Vertebrate cell culture as an experimental approach – limitations and solutions

Bridging the gap: advancing cancer cell culture to reveal key metabolic targets

Metabolic rewiring is a defining characteristic of cancer cells, driving their ability to proliferate. Leveraging these metabolic vulnerabilities for therapeutic purposes has a long and impactful history, with the advent of antimetabolites marking a significant breakthrough in cancer treatment. Despite this, only a few in vitro metabolic discoveries have been successfully translated into effective clinical therapies. This limited translatability is partially due to the use of simplistic in vitro models that do not accurately reflect the tumor microenvironment. This Review examines the effects of current cell culture practices on cancer cell metabolism and highlights recent advancements in establishing more physiologically relevant in vitro culture conditions and technologies, such as organoids. Applying these improvements may bridge the gap between in vitro and in vivo findings, facilitating the development of innovative metabolic therapies for cancer.

Promising Effects of Novel Supplement Formulas in Preventing Skin Aging in 3D Human Keratinocytes

Dietary intervention is considered a safe preventive strategy to slow down aging. This study aimed to evaluate the protective effects of a commercially available supplement and six simpler formulations against DNA damage in 3D human keratinocytes. The ingredients used are well known and were combined into various formulations to test their potential anti-aging properties. Firstly, we determined the formulations' safe concentration by evaluating cytotoxicity and cell viability through spectrophotometric assays. We then examined the presence of tumor p53 binding protein 1 and phosphorylated histone H2AX foci, which are markers of genotoxicity. The foci count revealed that a 24-h treatment with the supplement did not induce DNA damage, and significantly reduced DNA damage in cells exposed to neocarzinostatin for 2 h. Three of the simpler formulations showed similar results. Moreover, the antioxidant activity was tested using a recently developed whole cell-based chemiluminescent bioassay; results showed that a 24-h treatment with the supplement and three simpler formulations significantly reduced intracellular H2O2 after pro-oxidant injury, thus suggesting their possible antiaging effect. This study's originality lies in the use of a 3D human keratinocyte cell model and a combination of natural ingredients targeting DNA damage and oxidative stress, providing a robust evaluation of their anti-aging potential.

Choice of medium affects PBMC quantification, cell size, and downstream respiratory analysis

High-resolution respirometry (HRR) can assess peripheral blood mononuclear cell (PBMC) bioenergetics, but no standardized medium for PBMC preparation and HRR analysis exist. Here, we study the effect of four different media (MiR05, PBS, RPMI, Plasmax) on the count, size, and HRR (Oxygraph-O2k) of intact PBMCs. Remarkably, the cell count was 21 % higher when PBMCs were resuspended in MiR05 than in PBS or Plasmax, causing O2 flux underestimation during HRR due to inherent adjustments. Moreover, smaller cell size and cell aggregation was observed in MiR05. Based on our findings, we propose that Plasmax, PBS or RPMI is more suitable than MiR05 for HRR of intact PBMCs. We provide oxygen solubility factors for Plasmax and PBS and encourage further optimization of a standardized HRR protocol for intact PBMCs.

Oxygen levels affect oviduct epithelium functions in air-liquid interface culture

Key reproductive events such as fertilization and early embryonic development occur in the lumen of the oviduct. Since investigating these processes in vivo is both technically challenging and ethically sensitive, cell culture models have been established to reproduce the oviductal microenvironment. Compartmentalized culture systems, particularly air-liquid interface cultures (ALI; cells access the culture medium only from the basolateral cell side), result in highly differentiated oviduct epithelial cell cultures. The oxygen (O2) tension within the oviduct is 4-10% across species, and its reduced O2 content is presumed to be important for early reproductive processes. However, cell culture models of the oviduct are typically cultivated without O2 regulation and therefore at about 18% O2. To investigate the impact of O2 levels on oviduct epithelium functions in vitro, we cultured porcine oviduct epithelial cells (POEC) at the ALI using both physiological (5%) and supraphysiological (18%) O2 levels and two different media regimes. Epithelium architecture, barrier function, secretion of oviduct fluid surrogate (OFS), and marker gene expression were comparatively assessed. Under all culture conditions, ALI-POEC formed polarized, ciliated monolayers with appropriate barrier function. Exposure to 18% O2 accelerated epithelial differentiation and significantly increased the apical OFS volume and total protein content. Expression of oviduct genes and the abundance of OVGP1 (oviduct-specific glycoprotein 1) in the OFS were influenced by both O2 tension and medium choice. In conclusion, oviduct epithelial cells can adapt to a supraphysiological O2 environment. This adaptation, however, may alter their capability to replicate in vivo tissue characteristics.

Cardiac Organoids: A 3D Technology for Disease Modeling and Drug Screening

Cardiovascular diseases remain the leading cause of death worldwide; therefore, there is increasing attention to developing physiological-related in vitro cardiovascular tissue models suitable for personalized healthcare and preclinical test. Recently, more complex and powerful in vitro models have emerged for cardiac research. Human cardiac organoids (HCOs) are three-dimensional (3D) cellular constructs similar to in vivo organs. They are derived from pluripotent stem cells and can replicate the structure, function, and biogenetic information of primitive tissues. High-fidelity HCOs are closer to natural human myocardial tissue than animal and cell models to some extent, which helps to study better the development process of the heart and the occurrence of related diseases. In this review, we introduce the methods for constructing HCOs and the application of them, especially in cardiovascular disease modeling and cardiac drug screening. In addition, we propose the prospects and limitations of HCOs. In summary, we have introduced the research progress of HCOs and described their innovation and practicality of them in the biomedical field.

Vascularized microfluidic models of major organ structures and cancerous tissues

Organ-on-a-chip devices are powerful modeling systems that allow researchers to recapitulate the in vivo structures of organs as well as the physiological conditions those tissues are subject to. These devices are useful tools in modeling not only the behavior of a healthy organ but also in modeling disease pathology or the effects of specific drugs. The incorporation of fluidic flow is of great significance in these devices due to the important roles of physiological fluid flows in vivo. Recent developments in the field have led to the production of vascularized organ-on-a-chip devices, which can more accurately reproduce the conditions observed in vivo by recapitulating the vasculature of the organ concerned. This review paper will provide a brief overview of the history of organ-on-a-chip devices, before discussing developments in the production of vascularized organs-on-chips, and the implications these developments hold for the future of the field.

Hyperoxic exposure alters intracellular bioenergetics distribution in human pulmonary cells

AIMS

Pulmonary oxygen toxicity is caused by exposure to a high fraction of inspired oxygen, which damages multiple cell types within the lung. The cellular basis for pulmonary oxygen toxicity includes mitochondrial dysfunction. The aim of this study was to identify the effects of hyperoxic exposure on mitochondrial bioenergetic and dynamic functions in pulmonary cells.

MAIN METHODS

Mitochondrial respiration, inner membrane potential, dynamics (including motility), and distribution of mitochondrial bioenergetic capacity in two intracellular regions were quantified using cultured human lung microvascular endothelial cells, human pulmonary artery endothelial cells and A549 cells. Hyperoxic (95 % O₂) exposures lasted 24, 48 and 72 h, durations relevant to mechanical ventilation in intensive care settings.

KEY FINDINGS

Mitochondrial motility was altered following all hyperoxic exposures utilized in experiments. Inhomogeneities in inner membrane potential and respiration parameters were present in each cell type following hyperoxia. The partitioning of ATP-linked respiration was also hyperoxia-duration and cell type dependent. Hyperoxic exposure lasting 48 h or longer provoked the largest alterations in mitochondrial motility and the greatest decreases in ATP-linked respiration, with a suggestion of decreases in respiration complex protein levels.

SIGNIFICANCE

Hyperoxic exposures of different durations produce intracellular inhomogeneities in mitochondrial dynamics and bioenergetics in pulmonary cells. Oxygen therapy is utilized commonly in clinical care and can induce undesirable decrements in bioenergy function needed to maintain pulmonary cell function and viability. There may be adjunctive or prophylactic measures that can be employed during hyperoxic exposures to prevent the mitochondrial dysfunction that signals the presence of oxygen toxcity.

Dose and route dependent effects of the mycotoxin deoxynivalenol in a 3D gut-on-a-chip model with flow

Deoxynivalenol (DON) is the most prevalent mycotoxin in human food and is ubiquitously detected in human bodyfluids. DON leads to intestinal barrier dysfunction, as observed from animal- and cell culture models with the known disadvantages. Here we present the effects of DON in a gut-on-a-chip model, as the first study incorporating the effects of intestinal flow. Using the OrganoPlate 3-lane, Caco-2 cells were seeded against an extracellular matrix (ECM) and formed leak tight tubules. DON was then applied in different concentrations (3 μM to 300 μM) via the apical or the basolateral channel. Permeability was assessed using continuous TEER and barrier integrity assays (BIA). Zonulin-1, toxicity (LDH) and proinflammatory status (IL-8) was analyzed. DON exposure led to a dose dependent decrease in para-and transcellular barrier integrity, which was more sensitive to basal than apical application (route). Timelaps/Continuous TEER measurements however revealed bidirectional effects, with even TEER-inducing effects of lower concentrations (until 10 μM). IL-8 secretion into luminal supernatants was only induced by apical DON. Attributed to the flow, the barrier-disintegrating effects of DON start at higher concentrations than in other culture models. The barrier was more sensitive to basolateral DON, even though DON had to pass the ECM; and IL-8 secretion was independent of TEER-alterations. Thus, the gut-on-a chip model might be a good alternative to further characterize the bidirectional effects of DON with reasonable throughput incorporating flow.

Mass Spectrometry-Based Atlas of Extracellular Matrix Proteins across 25 Mouse Organs

The extracellular matrix (ECM) is a critical non-cellular component of multicellular organisms containing a variety of proteins, glycoproteins, and proteoglycans which have been implicated in a wide variety of essential biological processes, including development, wound healing, and aging. Due to low solubility, many ECM proteins have been underrepresented in previous proteomic datasets. Using an optimized three-step decellularization and ECM extraction method involving chaotrope extraction and digestion via hydroxylamine hydrochloride, we have generated coverage of the matrisome across 25 organs. We observe that the top 100 most abundant proteins from the ECM fractions of all tissues are generally present in all tissues, indicating that tissue matrices are principally composed of a shared set of ECM proteins. However, these proteins vary up to 4000-fold between tissues, resulting in highly unique matrix profiles even with the same primary set of proteins. A data reduction approach was used to reveal related networks of expressed ECM proteins across varying tissues, including basement membrane and collagen subtypes.

The role of glutamine metabolism in castration-resistant prostate cancer

Reprogramming of metabolism is a hallmark of tumors, which has been explored for therapeutic purposes. Prostate cancer (PCa), particularly advanced and therapy-resistant PCa, displays unique metabolic properties. Targeting metabolic vulnerabilities in PCa may benefit patients who have exhausted currently available treatment options and improve clinical outcomes. Among the many nutrients, glutamine has been shown to play a central role in the metabolic reprogramming of advanced PCa. In addition to amino acid metabolism, glutamine is also widely involved in the synthesis of other macromolecules and biomasses. Targeting glutamine metabolic network by maximally inhibiting glutamine utilization in tumor cells may significantly add to treatment options for many patients. This review summarizes the metabolic landscape of PCa, with a particular focus on recent studies of how glutamine metabolism alterations affect therapeutic resistance and disease progression of PCa, and suggests novel therapeutic strategies.

Nutritional compensation of the circadian clock is a conserved process influenced by gene expression regulation and mRNA stability

Compensation is a defining principle of a true circadian clock, where its approximately 24-hour period length is relatively unchanged across environmental conditions. Known compensation effectors directly regulate core clock factors to buffer the oscillator's period length from variables in the environment. Temperature Compensation mechanisms have been experimentally addressed across circadian model systems, but much less is known about the related process of Nutritional Compensation, where circadian period length is maintained across physiologically relevant nutrient levels. Using the filamentous fungus Neurospora crassa, we performed a genetic screen under glucose and amino acid starvation conditions to identify new regulators of Nutritional Compensation. Our screen uncovered 16 novel mutants, and together with 4 mutants characterized in prior work, a model emerges where Nutritional Compensation of the fungal clock is achieved at the levels of transcription, chromatin regulation, and mRNA stability. However, eukaryotic circadian Nutritional Compensation is completely unstudied outside of Neurospora. To test for conservation in cultured human cells, we selected top hits from our fungal genetic screen, performed siRNA knockdown experiments of the mammalian orthologs, and characterized the cell lines with respect to compensation. We find that the wild-type mammalian clock is also compensated across a large range of external glucose concentrations, as observed in Neurospora, and that knocking down the mammalian orthologs of the Neurospora compensation-associated genes CPSF6 or SETD2 in human cells also results in nutrient-dependent period length changes. We conclude that, like Temperature Compensation, Nutritional Compensation is a conserved circadian process in fungal and mammalian clocks and that it may share common molecular determinants.

Physiological Media in Studies of Cell Metabolism

Changes in cell metabolism accompany the development of a wide spectrum of pathologies including cancer, autoimmune, and inflammatory diseases. Therefore, usage of inhibitors of metabolic enzymes are considered a promising strategy for the development of therapeutic agents. However, the investigation of cellular metabolism is hampered by the significant impact of culture media, which interfere with many cellular processes, thus making cellular models irrelevant. There are numerous reports that show that the results from in vitro systems are not reproduced in in vivo models and patients. Over the last decade a novel approach has emerged, which consists of adaptation of the culture medium composition to that closer to the composition of blood plasma. In 2017‒2019, two plasma-like media were proposed, Plasmax and HPLM. In the review, we have summarized the drawbacks of common media and have analyzed changes in the metabolism of cells cultivated in common and plasma-like media in normal and pathological conditions.

Supraphysiological Oxygen Levels in Mammalian Cell Culture: Current State and Future Perspectives

Most conventional incubators used in cell culture do not regulate O2 levels, making the headspace O2 concentration ~18%. In contrast, most human tissues are exposed to 2-6% O2 (physioxia) in vivo. Accumulating evidence has shown that such hyperoxic conditions in standard cell culture practices affect a variety of biological processes. In this review, we discuss how supraphysiological O2 levels affect reactive oxygen species (ROS) metabolism and redox homeostasis, gene expression, replicative lifespan, cellular respiration, and mitochondrial dynamics. Furthermore, we present evidence demonstrating how hyperoxic cell culture conditions fail to recapitulate the physiological and pathological behavior of tissues in vivo, including cases of how O2 alters the cellular response to drugs, hormones, and toxicants. We conclude that maintaining physioxia in cell culture is imperative in order to better replicate in vivo-like tissue physiology and pathology, and to avoid artifacts in research involving cell culture.

Oxygen toxicity: cellular mechanisms in normobaric hyperoxia

In clinical settings, oxygen therapy is administered to preterm neonates and to adults with acute and chronic conditions such as COVID-19, pulmonary fibrosis, sepsis, cardiac arrest, carbon monoxide poisoning, and acute heart failure. In non-clinical settings, divers and astronauts may also receive supplemental oxygen. In addition, under current standard cell culture practices, cells are maintained in atmospheric oxygen, which is several times higher than what most cells experience in vivo. In all the above scenarios, the elevated oxygen levels (hyperoxia) can lead to increased production of reactive oxygen species from mitochondria, NADPH oxidases, and other sources. This can cause cell dysfunction or death. Acute hyperoxia injury impairs various cellular functions, manifesting ultimately as physiological deficits. Chronic hyperoxia, particularly in the neonate, can disrupt development, leading to permanent deficiencies. In this review, we discuss the cellular activities and pathways affected by hyperoxia, as well as strategies that have been developed to ameliorate injury.

Fibroblasts as an experimental model system for the study of comparative physiology

Mechanistic evaluations of processes that underlie organism-level physiology often require reductionist approaches. Dermal fibroblasts offer one such approach. These cells are easily obtained from minimally invasive skin biopsy, making them appropriate for the study of protected and/or logistically challenging species. Cell culture approaches permit extensive and fine-scale sampling regimes as well as gene manipulation techniques that are not feasible in vivo. Fibroblast isolation and culture protocols are outlined here for primary cells, and the benefits and drawbacks of immortalization are discussed. We show examples of physiological metrics that can be used to characterize primary cells (oxygen consumption, translation, proliferation) and readouts that can be informative in understanding cell-level responses to environmental stress (lactate production, heat shock protein induction). Importantly, fibroblasts may display fidelity to whole animal physiological phenotypes, facilitating their study. Fibroblasts from Antarctic Weddell seals show greater resilience to low temperatures and hypoxia exposure than fibroblasts from humans or rats. Fibroblast oxygen consumption rates are not affected by temperature stress in the heat-tolerant camel, whereas similar temperature exposures depress mitochondrial metabolism in fibroblasts from rhinoceros. Finally, dermal fibroblasts from a hibernator, the meadow jumping mouse, better resist experimental cooling than a fibroblast line from the laboratory mouse, with the hibernator demonstrating a greater maintenance of homeostatic processes such as protein translation. These results exemplify the parallels that can be drawn between fibroblast physiology and expectations in vivo, and provide evidence for the power of fibroblasts as a model system to understand comparative physiology and biomedicine.

Non-destructive monitoring of 3D cell cultures: new technologies and applications

3D cell cultures are becoming the new standard for cell-based in vitro research, due to their higher transferrability toward in vivo biology. The lack of established techniques for the non-destructive quantification of relevant variables, however, constitutes a major barrier to the adoption of these technologies, as it increases the resources needed for the experimentation and reduces its accuracy. In this review, we aim at addressing this limitation by providing an overview of different non-destructive approaches for the evaluation of biological features commonly quantified in a number of studies and applications. In this regard, we will cover cell viability, gene expression, population distribution, cell morphology and interactions between the cells and the environment. This analysis is expected to promote the use of the showcased technologies, together with the further development of these and other monitoring methods for 3D cell cultures. Overall, an extensive technology shift is required, in order for monolayer cultures to be superseded, but the potential benefit derived from an increased accuracy of in vitro studies, justifies the effort and the investment.

The Effect of Oxygen and Micronutrient Composition of Cell Growth Media on Cancer Cell Bioenergetics and Mitochondrial Networks

Cancer cell culture is routinely performed under superphysiologic O₂ levels and in media such as Dulbecco's Modified Eagle Medium (DMEM) with nutrient composition dissimilar to mammalian extracellular fluid. Recently developed cell culture media (e.g., Plasmax, Human Plasma-Like Medium (HPLM)), which are modeled on the metabolite composition of human blood plasma, have been shown to shift key cellular activities in several cancer cell lines. Similar effects have been reported with respect to O₂ levels in cell culture. Given these observations, we investigated how media composition and O₂ levels affect cellular energy metabolism and mitochondria network structure in MCF7, SaOS2, LNCaP, and Huh7 cells. Cells were cultured in physiologic (5%) or standard (18%) O₂ levels, and in physiologic (Plasmax) or standard cell culture media (DMEM). We show that both O₂ levels and media composition significantly affect mitochondrial abundance and network structure, concomitantly with changes in cellular bioenergetics. Extracellular acidification rate (ECAR), a proxy for glycolytic activity, was generally higher in cells cultured in DMEM while oxygen consumption rates (OCR) were lower. This effect of media on energy metabolism is an important consideration for the study of cancer drugs that target aspects of energy metabolism, including lactate dehydrogenase activity.

Oxidative phosphorylation system and cell culture media

Traditional culture media do not resemble the metabolic composition of human blood. The concentration of different metabolites in these media influences mitochondrial biogenesis and oxidative phosphorylation (OXPHOS) function. This knowledge is essential for the interpretation of results obtained from cellular models used for the study of OXPHOS function.