MKI67 an potential oncogene of oral squamous cell carcinoma via the high throughput technology

Effects of Induced Pluripotent Stem Cell-Derived Astrocytes on Cisplatin Sensitivity in Pediatric Brain Cancer Cells

Background: ATRTs and DIPGs are deadly pediatric brain tumors with poor prognosis. These tumors can develop resistance to chemotherapies, which may be significantly influenced by their microenvironment. Since astrocytes are the most abundant glial cell type in the brain microenvironment and may support tumor growth and chemoresistance, this study investigated the effects of induced pluripotent stem cell-derived astrocytes (iPSC-astrocytes) on cisplatin sensitivity in CHLA-05-ATRT and SF8628 (DIPG) cells. iPSCs provide an unlimited and standardized source of nascent astrocytes, which enables modeling the interaction between childhood brain tumor cells and iPSC-astrocytes within a controlled coculture system. Methods: To study the effects on tumor growth, the iPSC-astrocytes were cocultured with tumor cells. Additionally, the tumor cells were exposed to various concentrations of cisplatin to evaluate their chemosensitivity in the presence of astrocytes. Results: The paracrine interaction of iPSC-astrocytes with tumor cells upregulated astrocyte activation markers GFAP and STAT3 and promoted tumor cell proliferation. Moreover, the cisplatin treatment significantly decreased the viability of CHLA-05-ATRT and SF8628 cells. However, tumor cells exhibited reduced sensitivity to cisplatin in the coculture with iPSC-astrocytes. During cisplatin treatment, DIPG cells in particular showed upregulation of resistance markers, ERK1, STAT3, and MTDH, which are associated with enhanced proliferation and invasion. They also had increased expression of APEX1, which is involved in the base excision repair pathway following cisplatin-induced DNA damage. Conclusion: These findings underscore the significance of the tumor microenvironment in modulating tumor cell survival and chemosensitivity.

Co-isolation of human donor eye cells and development of oncogene-mutated melanocytes to study uveal melanoma

BACKGROUND

Uveal melanoma (UM) is the most common intraocular tumor in adults, arises either de novo from normal choroidal melanocytes (NCMs) or from pre-existing nevi that stem from NCMs and are thought to harbor UM-initiating mutations, most commonly in GNAQ or GNA11. However, there are no commercially available NCM cell lines, nor is there a detailed protocol for developing an oncogene-mutated CM line (MutCM) to study UM development. This study aimed to establish and characterize premalignant CM models from human donor eyes to recapitulate the cell populations at the origin of UM.

RESULTS

Given the precious value of human donor eyes for studying multiple ocular cell types, we validated a co-isolation protocol of both human NCMs and retinal pigment epithelial (RPE) cells from a single eye. To this end, NCMs and RPE cells were sequentially isolated from 20 donors, with success rates of 95% and 75%, respectively. MutCMs were generated from 10 donors using GNAQQ209L-carried lentivirus with high mutant copies (up to 98.8% of total GNAQ copies being mutant). NCM growth and behavior were characterized under different culture conditions (i.e., supplementation with serum and 12-O-tetradecanoylphorbol-13-acetate) to determine optimized protocols. Particularly, Matrigel™ coating induced spheroid growth under certain coating thickness and cell seeding density but did not improve NCM metabolic activity. Current methodologies in NCM isolation, culture, and research applications were summarized. Proteomic profiling of 4 NCMs, 1 MutCM, and 3 UMs allowed to discover significant differences in UMs including a downregulation of proteins linked to melanocyte differentiation and an upregulation of proteins involved in RNA metabolism. RNA sequencing revealed enriched pathways related to cancer, notably PI3K-Akt and MAPK signaling pathways, in MutCMs and UM cells compared to NCMs, providing insights into molecular changes in GNAQQ209L-mutated pre-cancer cell models and UM cells.

CONCLUSIONS

We successfully isolated and established NCM, RPE, and MutCM cell lines. We describe efficient methods for the isolation and growth of NCMs and report their phenotypic, proteomic, and transcriptomic characteristics, which will facilitate the investigation of UM development and progression. The co-isolated RPE cells could benefit research on other ocular pathologies, such as age-related macular degeneration.

Roles of NOC3L and DDX17 in acquired immunodeficiency complicated with viral myocarditis and osteoporosis

Acquired immunodeficiency syndrome is a systemic infectious disease caused by human immunodeficiency virus infection, which could attack the bones and heart. However, the relationship between Nuclear Complex Associated 3 Homolog (NOC3L) and DEAD box helicase 17 (DDX17) and acquired immunodeficiency complicated with viral myocarditis and osteoporosis is unclear. The acquired immune deficiency dataset GSE140713, GSE147162 and the osteoporosis dataset (GSE230665), and viral myocarditis dataset (GSE150392) configuration files were generated from gene expression omnibus. The differentially expressed genes (DEGs) were screened and performed weighted gene co-expression network analysis. Construction and analysis of protein-protein interaction network. Functional enrichment analysis, gene set enrichment analysis, immune infiltration analysis, gene expression heatmap, and comparative toxicogenomics database analysis were performed. TargetScan screens miRNAs of DEGs. Thousand three hundred thirty-five DEGs were identified. According to gene ontology, they are mainly concentrated in the regulation of RNA biosynthesis, cytoplasmic ribosome, and the DNA binding transcription factor activity. In Kyoto Encyclopedia of Genes and Genomes analysis, they are mainly concentrated in TGF-β signal pathway, Notch signaling pathway, cAMP signaling pathway, and Apelin signaling pathway. Gene set enrichment analysis shows that DEGs are mainly enriched in cytoplasmic ribosome, transcriptional regulator activity, DNA binding transcription factor activity, TGF-β signal pathway, and Notch signal pathway. In the enrichment project of Metascape, tyrosine kinase receptor signaling, growth regulation, and enzyme-linked receptor protein signaling pathways can be seen in the gene ontology enrichment project. Four core genes (NOC3L, WDR46, SDAD1, and DDX17) were obtained. Core genes (NOC3L, WDR46, SDAD1, and DDX17) were low expressed in both acquired immunodeficiency and osteoporosis samples. Comparative toxicogenomics database analysis showed that core genes (NOC3L, WDR46, SDAD1, and DDX17) were associated with inflammation necrosis. The expressions of NOC3L and DDX17 are low in acquired immunodeficiency combined with viral myocarditis and osteoporosis.

Single-cell RNA sequencing reveals hub genes of myocardial infarction-associated endothelial cells

BACKGROUND

Myocardial infarction (MI) is a cardiovascular disease that seriously threatens human health. Dysangiogenesis of endothelial cells (ECs) primarily inhibits recovery from MI, but the specific mechanism remains to be further elucidated.

METHODS

In this study, the single-cell RNA-sequencing data from both MI and Sham mice were analyzed by the Seurat Package (3.2.2). The number of ECs in MI and Sham groups were compared by PCA and tSNE algorithm. FindMarkers function of Seurat was used to analyze the DEGs between the MI and Sham groups. Then, the ECs was further clustered into 8 sub-clusters for trajectory analysis. The BEAM was used to analyze the branch point 3 and cluster the results. In addition, the DEGs in the microarray data set of MI and Sham mice were cross-linked, and the cross-linked genes were used to construct PPI networks. The key genes with the highest degree were identified and analyzed for functional enrichment. Finally, this study cultured human umbilical vein endothelial cells (HUVECs), established hypoxia models, and interfered with hub gene expression in cells. The impact of hub genes on the migration and tube formation of hypoxic-induced HUVECs were verified by Wound healing assays and tubule formation experiments.

RESULTS

The number and proportion of ECs in the MI group were significantly lower than those in the Sham group. Meantime, 225 DEGs were found in ECs between the MI and Sham groups. Through trajectory analysis, EC4 was found to play an important role in MI. Then, by using BEAM to analyze the branch point 3, and clustering the results, a total of 495 genes were found to be highly expressed in cell Fate2 (mainly EC4). In addition, a total of 194 DEGs were identified in Micro array dataset containing both MI and Sham mice. The hub genes (Timp1 and Fn1) with the highest degree were identified. Inhibiting Timp1 and Fn1 expression promoted the migration and tube formation of HUVECs.

CONCLUSIONS

Our data highlighted the non-linear dynamics of ECs in MI, and provided a foothold for analyzing cardiac homeostasis and pro-angiogenesis in MI.

Review of Disease-Specific microRNAs by Strategically Bridging Genetics and Epigenetics in Oral Squamous Cell Carcinoma

Oral squamous cell carcinoma (OSCC) is one of the most prevalent human malignancies and a global health concern with a poor prognosis despite some therapeutic advances, highlighting the need for a better understanding of its molecular etiology. The genomic landscape of OSCC is well-established and recent research has focused on miRNAs, which regulate gene expression and may be useful non-invasive biomarkers or therapeutic targets. A plethora of findings regarding miRNA expression have been generated, posing challenges for the interpretation and identification of disease-specific molecules. Hence, we opted to identify the most important regulatory miRNAs by bridging genetics and epigenetics, focusing on the key genes implicated in OSCC development. Based on published reports, we have developed custom panels of fifteen major oncogenes and five major tumor suppressor genes. Following a miRNA/target gene interaction analysis and a comprehensive study of the literature, we selected the miRNA molecules which target the majority of these panels that have been reported to be downregulated or upregulated in OSCC, respectively. As a result, miR-34a-5p, miR-155-5p, miR-124-3p, miR-1-3p, and miR-16-5p appeared to be the most OSCC-specific. Their expression patterns, verified targets, and the signaling pathways affected by their dysregulation in OSCC are thoroughly discussed.