Bioinformatics analysis of Ewing's sarcoma: Seeking key candidate genes and pathways

Zhang, Jinming; Zhang, Yao; Li, Ze; Wu, Haijian; Xun, Jianjun; Feng, Helin

doi:10.3892/ol.2019.10936

Cited by 4 publications

(2 citation statements)

References 47 publications

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“…Besides, ISG15 has been described to play a pro-tumoral role in various malignancies like bladder, nasopharyngeal, breast, hepatocellular or pancreatic cancer [18-24, 27-30, 44]. In sarcoma, a recent bioinformatics study into Ewing sarcoma, comparing tumour samples versus non-cancerous samples, identified ISG15 as one of the hub genes in a protein-protein interaction network (PPI) [45]. Conversely, ISG15 showed a protective anti-tumour role in glioblastoma and ovarian models [46,47].…”

Section: Discussionmentioning

confidence: 99%

ISG15 as a prognostic biomarker in solitary fibrous tumour

Mondaza-Hernandez

Moura

López-Álvarez

et al. 2022

Cell. Mol. Life Sci.

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Background Solitary fibrous tumour (SFT) is a rare mesenchymal malignancy that lacks robust prognostic and predictive biomarkers. Interferon-stimulated gene 15 (ISG15) is a ubiquitin-like modifier, associated with tumour progression, and with poor survival of SFT patients, as previous published by our group. Here, we describe the role of ISG15 in the biology of this rare tumour. Methods ISG15 expression was assessed by immunohistochemistry in tissue microarrays from SFT patients and tested for correlation with progression-free survival and overall survival (OS). The effects of ISG15 knockdown or induction were investigated for cancer stem cell (CSC) characteristics and for drug sensitivity in unique in vitro models of SFT. Results The prognostic value of ISG15 for OS was validated at protein level in malignant SFT patients, prospectively treated with pazopanib and enrolled in GEIS-32 trial. In SFT in vitro models, ISG15 knockdown lead to a decrease in the expression of CSC-related genes, including SOX2, NANOG, ALDH1A1, ABCB1 and ABCC1. Likewise, ISG15 downregulation decreased the clonogenic/ tumoursphere-forming ability of SFT cells, while enhancing apoptotic cell death after doxorubicin, pazopanib or trabectedin treatment in 3D cell cultures. The regulation of CSC-related genes by ISG15 was confirmed after inducing its expression with interferon-β1; ISG15 induction upregulated 1.28- to 451-fold the expression of CSC-associated genes. Conclusions ISG15 is a prognostic factor in malignant SFT, regulating the expression of CSC-related genes and CSCs maintenance. Our results suggest that ISG15 could be a novel therapeutic target in SFT, which could improve the efficacy of the currently available treatments.

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Section: Discussionmentioning

confidence: 99%

ISG15 as a prognostic biomarker in solitary fibrous tumour

Mondaza-Hernandez

Moura

López-Álvarez

et al. 2022

Cell. Mol. Life Sci.

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“…Nowadays, numerous researches have been published on many different cancer types. Similarly, ES is no exception, some key genes involved in metastasis and development [5][6][7][8]. However, these studies contain one or two datasets.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Analysis of Key Genes and Regulatory Elements in Ewing Sarcoma With Prognostic Values

Li¹,

Li²,

Zong³

et al. 2021

Preprint

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Background: Ewing sarcoma (ES) is one of the most common types of round cell mesenchymal neoplasms related to children and young adults. It is characterized by chromosomal translocations. However, that does not completely explain the ES proliferation and development. Methods: Several public data series (GSE45544, GSE68591, and GSE68776) were used to identify differentially expressed genes (DEGs) between ES and normal tissue. Furthermore, functional enrichment analysis and protein-protein interaction network of DEGs were performed. The regulatory network of DEGs and hub genes, survival analysis of hub genes was visualized. In addition, functional predictions of the candidate gene were analyzed. Results: A total of 142 DEGs 10 hub genes were identified. While out of them, only one candidate gene FGF7 was found to be suitable as a candidate gene. Conclusions: In conclusion, the DEGs, hub genes, and their regulatory molecules screened out in this research could contribute to comprehend the mechanisms in ES and provide potential research molecular for further study.

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Identification of Comorbidities, Genomic Associations, and Molecular Mechanisms for COVID‐19 Using Bioinformatics Approaches

Omit

Akhter

Rana

et al. 2023

BioMed Research International

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Several studies have been done to identify comorbidities of COVID-19. In this work, we developed an analytical bioinformatics framework to reveal COVID-19 comorbidities, their genomic associations, and molecular mechanisms accomplishing transcriptomic analyses of the RNA-seq datasets provided by the Gene Expression Omnibus (GEO) database, where normal and infected tissues were evaluated. Using the framework, we identified 27 COVID-19 correlated diseases out of 7,092 collected diseases. Analyzing clinical and epidemiological research, we noticed that our identified 27 diseases are associated with COVID-19, where hypertension, diabetes, obesity, and lung cancer are observed several times in COVID-19 patients. Therefore, we selected the above four diseases and performed assorted analyses to demonstrate the association between COVID-19 and hypertension, diabetes, obesity, and lung cancer as comorbidities. We investigated genomic associations with the cross-comparative analysis and Jaccard’s similarity index, identifying shared differentially expressed genes (DEGs) and linking DEGs of COVID-19 and the comorbidities, in which we identified hypertension as the most associated illness. We also revealed molecular mechanisms by identifying statistically significant ten pathways and ten ontologies. Moreover, to understand cellular physiology, we did protein-protein interaction (PPI) analyses among the comorbidities and COVID-19. We also used the degree centrality method and identified ten biomarker hub proteins (IL1B, CXCL8, FN1, MMP9, CXCL10, IL1A, IRF7, VWF, CXCL9, and ISG15) that associate COVID-19 with the comorbidities. Finally, we validated our findings by searching the published literature. Thus, our analytical approach elicited interconnections between COVID-19 and the aforementioned comorbidities in terms of remarkable DEGs, pathways, ontologies, PPI, and biomarker hub proteins.

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Bioinformatics analysis of Ewing's sarcoma: Seeking key candidate genes and pathways

Cited by 4 publications

References 47 publications

ISG15 as a prognostic biomarker in solitary fibrous tumour

ISG15 as a prognostic biomarker in solitary fibrous tumour

Comprehensive Analysis of Key Genes and Regulatory Elements in Ewing Sarcoma With Prognostic Values

Identification of Comorbidities, Genomic Associations, and Molecular Mechanisms for COVID‐19 Using Bioinformatics Approaches

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