Fluctuations in cell density alter protein markers of multiple cellular compartments, confounding experimental outcomes

The impact of cell density variations on nanoparticle uptake across bioprinted A549 gradients

Introduction

The safe-by-design of engineered nanoparticles (NPs) for any application requires a detailed understanding of how the particles interact with single cells. Most studies are based on two-dimensional, uniformly dense cell cultures, which do not represent the diverse and inhomogeneous cell environments found in situ. In-vitro models that accurately represent tissue complexity, including realistic cell densities, are essential to increase the predictive accuracy of studies on cell-NP interactions. This study uses a bioprinted cell gradient model to examine the relation between cell density and NP uptake in one dish.

Method

A549 lung epithelial cell density gradients within single inserts were produced with a bioprinter by modulating inter-droplet distances. After two days in culture, cells were exposed to Cy5-labeled silica NPs (SiO2 NPs, ∼112 nm, 20 μg/mL) for up to 48 h. Confocal fluorescence microscopy and 3D image analysis were used to quantify NP uptake, cell surface area, and cell volume. The relationship between NP uptake and the other parameters was then investigated statistically.

Results

Bioprinting enabled the creation of reproducible linear cell density gradients, allowing controlled modeling of density variations while preserving cell viability throughout the experiment. Increasing inter-droplet distances, from 0.1 mm to 0.6 mm, were used to achieve uniformly decreasing cell densities. SiO2 NP uptake per cell was around 50% higher in low-density regions compared to high-density areas across all time points, i.e., 6, 24, and 48 h post-exposure. This inverse relationship correlated with greater average cell surface area in lower-density regions, while differences in the proliferation rates of the A549 cells at varying densities did not significantly impact uptake, did not significantly impact uptake.

Conclusion

SiO2 NP uptake is significantly enhanced at lower cell densities, mainly due to the increased available surface area, revealing potential cell-NP interaction differences in tissues that present cell density variability. Our drop-on-demand bioprinting gradient model successfully supports the implementation of cell density gradients in in-vitro models to increase their relevance as new approach methodologies (NAMs) for next-generation risk assessment strategies.

Scalable lipid droplet microarray fabrication, validation, and screening

High throughput screening of small molecules and natural products is costly, requiring significant amounts of time, reagents, and operating space. Although microarrays have proven effective in the miniaturization of screening for certain biochemical assays, such as nucleic acid hybridization or antibody binding, they are not widely used for drug discovery in cell culture due to the need for cells to internalize lipophilic drug candidates. Lipid droplet microarrays are a promising solution to this problem as they are capable of delivering lipophilic drugs to cells at dosages comparable to solution delivery. However, the scalablility of the array fabrication, assay validation, and screening steps has limited the utility of this approach. Here we take several new steps to scale up the process for lipid droplet array fabrication, assay validation in cell culture, and drug screening. A nanointaglio printing process has been adapted for use with a printing press. The arrays are stabilized for immersion into aqueous solution using a vapor coating process. In addition to delivery of lipophilic compounds, we found that we are also able to encapsulate and deliver a water-soluble compound in this way. The arrays can be functionalized by extracellular matrix proteins such as collagen prior to cell culture as the mechanism for uptake is based on direct contact with the lipid delivery vehicles rather than diffusion of the drug out of the microarray spots. We demonstrate this method for delivery to 3 different cell types and the screening of 92 natural product extracts on a microarray covering an area of less than 0.1 cm2. The arrays are suitable for miniaturized screening, for instance in high biosafety level facilities where space is limited and for applications where cell numbers are limited, such as in functional precision medicine.

Integrative transcriptomic and proteomic profiling of the effects of cell confluency on gene expression

In this study we examine the impact of cell confluency on gene expression. We focused on Argonaute (AGO) protein dynamics and associated gene and protein expression in HEK293, A375, and SHSY5Y cell lines. As a consequence of cell confluency, AGO2 protein translocates into the nucleus. Therefore, we generated transcriptomic data using RNA sequencing to compare gene expression in subconfluent versus confluent cells, which highlighted significant alterations in gene regulation patterns directly corresponding to changes in cell density. Our study also encompasses miRNA profiling data obtained through small RNA sequencing, revealing miRNA expressional changes dependent on cellular confluency, as well as cellular localization. Finally, we derived proteomic data from mass spectrometry analyses following AGO1-4 immunoprecipitation, providing a comprehensive view of AGO interactome in both nuclear and cytoplasmic compartments under varying confluency. These datasets offer a detailed exploration of the cellular and molecular dynamics, influenced by cell confluency, presenting a valuable resource for further research in cellular biology, particularly in understanding the basic mechanisms of cell density in cancer cells.

Nanoscale Methods for Longitudinal Extraction of Intracellular Contents

Longitudinal analysis of intracellular contents including gene and protein expression is crucial for deciphering the fundamentally dynamic nature of cells. This offers invaluable insights into complex tissue composition and behavior, and drives progress in disease diagnosis, biomarker discovery, and drug development. Traditional longitudinal analysis workflows, involving the destruction of cells at various timepoints, limit insights to singular moments and fail to account for cellular heterogeneity. Current non-destructive approaches, like temporal modeling with single-cell ribonucleic acid sequencing (RNA-seq) and live-cell fluorescence imaging, either rely on biological assumptions or possess the risk of cellular perturbation. Recent advances in nanoscale technologies for non-destructive intracellular content extraction offer a promising solution to these challenges. These novel methods work at the nanoscale to non-destructively access cellular membranes and can be broadly classified into three mechanisms: tip-facilitated aspiration, membrane-based, and probe-based methods. This perspective focuses on these emerging nanotechnologies for repeated intracellular content extraction. Their potential in longitudinal analysis is discussed, the critical requirements for effective repeated sampling are addressed, and the suitability of each technique for various applications is explored. Furthermore, unresolved challenges in repeated sampling are highlighted to encourage further research in this growing field.

Metabolic alterations and cellular responses to β-Hydroxybutyrate treatment in breast cancer cells

BACKGROUND

The ketogenic diet (KD), based on high fat (over 70% of daily calories), low carbohydrate, and adequate protein intake, has become popular due to its potential therapeutic benefits for several diseases including cancer. Under KD and starvation conditions, the lack of carbohydrates promotes the production of ketone bodies (KB) from fats by the liver as an alternative source of metabolic energy. KD and starvation may affect the metabolism in cancer cells, as well as tumor characteristics. The aim of this study is to evaluate the effect of KD conditions on a wide variety of aspects of breast cancer cells in vitro.

METHODS

Using two cancer and one non-cancer breast cell line, we evaluate the effect of β-hydroxybutyrate (βHb) treatment on cell growth, survival, proliferation, colony formation, and migration. We also assess the effect of KB on metabolic profile of the cells. Using RNAseq analysis, we elucidate the effect of βHb on the gene expression profile.

RESULTS

Significant effects were observed following treatment by βHb which include effects on viability, proliferation, and colony formation of MCF7 cells, and different effects on colony formation of MDA-MB-231 cells, with no such effects on non-cancer HB2 cells. We found no changes in glucose intake or lactate output following βHb treatment as measured by LC-MS, but an increase in reactive oxygen species (ROS) level was detected. RNAseq analysis demonstrated significant changes in genes involved in lipid metabolism, cancer, and oxidative phosphorylation.

CONCLUSIONS

Based on our results, we conclude that differential response of cancer cell lines to βHb treatment, as alternative energy source or signal to alter lipid metabolism and oncogenicity, supports the need for a personalized approach to breast cancer patient treatment.

Conductive Polyisocyanide Hydrogels Inhibit Fibrosis and Promote Myogenesis

Reliable in vitro models closely resembling native tissue are urgently needed for disease modeling and drug screening applications. Recently, conductive biomaterials have received increasing attention in the development of in vitro models as they permit exogenous electrical signals to guide cells toward a desired cellular response. Interestingly, they have demonstrated that they promote cellular proliferation and adhesion even without external electrical stimulation. This paper describes the development of a conductive, fully synthetic hydrogel based on hybrids of the peptide-modified polyisocyanide (PIC-RGD) and the relatively conductive poly(aniline-co-N-(4-sulfophenyl)aniline) (PASA) and its suitability as the in vitro matrix. We demonstrate that incorporating PASA enhances the PIC-RGD hydrogel's electroactive nature without significantly altering the fibrous architecture and nonlinear mechanics of the PIC-RGD network. The biocompatibility of our model was assessed through phenotyping cultured human foreskin fibroblasts (HFF) and murine C2C12 myoblasts. Immunofluorescence analysis revealed that PIC-PASA hydrogels inhibit the fibrotic behavior of HFFs while promoting myogenesis in C2C12 cells without electrical stimulation. The composite PIC-PASA hydrogel can actively change the cell fate of different cell types, providing an attractive tool to improve skin and muscle repair.

The population context is a driver of the heterogeneous response of epithelial cells to interferons

Isogenic cells respond in a heterogeneous manner to interferon. Using a micropatterning approach combined with high-content imaging and spatial analyses, we characterized how the population context (position of a cell with respect to neighboring cells) of epithelial cells affects their response to interferons. We identified that cells at the edge of cellular colonies are more responsive than cells embedded within colonies. We determined that this spatial heterogeneity in interferon response resulted from the polarized basolateral interferon receptor distribution, making cells located in the center of cellular colonies less responsive to ectopic interferon stimulation. This was conserved across cell lines and primary cells originating from epithelial tissues. Importantly, cells embedded within cellular colonies were not protected from viral infection by apical interferon treatment, demonstrating that the population context-driven heterogeneous response to interferon influences the outcome of viral infection. Our data highlights that the behavior of isolated cells does not directly translate to their behavior in a population, placing the population context as one important factor influencing heterogeneity during interferon response in epithelial cells.

System Biology Approach in Investigating Epithelial-Mesenchymal Transition (EMT)

Epithelial-mesenchymal transition (EMT) is a trans-differentiating and reversible process that leads to dramatic cell phenotypic changes, enabling epithelial cells in acquiring mesenchymal phenotypes and behaviors. EMT plays a crucial role during embryogenesis, and occurs in several para-physiologic and pathological conditions, as during fibrosis or cancer development. EMT displays some hallmarks of critical transitions, as a sudden change in the overall configuration of a system in correspondence of specific tipping point around which a "catastrophic bifurcation" happens. The transition occurs when external conditions breach specific thresholds. This definition helps in highlighting two main aspects: (1) the change involves the overall system, rather than single, discrete components; (2) cues from the microenvironment play an irreplaceable role in triggering the transition. This evidence implies that critical transition should be ascertained focusing the investigation at the system level (rather than investigating only molecular parameters) in a well-defined context, as the transition is strictly dependent on the microenvironment in which it occurs. Therefore, we need a systems biology approach to investigate EMT across the Waddington-like epigenetic landscape wherein the participation of both internal and external cues can be studied to follow the extent and the main characteristics of the phenotypic transition. Herein, we suggest a set of systems parameters (motility, invasiveness) altogether with specific molecular/histological markers to identify those critical observables, which can be integrated into a comprehensive mechanistic model.

Cancer cell seeding density as a mechanism of chemotherapy resistance: a novel cancer cell density index based on IC50-Seeding Density Slope (ISDS) to assess chemosensitivity

Although the 50% inhibitory concentration (IC50) is a commonly used measurement of chemosensitivity in cancer cells, it has been known to vary with the density of the treated cells (in that more densely seeded cells are more resistant to chemotherapeutic agents). Indeed, density-dependent chemoresistance may be a significant independent mechanism of therapy resistance. We examine the nature of cell density-dependent chemoresistance and explore possible underlying mechanisms. CellTiter-Glo assays and ethidium homodimer staining revealed that response to chemotherapy is density-dependent in all cancer cell lines tested. Our results prompted us to develop a novel cancer cell seeding density index of chemosensitivity, the ISDS (IC50-Seeding Density Slope), which we propose can serve as an improved method of analyzing how cancer cells respond to chemotherapeutic treatment compared to the widely-used IC50. Furthermore, western blot analysis suggests that levels of autophagy and apoptotic markers are modulated by cancer cell density. Cell viability experiments using the autophagy inhibitor chloroquine showed that chloroquine's efficacy was reduced at higher cell densities and that chloroquine and cisplatin exhibited synergy at both higher and lower cell densities in TOV-21G cells. We discuss alternative mechanisms of density-dependent chemoresistance and in vivo/clinical applications, including challenges of adjuvant chemotherapy and minimal residual disease. Taken together, our findings show that cell density is a significant contributor in shaping cancer chemosensitivity, that the ISDS (aka the Ujwal Punyamurtula/Wafik El-Deiry or Ujwal-WAF Index) can be used to effectively assess cell viability and that this phenomenon of density-dependent chemoresistance may be leveraged for a variety of biologic and cancer therapeutic applications.

PI3K signaling through a biochemical systems lens

Following 3 decades of extensive research into PI3K signaling, it is now evidently clear that the underlying network does not equate to a simple ON/OFF switch. This is best illustrated by the multifaceted nature of the many diseases associated with aberrant PI3K signaling, including common cancers, metabolic disease, and rare developmental disorders. However, we are still far from a complete understanding of the fundamental control principles that govern the numerous phenotypic outputs that are elicited by activation of this well-characterized biochemical signaling network, downstream of an equally diverse set of extrinsic inputs. At its core, this is a question on the role of PI3K signaling in cellular information processing and decision making. Here, we review the determinants of accurate encoding and decoding of growth factor signals and discuss outstanding questions in the PI3K signal relay network. We emphasize the importance of quantitative biochemistry, in close integration with advances in single-cell time-resolved signaling measurements and mathematical modeling.

Cell culture-derived extracellular vesicles: Considerations for reporting cell culturing parameters

Cell culture-conditioned medium (CCM) is a valuable source of extracellular vesicles (EVs) for basic scientific, therapeutic and diagnostic applications. Cell culturing parameters affect the biochemical composition, release and possibly the function of CCM-derived EVs (CCM-EV). The CCM-EV task force of the Rigor and Standardization Subcommittee of the International Society for Extracellular Vesicles aims to identify relevant cell culturing parameters, describe their effects based on current knowledge, recommend reporting parameters and identify outstanding questions. While some recommendations are valid for all cell types, cell-specific recommendations may need to be established for non-mammalian sources, such as bacteria, yeast and plant cells. Current progress towards these goals is summarized in this perspective paper, along with a checklist to facilitate transparent reporting of cell culturing parameters to improve the reproducibility of CCM-EV research.

Proteomics reveals that cell density could affect the efficacy of drug treatment

In vitro cell biology study plays a fundamental role in biological and drug development research, but the repeatability and accuracy of cell studies remain to be low. Various uncertainties during the cell culture process could introduce bias into drug research. In this study, we evaluate the potential effects and underlying mechanisms induced by cell number differences in the cell seeding process. Normally, drug experiments are initiated 24 h after cell seeding, and the difference in the cell number at the time of inoculation leads to the difference in cell confluence (cell density) when drug research is conducted. While cell confluence is closely related to intercellular communication, surface protein interaction, cell autocrine as well as paracrine protein expression of cells, it might have a potential impact on the effect of biological studies such as drug treatment. This study used proteomics technology to comprehensively explore the different protein expression patterns between cells with different confluences. Due to the high sensitivity and high throughput of liquid chromatography-mass spectrometry (LC-MS/MS) detection, it was hired to evaluate the protein expression differences of Hep3B cells with 3 different confluences (30%, 50%, and 70%). The differential expressed proteins were analyzed by the Reactome pathway and the Gene Ontology (GO) pathway. Significant differences were identified across three confluences in terms of the number of proteins identified, the protein expression pattern, and the expression level of certain KEGG pathways. We found that those proteins involved in the cell cycle pathway were differently expressed: the higher the cell confluence, the higher these proteins expressed. A cell cycle inhibitor palbociclib was selected to further verify this observation. Palbociclib in the same dose was applied to cells with different confluence, the results indicated that the growth inhibition effect of palbociclib increases along with the increasing trend of cell cycle protein expression. The result indicated that cell density did influence the effect of drug treatment. Furthermore, three other drugs, cisplatin, paclitaxel, and imatinib, were used to treat the three liver cancer cell lines Hep3B, SUN387, and MHCC97, and a similar observation was obtained that drug effect would be different when the cell confluences were different. Therefore, selecting an appropriate number of cells for plating is vitally important at the beginning of a drug study.

Assay-ready Cryopreserved Cell Monolayers Enabled by Macromolecular Cryoprotectants

Cell monolayers underpin the discovery and screening of new drugs and allow for fundamental studies of cell biology and disease. However, current cryopreservation technologies do not allow cells to be stored frozen while attached to tissue culture plastic. Hence, cells must be thawed from suspension, cultured for several days or weeks, and finally transferred into multiwell plates for the desired application. This inefficient process consumes significant time handling cells, rather than conducting biomedical research or other value-adding activities. Here, we demonstrate that a synthetic macromolecular cryoprotectant enables the routine, reproducible, and robust cryopreservation of biomedically important cell monolayers, within industry-standard tissue culture multiwell plates. The cells are simply thawed with media and placed in an incubator ready to use within 24 h. Post-thaw cell recovery values were >80% across three cell lines with low well-to-well variance. The cryopreserved cells retained healthy morphology, membrane integrity, proliferative capacity, and metabolic activity; showed marginal increases in apoptotic cells; and responded well to a toxicological challenge using doxorubicin. These discoveries confirm that the cells are “assay-ready” 24 h after thaw. Overall, we show that macromolecular cryoprotectants can address a long-standing cryobiological challenge and offers the potential to transform routine cell culture for biomedical discovery.

The effect of hypoxia on PD-L1 expression in bladder cancer

INTRODUCTION

Recent data has demonstrated that hypoxia drives an immunosuppressive tumour microenvironment (TME) via various mechanisms including hypoxia inducible factor (HIF)-dependent upregulation of programmed death ligand 1 (PD-L1). Both hypoxia and an immunosuppressive TME are targetable independent negative prognostic factors for bladder cancer. Therefore we sought to investigate whether hypoxia is associated with upregulation of PD-L1 in the disease.

MATERIALS AND METHODS

Three human muscle-invasive bladder cancer cell lines (T24, J82, UMUC3) were cultured in normoxia (20% oxygen) or hypoxia (1 and 0.1% oxygen) for 24 h. Differences in PD-L1 expression were measured using Western blotting, quantitative polymerase chain reaction (qPCR) and flow cytometry (≥3 independent experiments). Statistical tests performed were unpaired t tests and ANOVA. For in silico work an hypoxia signature was used to apply hypoxia scores to muscle-invasive bladder cancers from a clinical trial (BCON; n = 142) and TCGA (n = 404). Analyses were carried out using R and RStudio and statistical tests performed were linear models and one-way ANOVA.

RESULTS

When T24 cells were seeded at < 70% confluence, there was decreased PD-L1 protein (p = 0.009) and mRNA (p < 0.001) expression after culture in 0.1% oxygen. PD-L1 protein expression decreased in both 0.1% oxygen and 1% oxygen in a panel of muscle-invasive bladder cancer cells: T24 (p = 0.009 and 0.001), J82 (p = 0.008 and 0.013) and UMUC3 (p = 0.003 and 0.289). Increasing seeding density decreased PD-L1 protein (p < 0.001) and mRNA (p = 0.001) expression in T24 cells grown in both 20 and 1% oxygen. Only when cells were 100% confluent, were PD-L1 protein and mRNA levels higher in 1% versus 20% oxygen (p = 0.056 and p = 0.037). In silico analyses showed a positive correlation between hypoxia signature scores and PD-L1 expression in both BCON (p = 0.003) and TCGA (p < 0.001) cohorts, and between hypoxia and IFNγ signature scores (p < 0.001 for both).

CONCLUSION

Tumour hypoxia correlates with increased PD-L1 expression in patient derived bladder cancer tumours. In vitro PD-L1 expression was affected by cell density and decreased PD-L1 expression was observed after culture in hypoxia in muscle-invasive bladder cancer cell lines. As cell density has such an important effect on PD-L1 expression, it should be considered when investigating PD-L1 expression in vitro.

High cell density increases glioblastoma cell viability under glucose deprivation via degradation of the cystine/glutamate transporter xCT (SLC7A11)

The cystine/glutamate transporter system x_c ^- consists of the light-chain subunit xCT (SLC7A11) and the heavy-chain subunit CD98 (4F2hc or SLC3A2) and exchanges extracellular cystine for intracellular glutamate at the plasma membrane. The imported cystine is reduced to cysteine and used for synthesis of GSH, one of the most important antioxidants in cancer cells. Because cancer cells have increased levels of reactive oxygen species, xCT, responsible for cystine-glutamate exchange, is overexpressed in many cancers, including glioblastoma. However, under glucose-limited conditions, xCT overexpression induces reactive oxygen species accumulation and cell death. Here we report that cell survival under glucose deprivation depends on cell density. We found that high cell density (HD) down-regulates xCT levels and increases cell viability under glucose deprivation. We also found that growth of glioblastoma cells at HD inactivates mTOR and that treatment of cells grown at low density with the mTOR inhibitor Torin 1 down-regulates xCT and inhibits glucose deprivation-induced cell death. The lysosome inhibitor bafilomycin A1 suppressed xCT down-regulation in HD-cultured glioblastoma cells and in Torin 1-treated cells grown at low density. Additionally, bafilomycin A1 exposure or ectopic xCT expression restored glucose deprivation-induced cell death at HD. These results suggest that HD inactivates mTOR and promotes lysosomal degradation of xCT, leading to improved glioblastoma cell viability under glucose-limited conditions. Our findings provide evidence that control of xCT protein expression via lysosomal degradation is an important mechanism for metabolic adaptation in glioblastoma cells.