Mechanisms underlying the development of malignant retinoblastoma (RB) remain largely unknown. The purpose of this study was to identify weighted genes that are associated with the progression of RB and to assess the usefulness of bioinformatic analysis in RB research. Bioinformatic analysis was performed to construct weighted gene co-expression and protein-protein interaction (PPI) networks and to predict long non-coding RNA (lncRNA)-microRNA (miRNA)-mRNA regulatory networks. RNA extracted from RB and adjacent retinal tissue was used to validate the results obtained from bioinformatic analysis, using a semi-quantitative PCR (qPCR) assay. Twenty-one modules were generated from 5000 most variably expressed genes. Both the light-yellow and red modules were significantly associated with the cellular anaplastic grade of RB. The genes clustered in the light-yellow module included protocadherin beta (PCDHBs) family members. The red module included 5 hub genes involved in cell division. According to the hypothesis that lncRNA may serve as a competing endogenous RNA (ceRNA) for miRNAs and modulates mRNA expression, a network was constructed between lncRNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and cell division-related mRNAs. PCR analysis using 23 tumor tissues and 5 adjacent retinal tissue showed increased expression of PCDHB5 in tumor samples, and supported the predicted upregulation of mitotic checkpoint serine/threonine kinase (BUB1) by MALAT1 via miR-495-3p. Our study highlights the importance of bioinformatic analysis in identifying potential markers and mechanisms associated with the malignant transformation of RB, and provides evidence to suggest that PCDHB5 and the ceRNA regulatory network of MALAT1/miR-495-3p/BUB1 are involved in the progression of RB.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1016/j.exer.2021.108730 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
A rare dominant allele determines seed coat color and improves seed oil content in .
Sci Adv
January 2025
College of Life Science and Technology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, China.
Yellow seed coat color (SCC) is a valuable trait in , which is significantly correlated to high seed oil content (SOC) and low seed lignocellulose content (SLC). However, no dominant yellow SCC genes were identified in . In this study, a dominant yellow SCC N53-2 was verified, and then 58,981 eQTLs and 25 trans-eQTL hotspots were identified in a double haploid population derived from N53-2 and black SCC material Ken-C8.
View Article and Find Full Text PDFcSTAR analysis identifies endothelial cell cycle as a key regulator of flow-dependent artery remodeling.
Sci Adv
January 2025
Yale Cardiovascular Research Center, Yale School of Medicine, New Haven, CT 06511, USA.
Fluid shear stress (FSS) from blood flow sensed by vascular endothelial cells (ECs) determines vessel behavior, but regulatory mechanisms are only partially understood. We used cell state transition assessment and regulation (cSTAR), a powerful computational method, to elucidate EC transcriptomic states under low shear stress (LSS), physiological shear stress (PSS), high shear stress (HSS), and oscillatory shear stress (OSS) that induce vessel inward remodeling, stabilization, outward remodeling, or disease susceptibility, respectively. Combined with a publicly available database on EC transcriptomic responses to drug treatments, this approach inferred a regulatory network controlling EC states and made several notable predictions.
View Article and Find Full Text PDFInvestigation of alpha-glucosidase inhibition activity of Artabotrys sumatranus leaf extract using metabolomics, machine learning and molecular docking analysis.
PLoS One
January 2025
Research Centre for Plant Conservation, Botanic Gardens and Forestry, National Research and Innovation Agency, Bogor, Indonesia.
One way to treat diabetes mellitus type II is by using α-glucosidase inhibitor, that will slow down the postprandial glucose intake. Metabolomics analysis of Artabotrys sumatranus leaf extract was used in this research to predict the active compounds as α-glucosidase inhibitors from this extract. Both multivariate statistical analysis and machine learning approaches were used to improve the confidence of the predictions.
View Article and Find Full Text PDFAnalysis of the stability of a predator-prey model including the memory effect, double Allee effect and Holling type-I functional response.
PLoS One
January 2025
Department of Mathematics and General Sciences, Prince Sultan University, Riyadh, Saudi Arabia.
This study proposes and analyses a revised predator-prey model that accounts for a twofold Allee impact on the rate of prey population expansion. Employing the Caputo fractional-order derivative, we account for memory impact on the suggested model. We proceed to examine the significant mathematical aspects of the suggested model, including the uniqueness, non-negativity, boundedness, and existence of solutions to the noninteger order system.
View Article and Find Full Text PDFQuantitative analysis of the dexamethasone side effect on human-derived young and aged skeletal muscle by myotube and nuclei segmentation using deep learning.
Bioinformatics
January 2025
Department of Robotics & Mechatronics Engineering, DGIST, Daegu, 42988, South Korea.
Motivation: Skeletal muscle cells (skMCs) combine together to create long, multi-nucleated structures called myotubes. By studying the size, length, and number of nuclei in these myotubes, we can gain a deeper understanding of skeletal muscle development. However, human experimenters may often derive unreliable results owing to the unusual shape of the myotube, which causes significant measurement variability.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!