Bio-EdIP: An automatic approach for in vitro cell confluence images quantification

An automated in vitro wound healing microscopy image analysis approach utilizing U-net-based deep learning methodology

BACKGROUND

The assessment of in vitro wound healing images is critical for determining the efficacy of the therapy-of-interest that may influence the wound healing process. Existing methods suffer significant limitations, such as user dependency, time-consuming nature, and lack of sensitivity, thus paving the way for automated analysis approaches.

METHODS

Hereby, three structurally different variations of U-net architectures based on convolutional neural networks (CNN) were implemented for the segmentation of in vitro wound healing microscopy images. The developed models were fed using two independent datasets after applying a novel augmentation method aimed at the more sensitive analysis of edges after the preprocessing. Then, predicted masks were utilized for the accurate calculation of wound areas. Eventually, the therapy efficacy-indicator wound areas were thoroughly compared with current well-known tools such as ImageJ and TScratch.

RESULTS

The average dice similarity coefficient (DSC) scores were obtained as 0.958 ∼ 0.968 for U-net-based deep learning models. The averaged absolute percentage errors (PE) of predicted wound areas to ground truth were 6.41%, 3.70%, and 3.73%, respectively for U-net, U-net++, and Attention U-net, while ImageJ and TScratch had considerable averaged error rates of 22.59% and 33.88%, respectively.

CONCLUSIONS

Comparative analyses revealed that the developed models outperformed the conventional approaches in terms of analysis time and segmentation sensitivity. The developed models also hold great promise for the prediction of the in vitro wound area, regardless of the therapy-of-interest, cell line, magnification of the microscope, or other application-dependent parameters.

Modulatory Effect of Chlorogenic Acid and Coffee Extracts on Wnt/β-Catenin Pathway in Colorectal Cancer Cells

The Wnt/β-Catenin pathway alterations present in colorectal cancer (CRC) are of special interest in the development of new therapeutic strategies to impact carcinogenesis and the progression of CRC. In this context, different polyphenols present in natural products have been reported to have modulatory effects against the Wnt pathway in CRC. In this study, we evaluate the effect of two polyphenol-rich coffee extracts and chlorogenic acid (CGA) against SW480 and HT-29 CRC cells. This involved the use of MTT and SRB techniques for cell viability; wound healing and invasion assay for the evaluation of the migration and invasion process; T cell factor (TCF) reporter plasmid for the evaluation of transciption factor (TCF) transcriptional activity; polymerase chain reaction (PCR) of target genes and confocal fluorescence microscopy for β-Catenin and E-Cadherin protein fluorescence levels; and subcellular localization. Our results showed a potential modulatory effect of the Wnt pathway on CRC cells, and we observed a reduction in the transcriptional activity of β-catenin. All the results were prominent in SW480 cells, where the Wnt pathway deregulation has more relevance and implies a constitutive activation of the signaling pathway. These results establish a starting point for the discovery of a mechanism of action associated with these effects and corroborate the anticancer potential of polyphenols present in coffee, which could be explored as chemopreventive molecules or as adjunctive therapy in CRC.

A pH Monitoring Algorithm for Orifice Plate Culture Medium

Recently, there has been renewed interest in cell therapy, which plays a key role in the clinical research of genetic diseases, advanced blood disease, and other diseases. It shows considerable clinical application value and is known as “the new pillar of future medicine”. Automatic cell culture and operation technology is the key to ensuring scale, standardization, and stability between batches of therapeutic cells. The pH of the cell culture medium is vital for cell growth. Most cells are suitable for growth at pH 7.2~7.4. A pH of cell culture medium lower than 6.8 or higher than 7.6 is harmful to cells, and cells will degenerate or even die. At present, the monitoring method of cell culture medium pH of automatic cell culture equipment is mainly a visual observation method, which can not accurately or quickly reflect changes in the cell culture medium. To address the issue of monitoring of cell culture fluid pH for automated cell culture equipment and the inability to employ invasive sensors to measure pH during well plate culture, a pH monitoring method for orifice plate culture medium algorithm based on HSV (hue, saturation, value) model is proposed by studying the changes of cell culture medium in the process of cell culture. The research presented here reveals the laws of cell culture fluid pH change and its color moment, and the intelligent monitoring of cell culture fluid pH was successfully achieved. The problem of non-destructive monitoring of the pH of cell culture fluids in well plates is also addressed.

Biological Impact of Phenolic Compounds from Coffee on Colorectal Cancer

Colorectal cancer is one of the leading death-related diseases worldwide, usually induced by a multifactorial and complex process, including genetic and epigenetic abnormalities and the impact of diet and lifestyle. In the present study, we evaluated the biological impact of two of the main coffee polyphenols, chlorogenic acid (CGA) and caffeic acid (CA), as well as two polyphenol-rich coffee extracts (green coffee extract and toasted coffee Extract) against SW480 and SW620 colorectal cancer cells. First, the total phenolic content and the antioxidant capability of the extracts were determined. Then, cytotoxicity was evaluated by MTT and SBR. Finally, a wound healing assay was performed to determine the impact on the cell migration process. The results showed a cytotoxic effect of all treatments in a time and dose-dependent manner, which decreased the viability in both cell lines at 24 h and 48 h; likewise, the migration capability of cells decreased with low doses of treatments. These results suggest the potential of coffee to modulate biological mechanisms involved in colorectal cancer development; however, more studies are required to understand the mechanistic insights of these observations.

Quantifying Cell Confluency by Plasmonic Nanodot Arrays to Achieve Cultivating Consistency

The determination of cell confluency and subculture timing for cell culture consistency is crucial in the field of cell-based research, but there is no universal standard concerning optimal confluence. In this study, gold nanodot arrays on glass substrates were used as culture substrates, and their spectral shifts of localized surface plasmon resonance (LSPR) were employed to monitor cell growth and quantify cell confluency. Experiments including cell counting, metabolic activity, focal adhesion, and cell cycle were also performed to confirm the cell growth monitoring accuracy of the LSPR signals. The LSPR signal exhibited the same trends like the increase of cell numbers and cell metabolic activity and reached the maximum as the cell growth achieved confluency, suggesting its great capability as an effective indicator to predict suitable subculture timing. The proposed sensing approach is a noninterventional, nondestructive, real-time, and useful tool to help biologists quantify the optimal subculture timing, achieve cell culture consistency, and obtain reproducible experimental results efficiently.

Antiproliferative Effects of Epigenetic Modifier Drugs Through E-cadherin Up-regulation in Liver Cancer Cell Lines

INTRODUCTION AND AIM

Epigenetic alterations play an essential role in cancer onset and progression, thus studies of drugs targeting the epigenetic machinery are a principal concern for cancer treatment. Here, we evaluated the potential of the combination of the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine (5aza-dC) and the pan-deacetylase inhibitor Trichostatin A (TSA), at low cytotoxic concentrations, to modulate the canonical Wnt/β-catenin pathway in liver cancer cells.

MATERIAL AND METHODS

Pyrosequencing was used for DNA methylation analyses of LINE-1 sequences and the Wnt/β-catenin pathway antagonist DKK3, SFRP1, WIF1 and CDH1. qRT-PCR was employed to verify the expression of the antagonist. Pathway regulation were evaluated looking at the expression of β-catenin and E-cadherin by confocal microscopy and the antitumoral effects of the drugs was studied by wound healing and clonogenic assays.

RESULTS

Our result suggest that 5aza-dC and TSA treatments were enough to induce a significant expression of the pathway antagonists, decrease of β-catenin protein levels, re-localization of the protein to the plasma membrane, and pathway transcriptional activity reduction. These important effects exerted an antitumoral outcome shown by the reduction of the migration and clonogenic capabilities of the cells.

CONCLUSION

We were able to demonstrate Wnt/ β-catenin pathway modulation through E-cadherin up-regulation induced by 5aza-dC and TSA treatments, under an activation-pathway background, like CTNNB1 and TP53 mutations. These findings provide evidences of the potential effect of epigenetic modifier drugs for liver cancer treatment. However, further research needs to be conducted, to determine the in vivo potential of this treatment regimen for the management of liver cancer.

Accurate Region-of-Interest Recovery Improves the Measurement of the Cell Migration Rate in the In Vitro Wound Healing Assay

The wound healing assay is widely used for the quantitative analysis of highly regulated cellular events. In this essay, a wound is voluntarily produced on a confluent cell monolayer, and then the rate of wound reduction (WR) is characterized by processing images of the same regions of interest (ROIs) recorded at different time intervals. In this method, sharp-image ROI recovery is indispensable to compensate for displacements of the cell cultures due either to the exploration of multiple sites of the same culture or to transfers from the microscope stage to a cell incubator. ROI recovery is usually done manually and, despite a low-magnification microscope objective is generally used (10x), repositioning imperfections constitute a major source of errors detrimental to the WR measurement accuracy. We address this ROI recovery issue by using pseudoperiodic patterns fixed onto the cell culture dishes, allowing the easy localization of ROIs and the accurate quantification of positioning errors. The method is applied to a tumor-derived cell line, and the WR rates are measured by means of two different image processing software. Sharp ROI recovery based on the proposed method is found to improve significantly the accuracy of the WR measurement and the positioning under the microscope.