Direct tool for quantitative analysis of cell/object dynamic behavior - metastasis and far beyond

INTRODUCTION

The dynamics and depth of invasion as well as the ability of cancer cells to penetrate the walls of  lymphatic or blood vessels represent critical survival-influencing factors in cancer patients. Depending on the cell type and tissue environment, cancer cell invasion differ in terms of motility mechanism and migration modes. Thus, there is the need of effective models allowing not only for single cell invasion potential assessment but also for collective migration and expansive growth evaluation in 3D microenvironment e.g. basement membranes. To meet this task, the specimens should be compared and analyzed in terms of the dynamics of movement and the evolution of the shape.

OBJECTIVES

Our main objective was development of the mathematical method that enables fast and credible calculation of parameters of shape and position, namely standard deviations (σ_X, σ_Y), centroid position (μ_X, μ_Y) and correlation coefficient ρ, based only on the contour of the aggregate.

METHODS

In order to accomplish this goal we measured geometrical properties of aggregates of RGM1 cells seeded in 3D Geltrex basement membrane. Referential microscopic images were taken 24 and 48 h after seeding and cell group dynamics was registered over 8 h periods using time lapse microscopy.

RESULTS

Based on gathered data, we managed to develop and fully test universal numerical tool allowing for estimation of statistical parameters of cell groups and aggregates which then allows for the precise evaluation of their behavior within microenvironment with time.

CONCLUSION

We conclude, that our tool is suitable for any research on the metastatic potential and motility of cancer cells in a given microenvironment, regardless of the migration mechanism, which together with the advanced analysis like cell single-cell transcriptomic, proteomic, and chromatin accessibility data may allow to identify precise targets for anti-cancer therapies, to predict the degree of malignancy of neoplastic lesions as well as it can be useful during architecting therapeutic strategies. Moreover, the developed tool seems to be broadly applicable for assessment of behavioural dynamics of any population.

Inhibitory role of LINC00332 in gastric cancer progression through regulating cell EMT and stemness

OBJECTIVE

Gastric cancer (GC) is one of the most common lethal malignancies worldwide. The molecular mechanisms underlying GC early detection are poorly understood. Identifying potential coding and non-coding markers and related pathways in the GC progression is essential. Some Long non-coding RNAs (lncRNAs) reportedly play vital roles during gastric GC development. However, the clinical significance and biological function of LINC00332 in GC remain largely unclear.

METHODS

The gene expression patterns of GC from an RNAseq dataset (GSE122401) were retrieved from the Gene Expression Omnibus (GEO) database to recognize differentially expressed genes (DEGs) and lncRNAs (DELs) between normal and GC samples through several bioinformatic analysis. The expression of LINC00332 and MMP-13 as a target gene was quantified in fresh frozen tissues obtained from GC patients. In addition, we investigated the potential function of LINC00332 in silico and in vitro.

RESULTS

The expressions of LINC00332 and MMP-13 were significantly downregulated and upregulated in GC tissues, respectively. A significant inverse correlation between LINC00332 and MMP-13 mRNA expression was observed in tumor samples. The mRNA expression level of mesenchymal markers, stem cell factors, and MMP genes were significantly decreased after the LINC00332 ectopic expression, while epithelial markers expression was significantly increased. The LINC00332 overexpression markedly repressed proliferation, migration, and invasion and did not induce apoptosis in AGS cells. In addition, LINC00332 overexpression notably promoted the E-cadherin protein expression. Moreover, LINC00332 significantly decreased the cisplatin resistance.

CONCLUSION

Our findings indicated that LINC00332 may be a critical anti-EMT factor and provided a new efficient therapeutic strategy for GC treatment.

Identification of hub pathways and drug candidates in gastric cancer through systems biology

Gastric cancer is the fourth cause of cancer death globally, and gastric adenocarcinoma is its most common type. Efforts for the treatment of gastric cancer have increased its median survival rate by only seven months. Due to the relatively low response of gastric cancer to surgery and adjuvant therapy, as well as the complex role of risk factors in its incidences, such as protein-pomp inhibitors (PPIs) and viral and bacterial infections, we aimed to study the pathological pathways involved in gastric cancer development and investigate possible medications by systems biology and bioinformatics tools. In this study, the protein-protein interaction network was analyzed based on microarray data, and possible effective compounds were discovered. Non-coding RNA versus coding RNA interaction network and gene-disease network were also reconstructed to better understand the underlying mechanisms. It was found that compounds such as amiloride, imatinib, omeprazole, troglitazone, pantoprazole, and fostamatinib might be effective in gastric cancer treatment. In a gene-disease network, it was indicated that diseases such as liver carcinoma, breast carcinoma, liver fibrosis, prostate cancer, ovarian carcinoma, and lung cancer were correlated with gastric adenocarcinoma through specific genes, including hgf, mt2a, mmp2, fbn1, col1a1, and col1a2. It was shown that signaling pathways such as cell cycle, cell division, and extracellular matrix organization were overexpressed, while digestion and ion transport pathways were underexpressed. Based on a multilevel systems biology analysis, hub genes in gastric adenocarcinoma showed participation in the pathways such as focal adhesion, platelet activation, gastric acid secretion, HPV infection, and cell cycle. PPIs are hypothesized to have a therapeutic effect on patients with gastric cancer. Fostamatinib seems a potential therapeutic drug in gastric cancer due to its inhibitory effect on two survival genes. However, these findings should be confirmed through experimental investigations.