Exploration of potential key pathways and genes in multiple ocular cancers through bioinformatics analysis

Wan, Qi; Tang, Jing

doi:10.1007/s00417-019-04410-2

Cited by 13 publications

(9 citation statements)

References 31 publications

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“…GSEA is a computational method (https://software.broadinstitute.org/gsea/index.jsp) used to assess correlations between pathways and gene expression [15]. To identify the correlations between common gene expression and related pathways in esophageal cancer, GSEA was used to look for significant differences between high expression and low expression.…”

Section: E920355-4mentioning

confidence: 99%

SPP1 and FN1 associated with progression and prognosis of esophageal cancer identified by integrated expression profiles analysis

Wang

Pang

et al. 2020

Med Sci Monit

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Background: Esophageal cancer is a malignant tumor with a complex pathogenesis and a poor 5-year survival rate, which encourages researchers to explore its molecular mechanisms deeper to improve the prognosis. Material/Methods: DEGs were from 4 Gene Expression Omnibus (GEO) databases (GSE92396, GSE20347, GSE23400, and GSE45168) including 87 esophageal tumor samples and 84 normal samples. We performed Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, Protein-Protein interaction (PPI) analysis, and GeneMANIA to identify the DEGs. Gene set enrichment analysis (GSEA) and Kaplan-Meier survival analyses were performed. Results: There was an overlapping subset consisting of 120 DEGs that was present in all esophageal tumor samples. The DEGs were enriched in extracellular matrix (ECM)-receptor interaction, as well as focal adhesion and transcriptional mis-regulation in cancer. The 2 most crucial regulatory pathways in esophageal cancer were the amebiasis pathway and the PI3K-Akt signaling pathway. Secreted phosphoprotein 1 (SPP1) and fibronectin 1 (FN1) were selected and verified in an independent cohort and samples using the TCGA and GTEx projects. Gene set enrichment analysis (GSEA) showed that proteasome and nucleotide excision repair were 2 most differentially enriched pathways in the SPP1 high-expression phenotype, and ECM-receptor interaction and focal adhesion in FN1 high-expression phenotype. Kaplan-Meier survival analysis showed that SPP1 and FN1 were significantly positively related to overall survival and had the potential to predict patient relapse. Conclusions: Our analysis is the first to show that SPP1 and FN1 might work as biological markers of progression and prognosis in esophageal carcinoma (ESCA).

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Section: E920355-4mentioning

confidence: 99%

SPP1 and FN1 associated with progression and prognosis of esophageal cancer identified by integrated expression profiles analysis

Wang

Pang

et al. 2020

Med Sci Monit

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“…Although a handful of ndings have demonstrated the critical role of m 6 A modi cation in UM tumorigenesis, little is known about the effects of the newly discovered reader, IGF2BPs, in UM [40,41]. Wan et al reported that the transcription of IGF2BP3 is widely upregulated in multiple ocular cancers, including UM [42]. The survival analysis using TCGA further indicates that IGF2BP3 can act as an independent predictor for prognosis in UM.…”

Section: Discussionmentioning

confidence: 99%

Hsa_Circ_0053943 Drives Uveal Melanoma Progression via Regulating N6-Methyladenosine Modification of EGFR with IGF2BP3

Zhao

Wang

et al. 2022

SSRN Journal

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“…29 In another study, IGF2BP3 was differentially expressed among three ocular cancers. 30 In CRC, increased IGF2BP3 expression has been shown to promote the invasive pattern of CRC in vitro and vivo . 31 Moreover, IGF2BP3 can be considered as a possible oncogene and target of miR-34a in gastric carcinogenesis.…”

Section: Discussionmentioning

confidence: 99%

Gene signature and prognostic merit of M6a regulators in colorectal cancer

Zhang

Cheng

Wang

et al. 2020

Exp Biol Med (Maywood)

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Although new diagnostic techniques and treatments are increasingly updated, the clinical outcomes of CRC patients are still not encouraging with a low survival rate. N6-methyladenosine as a popular modification on mRNA is associated with multiple types of cancers. Our purpose is to evaluate gene signature and prognostic ability of N6-methyladenosine in CRC. We used the gene expression, copy number variation, simple nucleotide variation and clinical messages from The Cancer Genome Atlas database. We first identified mutation and copy number variations of N6-methyladenosine regulatory genes in both colon adenocarcinoma and rectum adenocarcinoma. Fourteen of all 17 N6-methyladenosine regulatory genes were related with higher mRNA expression, whereas deletion leads to reduced expression. Using univariate Cox regression analysis, RBM15, YTHDC2, and METTL14 genes in the rectum adenocarcinoma samples were conspicuously associated with the prognosis of patients. Based on the least absolute shrinkage and selection operator regression models, we built a 2-gene (YTHDC2 and IGF2BP3) signature of N6-methyladenosine regulators with prognostic ability. The 1-, 3-, and 5-year AUCs of this signature were all greater than 0.6, and the P-value for risk prediction for patients was also less than 0.0001. Moreover, high IGF2BP3 gene expression was significantly associated with IFN-γ in colon adenocarcinoma , and related to the azurophil granule membrane pathway in rectum adenocarcinoma. High YTHDC2 expression in colon adenocarcinoma is closely related to cell energy metabolism. In the rectum adenocarcinoma, high YTHDC2 gene expression is related to the cell centrosome pathway. In conclusion, for the first time, we identified genetic changes of N6-methyladenosine modulators and built a prognostic gene signature in CRC. Impact statement Although new diagnostic techniques and treatments are increasingly updated for CRC, the clinical outcomes of CRC patients are still not encouraging with a low survival rate. N6-methyladenosine (m6A) as a popular modification on mRNA is associated with multiple types of cancers. Our purpose is to identify gene signature and prognostic ability of m6A modulators in CRC. For the first time, we identified genetic changes of m6A modulators and built prognostic gene signature in CRC, which may provide effective targets for the diagnosis and management of CRC.

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Exploration of potential key pathways and genes in multiple ocular cancers through bioinformatics analysis

Cited by 13 publications

References 31 publications

SPP1 and FN1 associated with progression and prognosis of esophageal cancer identified by integrated expression profiles analysis

SPP1 and FN1 associated with progression and prognosis of esophageal cancer identified by integrated expression profiles analysis

Hsa_Circ_0053943 Drives Uveal Melanoma Progression via Regulating N6-Methyladenosine Modification of EGFR with IGF2BP3

Gene signature and prognostic merit of M6a regulators in colorectal cancer

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