ICDM-GEHC: identifying cancer driver module based on graph embedding and hierarchical clustering

Complex & Intelligent Systems, Journal Year: 2024, Volume and Issue: 10(3), P. 3411 - 3427

Published: Feb. 3, 2024

Abstract Due to the high heterogeneity of cancers, it is rather essential explore driver modules with help gene mutation data as well known interactions between genes/proteins. Unfortunately, latent false positive are inevitable in Protein-Protein Interaction (PPI) network. Hence presented method, a new weight evaluation index, based on gene-microRNA network somatic profile, introduced for weighting PPI first. Subsequently, vertices weighted hierarchically clustered by measuring Mahalanobis distance their feature vectors, extracted graph embedding method Node2vec. Finally, heuristic process dropping and extracting conducted clusters produce group modules. Numerous experiment results demonstrate that proposed exhibits superior performance four cutting-edge identification methods most cases regarding capability recognizing acknowledged cancer-related genes, generating having relatively coverage mutual exclusivity, significantly enriched specific types cancers. The majority genes identified involved signaling pathways, or have been reported be carcinogenic literature. Furthermore, many cancer related detected actually omitted comparison methods, which has verified experiments.

Language: Английский

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The mechanism of ITGB4 in tumor migration and invasion

Frontiers in Oncology, Journal Year: 2024, Volume and Issue: 14

Published: Aug. 7, 2024

Integrin β4 (ITGB4) is a transmembrane protein that functions as mechanosensor, mediating the bidirectional exchange of information between intracellular and extracellular matrices. ITGB4 plays critical role in cell adhesion, migration, signaling. Numerous studies have implicated key facilitator tumor migration invasion. This review provides foundational description mechanisms by which regulates invasion through pathways involving focal adhesion kinase (FAK), B (AKT), matrix metalloproteinases (MMPs). These encompass epithelial-mesenchymal transition (EMT), phosphorylation, methylation associated molecules. Additionally, this explores prevalent clinical tumors, including those digestive system, breast, prostate.

Language: Английский

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ING3 inhibits the malignant progression of lung adenocarcinoma by negatively regulating ITGB4 expression to inactivate Src/FAK signaling

Cellular Signalling, Journal Year: 2024, Volume and Issue: 117, P. 111066 - 111066

Published: Jan. 27, 2024

Language: Английский

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Chromatin remodeling with combined FACT and BET inhibition disrupts oncogenic transcription in Diffuse Midline Glioma

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 9, 2024

Abstract Aberrant epigenetic regulation is a hallmark of Diffuse Midline Glioma (DMG), an incurable pediatric brain tumor. The H3K27M driver histone mutation leads to transcriptional dysregulation, indicating that targeting the epigenome and transcription may be key therapeutic strategies against this highly aggressive cancer. One such target Facilitates Chromatin Transcription (FACT) chaperone. We found FACT enriched at developmental gene promoters, coinciding with regions open chromatin binding motifs core DMG regulatory factors. Furthermore, interacted co-localized Bromodomain Extra-Terminal Domain (BET) protein BRD4 promoters enhancers, suggesting functional cooperation between in DMG. In vitro , combinatorial approach using inhibitor CBL0137, coupled BET inhibition revealed potent synergistic cytotoxicity across range cultures, H3K27M-mutant cells demonstrating heightened sensitivity. These results were recapitulated vivo significantly extending survival three independent orthotopic PDX models Mechanistically, we show CBL0137 treatment decreased accessibility, synergizing disrupt transcription, silencing several oncogenes including MYC, PDGFRA MDM4 as well causing alterations splicing landscape. Combined, these data highlight promise simultaneously DMG, proposing novel strategy for combating devastating

Language: Английский

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Identification and Comprehensive Analysis of circRNA-miRNA-mRNA Regulatory Networks in A2780 Cells Treated with Resveratrol

Genes, Journal Year: 2024, Volume and Issue: 15(7), P. 965 - 965

Published: July 22, 2024

Ovarian cancer (OC) is one of the most commonplace gynecological malignancies. This study explored effects resveratrol (RES) on OC cell proliferation and apoptosis. Proliferation activity was measured for A2780 cells treated with RES 24 h 48 at concentrations 0, 10, 25, 50, 75, 100, 150, 200, 300 μM. RNA sequencing (RNA-seq) performed to analyze circular (circRNA), microRNA (miRNA), messenger (mRNA) expression spectrum. The differentially expressed genes included 460 circRNAs, 1988 miRNAs, 1671 mRNAs, they were subjected analyses including Gene Ontology, Kyoto Encyclopedia Genes Genomes (KEGG), Reactome enrichment. We selected signaling pathways enriched in processes by mRNA KEGG, comprehensively analyzed circRNA-miRNA-mRNA regulatory network, verified several miRNAs network diagram using quantitative real-time polymerase chain reaction. data showed that or decreased increasing RES. we constructed provides new insights into ability inhibit promote apoptosis cells.

Language: Английский

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Integrin α6 and integrin β4 in exosomes promote lung metastasis of colorectal cancer

Journal of Cancer Research and Therapeutics, Journal Year: 2024, Volume and Issue: 20(7), P. 2082 - 2093

Published: Dec. 1, 2024

Language: Английский

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