challenges associated with cancer organoid culture and highlights recent multidisciplinary advancements in the field with a specific focus on standardizing liver cancer organoid culture. We discuss the non-standardized aspects, including tissue sources, processing techniques, medium formulations, and matrix materials, that contribute to technical variability. Furthermore, we emphasize the need to establish reproducible platforms that accurately preserve the genetic, proteomic, morphological, and pharmacotypic features of the parent tumor. At the end of each section, our focus shifts to organoid culture standardization in primary liver cancer. By addressing these challenges, we can enhance the reproducibility and clinical translation of cancer organoid systems, enabling their potential applications in precision medicine, drug screening, and preclinical research.

Biochemical and functional characterization of heat-inactivated coelomic fluid from earthworms as a potential alternative for fetal bovine serum in animal cell culture

Fetal bovine serum (FBS) plays a pivotal role in animal cell culture. Due to ethical and scientific issues, searching for an alternative, comprising the three R's (Refinement, Reduction and Replacement) gained global attention. In this context, we have identified the heat inactivated coelomic fluid (HI-CF) of the earthworm, Perionyx excavatus as a potential alternative for FBS. Briefly, we formulated HI-CF (f-HICF) containing serum free medium which can aid the growth, attachment, and proliferation of adherent cells, similar to FBS. In this study, we investigated the biochemical characterization, sterility, stability, formulation, and functional analysis of HI-CF as a supplement in culturing animal cells. Notably, vitamins, micronutrients, proteins, lipids, and trace elements are identified and compared with FBS for effective normalization of the serum free media. HI-CF is tested to be devoid of endotoxin and mycoplasma contamination thus can qualify the cell culture grade. The f-HICF serum free media was prepared, optimised, and tested with A549, HeLa, 3T3, Vero and C2C12 cell lines. Our results conclude that f-HICF is a potential alternative to FBS, in accordance with ethical concern; compliance with 3R's; lack of unintended antibody interactions; presence of macro and micronutrients; simple extraction; cost-effectiveness and availability.

A systematic review of patient-derived tumor organoids generation from malignant effusions

This review assesses the possibility of utilizing malignant effusions (MEs) for generating patient-derived tumor organoids (PDTOs). Obtained through minimally invasive procedures MEs broaden the spectrum of organoid sources beyond resection specimens and tissue biopsies. A systematic search yielded 11 articles, detailing the successful generation of 190 ME-PDTOs (122 pleural effusions, 54 malignant ascites). Success rates ranged from 33% to 100%, with an average of 84% and median of 92%. A broad and easily applicable array of techniques can be employed, encompassing diverse collection methods, variable centrifugation speeds, and the inclusion of approaches like RBC lysis buffer or centrifuged ME supernatants supplementation, enhancing the versatility and accessibility of the methodology. ME-PDTOs were found to recapitulate primary tumor characteristics and were primarily used for drug screening applications. Thus, MEs are a reliable source for developing PDTOs, emphasizing the need for further research to maximize their potential, validate usage, and refine culturing processes.

Long-Term Porcine Retina Explants as an Alternative to In Vivo Experimentation

Purpose

The porcine retina represents an optimal model system to study treatment approaches for inherited retinal dystrophies owing to close anatomical similarities to the human retina, including a cone enriched visual streak. The aim of this work was to establish a protocol to keep explants in culture for up to 28 days with good morphological preservation.

Methods

Two to four retina explants per eye were obtained from the central part of the retina and transferred onto a membrane insert with the photoreceptors facing down. Different medium compositions using Neurobasal-A medium containing 100 or 450 mg/dL glucose and combinations of fetal calf serum, B-27 with or without insulin and N-2 were tested. We developed a tissue quality score with robust markers for different retinal cell types (protein kinase C alpha, peanut agglutinin and 4',6-diamidino-2-phenylindol).

Results

Retinae were kept until 28 days with only little degradation. The best results were attained using Neurobasal-A medium containing 100 mg/dL glucose supplemented with B-27 containing insulin and N-2. For an easy preparation process, it is necessary to minimize transport time and keep the eyes on ice until dissected. Heat-mediated decontamination by the butcher has to be avoided.

Conclusions

Using a standardized protocol, porcine retina explants represent an easy to handle intermediate model between in vitro and in vivo experimentation. This model system is robustly reproducible and contributes to the implementation of the 3R principle to minimize animal experimentation.

Translational Relevance

This model can be used to test future therapeutic approaches for inherited retinal dystrophies.

Xeno-Free 3D Bioprinted Liver Model for Hepatotoxicity Assessment

Three-dimensional (3D) bioprinting is one of the most promising methodologies that are currently in development for the replacement of animal experiments. Bioprinting and most alternative technologies rely on animal-derived materials, which compromises the intent of animal welfare and results in the generation of chimeric systems of limited value. The current study therefore presents the first bioprinted liver model that is entirely void of animal-derived constituents. Initially, HuH-7 cells underwent adaptation to a chemically defined medium (CDM). The adapted cells exhibited high survival rates (85-92%) after cryopreservation in chemically defined freezing media, comparable to those preserved in standard medium (86-92%). Xeno-free bioink for 3D bioprinting yielded liver models with high relative cell viability (97-101%), akin to a Matrigel-based liver model (83-102%) after 15 days of culture. The established xeno-free model was used for toxicity testing of a marine biotoxin, okadaic acid (OA). In 2D culture, OA toxicity was virtually identical for cells cultured under standard conditions and in CDM. In the xeno-free bioprinted liver model, 3-fold higher concentrations of OA than in the respective monolayer culture were needed to induce cytotoxicity. In conclusion, this study describes for the first time the development of a xeno-free 3D bioprinted liver model and its applicability for research purposes.

Comparison between Platelet Lysate, Platelet Lysate Serum, and Fetal Bovine Serum as Supplements for Cell Culture, Expansion, and Cryopreservation

As cell culture supplements, human platelet lysate (PL) and human platelet lysate serum (PLS) are alternatives to fetal bovine serum (FBS) due to FBS-related issues such as ethical concerns, variability between batches, and the possible introduction of xenogenic contaminants. This study compared the composition and efficacy of PL, PLS, and FBS as supplements in the culture and cryopreservation of human dermal fibroblasts, Wharton's jelly-derived mesenchymal stem cells (WJ-MCS), and adipose tissue (AdMSC). Biochemical components, some growth factors, and cytokines present in each of them were analyzed; in addition, the cells were cultured in media supplemented with 5% PL, 5% PLS, and 10% FBS and exposed to different freezing and thawing solutions with the supplements under study. Biochemical parameters were found to be similar in PL and PLS compared to FBS, with some differences in fibrinogen and calcium concentration. Growth factors and cytokines were higher in PL and PLS compared to FBS. Cell proliferation and morphology showed no significant differences between the three culture media. Regarding the cryopreservation and thawing of cells, better results were obtained with PLS and FBS. In conclusion, PL and PLS are an excellent choice to replace the standard supplement of animal origin (FBS) in the media used for the culture and cryopreservation of fibroblasts, WJ-MSC, and AdMSC.

Challenges in developing cell culture media using machine learning

Microbial and mammalian cells are widely used in the food, pharmaceutical, and medical industries. Developing or optimizing culture media is essential to improve cell culture performance as a critical technology in cell culture engineering. Methodologies for media optimization have been developed to a great extent, such as the approaches of one-factor-at-a-time (OFAT) and response surface methodology (RSM). The present review introduces the emerging machine learning (ML) technology in cell culture engineering by combining high-throughput experimental technologies to develop highly efficient and effective culture media. The commonly used ML algorithms and the successful applications of employing ML in medium optimization are summarized. This review highlights the benefits of ML-assisted medium development and guides the selection of the media optimization method appropriate for various cell culture purposes.

Secretome as a Tool to Treat Neurological Conditions: Are We Ready?

Due to their characteristics, mesenchymal stem cells (MSCs) are considered a potential therapy for brain tissue injury or degeneration. Nevertheless, despite the promising results observed, there has been a growing interest in the use of cell-free therapies in regenerative medicine, such as the use of stem cell secretome. This review provides an in-depth compilation of data regarding the secretome composition, protocols used for its preparation, as well as existing information on the impact of secretome administration on various brain conditions, pointing out gaps and highlighting relevant findings. Moreover, due to the ability of MSCs to respond differently depending on their microenvironment, preconditioning of MSCs has been used to modulate their composition and, consequently, their therapeutic potential. The different strategies used to modulate the MSC secretome were also reviewed. Although secretome administration was effective in improving functional impairments, regeneration, neuroprotection, and reducing inflammation in brain tissue, a high variability in secretome preparation and administration was identified, compromising the transposition of preclinical data to clinical studies. Indeed, there are no reports of the use of secretome in clinical trials. Despite the existing limitations and lack of clinical data, secretome administration is a potential tool for the treatment of various diseases that impact the CNS.

In vitro formation and extended culture of highly metabolically active and contractile tissues

3D cell culture models have gained popularity in recent years as an alternative to animal and 2D cell culture models for pharmaceutical testing and disease modeling. Polydimethylsiloxane (PDMS) is a cost-effective and accessible molding material for 3D cultures; however, routine PDMS molding may not be appropriate for extended culture of contractile and metabolically active tissues. Failures can include loss of culture adhesion to the PDMS mold and limited culture surfaces for nutrient and waste diffusion. In this study, we evaluated PDMS molding materials and surface treatments for highly contractile and metabolically active 3D cell cultures. PDMS functionalized with polydopamine allowed for extended culture duration (14.8 ± 3.97 days) when compared to polyethylamine/glutaraldehyde functionalization (6.94 ± 2.74 days); Additionally, porous PDMS extended culture duration (16.7 ± 3.51 days) compared to smooth PDMS (6.33 ± 2.05 days) after treatment with TGF-β2 to increase culture contraction. Porous PDMS additionally allowed for large (13 mm tall × 8 mm diameter) constructs to be fed by diffusion through the mold, resulting in increased cell density (0.0210 ± 0.0049 mean nuclear fraction) compared to controls (0.0045 ± 0.0016 mean nuclear fraction). As a practical demonstration of the flexibility of porous PDMS, we engineered a vascular bioartificial muscle model (VBAM) and demonstrated extended culture of VBAMs anchored with porous PDMS posts. Using this model, we assessed the effect of feeding frequency on VBAM cellularity. Feeding 3×/week significantly increased nuclear fraction at multiple tissue depths relative to 2×/day. VBAM maturation was similarly improved in 3×/week feeding as measured by nuclear alignment (23.49° ± 3.644) and nuclear aspect ratio (2.274 ± 0.0643) relative to 2x/day (35.93° ± 2.942) and (1.371 ± 0.1127), respectively. The described techniques are designed to be simple and easy to implement with minimal training or expense, improving access to dense and/or metabolically active 3D cell culture models.

Integrating intracellular and extracellular proteomic profiling for in-depth investigations of cellular communication in a model of prostate cancer

Cellular communication is essential for cell-cell interactions, maintaining homeostasis and progression of certain disease states. While many studies examine extracellular proteins, the holistic extracellular proteome is often left uncaptured, leaving gaps in our understanding of how all extracellular proteins may impact communication and interaction. We used a cellular-based proteomics approach to more holistically profile both the intracellular and extracellular proteome of prostate cancer. Our workflow was generated in such a manner that multiple experimental conditions can be observed with the opportunity for high throughput integration. Additionally, this workflow is not limited to a proteomic aspect, as metabolomic and lipidomic studies can be integrated for a multi-omics workflow. Our analysis showed coverage of over 8000 proteins while also garnering insights into cellular communication in the context of prostate cancer development and progression. Identified proteins covered a variety of cellular processes and pathways, allowing for the investigation of multiple aspects into cellular biology. This workflow demonstrates advantages for integrating intra- and extracellular proteomic analyses as well as potential for multi-omics researchers. This approach possesses great value for future investigations into the systems biology aspects of disease development and progression.

Effect assessment of a type of xeno-free and serum-free human adipose-derived mesenchymal stem cells culture medium by proliferation and differentiation capacities

Human mesenchymal stem cells (hMSCs) possess broad prospects in pre-clinical research. In vitro amplification of hMSCs requires appropriate medium to reach the number of seed cells with clinical significance. However, the uncertainty of the heterologous components of the traditional fetal bovine serum (FBS) culture medium has great safety risks. Moreover, existing commercial hMSCs medium is very expensive, therefore a safer and more optimal hMSCs medium is urgently needed. Accordingly, we developed five components adipose-derived hMSCs (hADMSCs) medium without xenogenic components, named E5 SFM. which is mainly composed of knockout serum replacement (KSR), and additionally four components such as fibroblast growth factor and transferrin. Here, we mainly compared the E5 SFM with traditional FBS-containing medium and a commercial medium by surface markers testing, proliferation assay as well as osteogenic, adipogenic and chondrogenic differentiation assessment. We demonstrated that hADMSCs cultured in the E5 SFM showed similar morphological characteristics and immunophenotypes to those in other media. Notably, cell proliferative capability was similar to that in the commercial medium, but higher than that in the FBS-containing medium and other media. Additionally, their capabilities of adipogenic and osteogenic differentiation were significantly higher than those of other media. Consequently, we concluded that the E5 SFM medium can not only effectively promote cell proliferation of hMSCs, but also has optimal differentiative capacity and clear and simple ingredients.

The interaction between the environment and embryo development in assisted reproduction

It can be assumed that the natural processes of selection and developmental condition in the animal provide the best prerequisites for embryogenesis resulting in pregnancy and subsequent birth of a healthy neonate. In contrast, circumventing the natural selection mechanisms and all developmental conditions in a healthy animal harbors the risk of counteracting, preventing or reducing the formation of embryos or substantially restricting their genesis. Considering these facts, it seems to be obvious that assisted reproductive techniques focusing on early embryonic stages serve an expanded and unselected germ cell pool of oocytes and sperm cells, and include the culture of embryos outside their natural habitat during and after fertilization for manipulation and diagnostic purposes, and for storage. A significant influence on the early embryonic development is seen in the extracorporeal culture of bovine embryos (in vitro) or stress on the animal organism (in vivo). The in vitro production per se and metabolic as well as endocrine changes in the natural environment of embryos represent adequate models and serve for a better understanding. The purpose of this review is to give a brief presentation of recent techniques aimed at focusing more on the complex processes in the Fallopian tube to contrast in vivo and in vitro prerequisites and abnormalities in early embryonic development and serve to identify potential new ways to make the use of ARTs more feasible.

Enhanced Expansion of Human Pluripotent Stem Cells and Somatic Cell Reprogramming Using Defined and Xeno-Free Culture Conditions

Human embryonic stem cells and induced pluripotent stem cells (hPSC) have an unprecedented opportunity to revolutionize the fields of developmental biology as well as tissue engineering and regenerative medicine. However, their applications have been significantly limited by the lack of chemically defined and xeno-free culture conditions. The demand for the high-quality and scaled-up production of cells for use in both research and clinical studies underscores the need to develop tools that will simplify the in vitro culture process while reducing the variables. Here, we describe a systematic study to identify the optimal conditions for the initial cell attachment of hPSC to tissue culture dishes grafted with polymers of N-(3-Sulfopropyl)-N-Methacryloxyethyl-N, N-Dimethylammoniun Betaine (PMEDSAH) in combination with chemically defined and xeno-free culture media. After testing multiple supplements and chemicals, we identified that pre-conditioning of PMEDSAH grafted plates with 10% human serum (HS) supported the initial cell attachment, which allowed for the long-term culture and maintenance of hPSC compared to cells cultured on Matrigel-coated plates. Using this culture condition, a 2.1-fold increase in the expansion of hPSC was observed without chromosomal abnormalities. Furthermore, this culture condition supported a higher reprogramming efficiency (0.37% vs. 0.22%; p < 0.0068) of somatic cells into induced pluripotent stem cells compared to the non-defined culture conditions. This defined and xeno-free hPSC culture condition may be used in obtaining the large populations of hPSC and patient-derived iPSC required for many applications in regenerative and translational medicine.

Production of Tissue-Engineered Skin Substitutes for Clinical Applications: Elimination of Serum

Tissue-engineered skin substitutes (TESs) are used as a treatment for severe burn injuries. Their production requires culturing both keratinocytes and fibroblasts. The methods to grow these cells have evolved over the years, but bovine serum is still commonly used in the culture medium. Because of the drawbacks associated with the use of serum, it would be advantageous to use serum-free media for the production of TESs. In a previous study, we developed a serum-free medium (Surge SFM) for the culture of keratinocytes. Herein, we tested the use of this medium, together with a commercially available serum-free medium for fibroblasts (Prime XV), to produce serum-free TESs. Our results show that serum-free TESs are macroscopically and histologically similar to skin substitutes produced with conventional serum-containing media. TESs produced with either culture media expressed keratin 14, Ki-67, transglutaminase 1, filaggrin, type I and IV collagen, and fibronectin comparably. Mechanical properties, such as contraction and tensile strength, were comparable between TESs cultured with and without serum. Serum-free TESs were also successfully grafted onto athymic mice for a six-month period. In conclusion, Surge SFM and Prime XV serum-free media could be used to produce high quality clinical-grade skin substitutes.

Expansion of bovine skeletal muscle stem cells from spinner flasks to benchtop stirred-tank bioreactors for up to 38 days

Introduction

Successful long-term expansion of skeletal muscle satellite cells (MuSCs) on a large scale is fundamental for cultivating animal cells for protein production. Prerequisites for efficient cell expansion include maintaining essential native cell activities such as cell adhesion, migration, proliferation, and differentiation while ensuring consistent reproducibility.

Method

This study investigated the growth of bovine MuSC culture using low-volume spinner flasks and a benchtop stirred-tank bioreactor (STR).

Results and discussion

Our results showed for the first time the expansion of primary MuSCs for 38 days in a bench-top STR run with low initial seeding density and FBS reduction, supported by increased expression of the satellite cell marker PAX7 and reduced expression of differentiation-inducing genes like MYOG, even without adding p38-MAPK inhibitors. Moreover, the cells retained their ability to proliferate, migrate, and differentiate after enzymatic dissociation from the microcarriers. We also showed reproducible results in a separate biological benchtop STR run.

Multi-objective Bayesian algorithm automatically discovers low-cost high-growth serum-free media for cellular agriculture application

In this work, we applied a multi-information source modeling technique to solve a multi-objective Bayesian optimization problem involving the simultaneous minimization of cost and maximization of growth for serum-free C2C12 cells using a hyper-volume improvement acquisition function. In sequential batches of custom media experiments designed using our Bayesian criteria, collected using multiple assays targeting different cellular growth dynamics, the algorithm learned to identify the trade-off relationship between long-term growth and cost. We were able to identify several media with > 100 % more growth of C2C12 cells than the control, as well as a medium with 23% more growth at only 62.5% of the cost of the control. These algorithmically generated media also maintained growth far past the study period, indicating the modeling approach approximates the cell growth well from an extremely limited data set.

Longitudinal characterization of TK6 cells sequentially adapted to animal product-free, chemically defined culture medium: considerations for genotoxicity studies

Introduction: In vitro approaches are an essential tool in screening for toxicity of new chemicals, products and therapeutics. To increase the reproducibility and human relevance of these in vitro assessments, it is advocated to remove animal-derived products such as foetal bovine serum (FBS) from the cell culture system. Currently, FBS is routinely used as a supplement in cell culture medium, but batch-to-batch variability may introduce inconsistency in inter- and intra-lab assessments. Several chemically defined serum replacements (CDSR) have been developed to provide an alternative to FBS, but not every cell line adapts easily and successfully to CDSR-supplemented medium, and the long-term effect on cell characteristics remains uncertain. Aim: The aim of this study was to adapt the TK6 cell line to animal-product free CDSR-supplemented medium and evaluate the long-term effects on cell health, growth, morphology, phenotype, and function. This included a provisional assessment to determine the suitability of the transitioned cell line for standardised genotoxicity testing using the "in vitro mammalian cell micronucleus test" (OECD TG 487). Materials and methods: Gradual adaptation and direct adaptation methodologies were compared by assessing the cell proliferation, size and viability every passage until the cells were fully adapted to animal-free CDSR. The metabolic activity and membrane integrity was assessed every 4-8 passages by PrestoBlue and CytoTox-ONE™ Homogeneous Membrane Integrity Assay respectively. A detailed morphology study by high content imaging was performed and the expression of cell surface markers (CD19 and CD20) was conducted via flow cytometry to assess the potential for phenotypic drift during longer term culture of TK6 in animal-free conditions. Finally, functionality of cells in the OECD TG 487 assay was evaluated. Results: The baseline characteristics of TK6 cells cultured in FBS-supplemented medium were established and variability among passages was used to set up acceptance criteria for CDSR adapted cells. TK6 were adapted to CDSR supplemented medium either via direct or gradual transition reducing from 10% v/v FBS to 0% v/v FBS. The cell growth rate was compromised in the direct adaptation and therefore the gradual adaptation was preferred to investigate the long-term effects of animal-free CDSR on TK6 cells. The new animal cells showed comparable (p > 0.05) viability and cell size as the parent FBS-supplemented cells, with the exception of growth rate. The new animal free cells showed a lag phase double the length of the original cells. Cell morphology (cellular and nuclear area, sphericity) and phenotype (CD19 and CD20 surface markers) were in line (p > 0.05) with the original cells. The new cells cultured in CDSR-supplemented medium performed satisfactory in a pilot OECD TG 487 assay with compounds not requiring metabolic activation. Conclusion: TK6 cells were successfully transitioned to FBS- and animal product-free medium. The new cell cultures were viable and mimicked the characteristics of FBS-cultured cells. The gradual transition methodology utilised in this study can also be applied to other cell lines of interest. Maintaining cells in CDSR-supplemented medium eliminates variability from FBS, which in turn is likely to increase the reproducibility of in vitro experiments. Furthermore, removal of animal derived products from cell culture techniques is likely to increase the human relevance of in vitro methodologies.

A global perspective on a new paradigm shift in bio-based meat alternatives for healthy diet

A meat analogue is a casserole in which the primary ingredient is something other than meat. It goes by various other names, such as meat substitute, fake meat, alternative meat, and imitation meat. Consumers growing interest in improving their diets and the future of the planet have contributed to the move towards meat substitutes. This change is due to the growing popularity of low-fat and low-calorie diets, the rise of flexitarians, the spread of animal diseases, the loss of natural resources, and the need to cut down on carbon emissions, which lead to greenhouse effects. Plant-based meat, cultured meat, algal protein-based meat, and insect-based meat substitutes are available on the market with qualities like appearance and flavor similar to those of traditional meat. Novel ingredients like mycoprotein and soybean leg haemoglobin are mixed in with the more traditional soy proteins, cereals, green peas, etc. Plant-based meat is currently more popular in the West, but the growing interest in this product in Asian markets indicates the industry in this region will expand rapidly in the near future. Future growth in the food sector can be anticipated from technologies like lab-grown meat and its equivalents that do not require livestock breeding. Insect-based products also hold great potential as a new source of protein for human consumption. However, product safety and quality should be considered along with other factors such as marketability and affordability.