Identification of potential biomarkers associated with poor prognosis in oral squamous cell carcinoma through integrated bioinformatics analysis: A pilot study

Bayat, Zeynab; Farhadi, Zohre; Taherkhani, Amir

doi:10.1016/j.genrep.2021.101243

Cited by 16 publications

(14 citation statements)

References 127 publications

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“…Despite advances in the diagnosis and treatment of OSCC in recent decades, its five-year survival rate remains low [ 18 ]. With the development of bioinformatics, the understanding of OSCC has gradually broadened and deepened [ 19 , 20 ]. Chai et al performed a genome-wide CRISPR-Cas9 screen of OSCC cells and identified YAP1 and WWTR1 as key genes [ 21 ].…”

Section: Discussionmentioning

confidence: 99%

[Retracted] Comprehensive and Integrated Analysis Identifies ZEB1 as a Key Novel Gene in Oral Squamous Cell Carcinoma

Tao

et al. 2022

Contrast Media & Molecular Imaging

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Oral squamous cell carcinoma (OSCC) is the most common head and neck cancer with a poor prognosis. Therefore, it is crucial to explore molecular prognostic biomarkers for OSCC. ZEB1 (also known as δEF1) is a member of the zinc finger E-box binding protein family of transcription factors involved in various biological processes, including tumorigenesis, progression, and metastasis. Recent evidence suggests that ZEB1 has a role in the tumorigenicity of oral epithelial cells, although its mode of action needs to be investigated further. To better understand the relationship between ZEB1 and OSCC, we transfected the ZEB1-overexpressing oral squamous cell lines SCC9 and SCC25 with lentivirus and then extracted RNA from the cells for gene expression analysis. Furthermore, the GSE30784 dataset was downloaded from the Gene Expression Omnibus (GEO) database to identify potential biomarkers of OSCC and to assess the potential mechanisms. The criteria for identification of their DEGs were |logFC| > 1 and P < 0.05. Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) analyses were also carried out. Integrating the data from the PPI network and survival analysis identified that ZEB1 might be an independent prognostic biomarker in OSCC. In conclusion, integrated bioinformatics and microarray analysis identified the critical gene ZEB1 linked to the overall survival (OS) of patients with OSCC. ZEB1 could be applied as a prognostic biomarker to forecast the survival of patients with OSCC and might indicate innovative therapeutic indicators for OSCC.

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Section: Discussionmentioning

confidence: 99%

[Retracted] Comprehensive and Integrated Analysis Identifies ZEB1 as a Key Novel Gene in Oral Squamous Cell Carcinoma

Tao

et al. 2022

Contrast Media & Molecular Imaging

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“…A significant part in promoting the signaling pathways connected to programmed cell death is played by cytochrome c (CYCS) [ 51 ]. However, CYCS is a poor prognostic indicator in the majority of malignancies, which may be a result of a malignant tissue response [ 52 , 53 ]. Thrombospondin-1 (THBS1) is an adhesive glycoprotein.…”

Section: Discussionmentioning

confidence: 99%

Pathogenesis and prognosis of primary oral squamous cell carcinoma based on microRNAs target genes: a systems biology approach

Taherkhani¹,

Dehto²,

Jamshidi³

et al. 2022

Genomics Inform

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Oral squamous cell carcinoma (OSCC) is the most prevalent head and neck malignancy, with frequent cervical lymph-node metastasis, leading to a poor prognosis in OSCC patients. The present study aimed to identify potential markers, including microRNAs (miRNAs) and genes, significantly involved in the etiology of early-stage OSCC. Additionally, the main OSCC's dysregulated Gene Ontology annotations and significant signaling pathways were identified. The dataset GSE45238 underwent multivariate statistical analysis in order to distinguish primary OSCC tissues from healthy oral epithelium. Differentially expressed miRNAs (DEMs) with the criteria of p-value < 0.001 and |Log2 fold change| > 1.585 were identified in the two groups, and subsequently, validated targets of DEMs were identified. A protein interaction map was constructed, hub genes were identified, significant modules within the network were illustrated, and significant pathways and biological processes associated with the clusters were demonstrated. Using the GEPI2 database, the hub genes' predictive function was assessed. Compared to the healthy controls, main OSCC had a total of 23 DEMs. In patients with head and neck squamous cell carcinoma (HNSCC), upregulation of CALM1, CYCS, THBS1, MYC, GATA6, and SPRED3 was strongly associated with a poor prognosis. In HNSCC patients, overexpression of PIK3R3, GIGYF1, and BCL2L11 was substantially correlated with a good prognosis. Besides, “proteoglycans in cancer” was the most significant pathway enriched in the primary OSCC. The present study results revealed more possible mechanisms mediating primary OSCC and may be useful in the prognosis of the patients with early-stage OSCC.

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“…2). [67,[80][81][82][83]. The most significant pathways and GO terms enriched in H. pylori-induced GC are demonstrated in Fig.…”

Section: Protein Interaction Map Clustering and Functional Analysesmentioning

confidence: 96%

“…The Reactome database [79] and the ClueGO tool were used for pathway and GO annotation analyses, respectively. The minimum number of enriched genes as two, besides the false discovery rate (FDR) as < 0.05 [67,68,[80][81][82][83], were assigned meaningful for the affected pathways and BP terms in H. pylori-induced GC.…”

Section: Pim Construction Module Detection and Functional Analysismentioning

confidence: 99%

“…Furthermore, the Cox proportional hazards regression model was utilized to determine the corrected hazard ratios (HR) and 95% confidence intervals of hub genes and evaluate the prognostic factors' independence. The prognostic impact of markers with the HR and log-rank test p < 0.05 [67,[80][81][82][83] were statistically considered meaningful.…”

Section: Survival Analysismentioning

confidence: 99%

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Prognostic biomarkers and molecular pathways mediating Helicobacter pylori–induced gastric cancer: a network-biology approach

2023

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Cancer of the stomach is the second most frequent cancer-related death worldwide. The survival rate of patients with gastric cancer (GC) remains fragile. There is a requirement to discover biomarkers for prognosis approaches. Helicobacter pylori in the stomach is closely associated with the progression of GC. We identified the genes associated with poor/favorable prognosis in H. pylori–induced GC. Multivariate statistical analysis was applied on the Gene Expression Omnibus (GEO) dataset GSE54397 to identify differentially expressed miRNAs (DEMs) in gastric tissues with H. pylori–induced cancer compared with the H. pylori–positive with non-cancerous tissue. A protein interaction map (PIM) was built and subjected to DEMs targets. The enriched pathways and biological processes within the PIM were identified based on substantial clusters. Thereafter, the most critical genes in the PIM were illustrated, and their prognostic impact in GC was investigated. Considering p-value less than 0.01 and |Log2 fold change| as >1, five microRNAs demonstrated significant changes among the two groups. Gene functional analysis revealed that the ubiquitination system, neddylation pathway, and ciliary process are primarily involved in H. pylori–induced GC. Survival analysis illustrated that the overexpression of DOCK4, GNAS, CTGF, TGF-b1, ESR1, SELE, TIMP3, SMARCE1, and TXNIP was associated with poor prognosis, while increased MRPS5 expression was related to a favorable prognosis in GC patients. DOCK4, GNAS, CTGF, TGF-b1, ESR1, SELE, TIMP3, SMARCE1, TXNIP, and MRPS5 may be considered prognostic biomarkers for H. pylori–induced GC. However, experimental validation is necessary in the future.

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Identification of potential biomarkers associated with poor prognosis in oral squamous cell carcinoma through integrated bioinformatics analysis: A pilot study

Cited by 16 publications

References 127 publications

[Retracted] Comprehensive and Integrated Analysis Identifies ZEB1 as a Key Novel Gene in Oral Squamous Cell Carcinoma

[Retracted] Comprehensive and Integrated Analysis Identifies ZEB1 as a Key Novel Gene in Oral Squamous Cell Carcinoma

Pathogenesis and prognosis of primary oral squamous cell carcinoma based on microRNAs target genes: a systems biology approach

Prognostic biomarkers and molecular pathways mediating Helicobacter pylori–induced gastric cancer: a network-biology approach

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