Profiling of the Prognostic Role of Extracellular Matrix-Related Genes in Neuroblastoma Using Databases and Integrated Bioinformatics
Authors
Publication Date
2022-05-19Journal Title
Onco
ISSN
2673-7523
Publisher
MDPI AG
Volume
2
Issue
2
Pages
85-112
Language
en
Type
Article
This Version
VoR
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Jahangiri, L. (2022). Profiling of the Prognostic Role of Extracellular Matrix-Related Genes in Neuroblastoma Using Databases and Integrated Bioinformatics. Onco, 2 (2), 85-112. https://doi.org/10.3390/onco2020007
Abstract
<jats:p>A complex interaction occurs between cancer cells and the extracellular matrix (ECM) in the tumour microenvironment (TME). In this study, the expressions and mutational profiles of 964 ECM-related genes and their correlations with patient overall survival (OS) in neuroblastoma, an aggressive paediatric malignancy, were investigated using cBioPortal and PCAT databases. Furthermore, extended networks comprising protein-protein, protein-long non-coding RNA (lncRNA), and protein-miRNA of 12 selected ECM-related genes were established. The higher expressions of 12 ECM-related genes, AMBN, COLQ, ELFN1, HAS3, HSPE1, LMAN1, LRP5, MUC6, RAMP2, RUVBL2, SSBP1 and UMOD in neuroblastoma patients displayed a significant correlation with patient OS, while similar associations with neuroblastoma patient risk groups, histology and MYCN amplification were obtained. Furthermore, extended gene networks formed by these 12 ECM-related genes were established using Cytoscape, STRING, MSigDB/BioGRID, GeneMANIA and Omicsnet. Finally, the implications of the 12 ECM-related genes in other cancers were revealed using GEPIA2 and the Human Pathology Atlas databases. This meta-analysis showed the significance of these 12 ECM-related genes as putative prognostic predictors in neuroblastoma and other cancers.</jats:p>
Keywords
neuroblastoma, solid tumours, tumour microenvironment, gene networks, extracellular matrix, lncRNAs and miRNAs
Identifiers
External DOI: https://doi.org/10.3390/onco2020007
This record's URL: https://www.repository.cam.ac.uk/handle/1810/337359
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Licence:
https://creativecommons.org/licenses/by/4.0/
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