scholarly journals The prognostic and clinical significance of IFI44L aberrant downregulation in patients with oral squamous cell carcinoma

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Deming Ou ◽  
Ying Wu
Keyword(s):  
Gene Expression ◽  
Squamous Cell Carcinoma ◽  
Survival Analysis ◽  
Oral Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Gene Set Enrichment Analysis ◽  
Cox Regression Analysis ◽  
Gene Pairs ◽  
Study Gene Expression

Abstract Background It is a basic task in high-throughput gene expression profiling studies to identify differentially expressed genes (DEGs) between two phenotypes. RankComp, an algorithm, could analyze the highly stable within-sample relative expression orderings (REOs) of gene pairs in a particular type of human normal tissue that are widely reversed in the cancer condition, thereby detecting DEGs for individual disease samples measured by a particular platform. Methods In the present study, Gene Expression Omnibus (GEO) Series (GSE) GSE75540, GSE138206 were downloaded from GEO, by analyzing DEGs in oral squamous cell carcinoma based on online datasets using the RankComp algorithm, using the Kaplan-Meier survival analysis and Cox regression analysis to survival analysis, Gene Set Enrichment Analysis (GSEA) to explore the potential molecular mechanisms underlying. Results We identified 6 reverse gene pairs with stable REOs. All the 12 genes in these 6 reverse gene pairs have been reported to be associated with cancers. Notably, lower Interferon Induced Protein 44 Like (IFI44L) expression was associated with poorer overall survival (OS) and Disease-free survival (DFS) in oral squamous cell carcinoma patients, and IFI44L expression showed satisfactory predictive efficiency by receiver operating characteristic (ROC) curve. Moreover, low IFI44L expression was identified as risk factors for oral squamous cell carcinoma patients’ OS. IFI44L downregulation would lead to the activation of the FRS-mediated FGFR1, FGFR3, and downstream signaling pathways, and might play a role in the PI3K-FGFR cascades. Conclusions Collectively, we identified 6 reverse gene pairs with stable REOs in oral squamous cell carcinoma, which might serve as gene signatures playing a role in the diagnosis in oral squamous cell carcinoma. Moreover, high expression of IFI44L, one of the DEGs in the 6 reverse gene pairs, might be associated with favorable prognosis in oral squamous cell carcinoma patients and serve as a tumor suppressor by acting on the FRS-mediated FGFR signaling.

scholarly journals Identification of a Transcriptional Prognostic Signature From Five Metabolic Pathways in Oral Squamous Cell Carcinoma

2020 ◽  
Vol 10 ◽  
Author(s):  
Xiang Wu ◽  
Yuan Yao ◽  
Zhongwu Li ◽  
Han Ge ◽  
Dongmiao Wang ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Oral Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Roc Curve ◽  
Metabolic Pathways ◽  
Gene Set Enrichment Analysis ◽  
Enrichment Score ◽  
Prognostic Signature ◽  
Cox Regression Analysis

Dysregulated metabolic pathways have been appreciated to be intimately associated with tumorigenesis and patient prognosis. Here, we sought to develop a novel prognostic signature based on metabolic pathways in patients with primary oral squamous cell carcinoma (OSCC). The original RNA-seq data of OSCC from The Cancer Genome Atlas (TCGA) project and Gene Expression Omnibus (GEO) database were transformed into a metabolic pathway enrichment score matrix by single-sample gene set enrichment analysis (ssGSEA). A novel prognostic signature based on metabolic pathways was constructed by LASSO and stepwise Cox regression analysis in the training cohort and validated in both testing and validation cohorts. The optimal cut-off value was obtained using the Youden index by receiver operating characteristic (ROC) curve. The overall survival curves were plotted by the Kaplan-Meier method. A time-dependent ROC curve analysis with 1, 3, 5 years as the defining point was performed to evaluate the predictive value of this prognostic signature. A 5-metabolic pathways prognostic signature (5MPS) for OSCC was constructed which stratified patients into subgroups with favorable or inferior survival. It served as an independent prognostic factor for patient survival and had a satisfactory predictive performance for OSCC. Our results developed a novel prognostic signature based on dysregulated metabolic pathways in OSCC and provided support for aberrant metabolism underlying OSCC tumorigenesis.

scholarly journals A glycolysis-based three-gene signature predicts survival in patients with lung squamous cell carcinoma

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Guichuan Huang ◽  
Jing Zhang ◽  
Ling Gong ◽  
Yi Huang ◽  
Daishun Liu
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Risk Score ◽  
Squamous Cell ◽  
Cox Regression ◽  
Lung Squamous Cell Carcinoma ◽  
Gene Signature ◽  
Gene Set Enrichment Analysis ◽  
Related Gene ◽  
Cox Regression Analysis

Abstract Background Lung cancer is one of the most lethal and most prevalent malignant tumors worldwide, and lung squamous cell carcinoma (LUSC) is one of the major histological subtypes. Although numerous biomarkers have been found to be associated with prognosis in LUSC, the prediction effect of a single gene biomarker is insufficient, especially for glycolysis-related genes. Therefore, we aimed to develop a novel glycolysis-related gene signature to predict survival in patients with LUSC. Methods The mRNA expression files and LUSC clinical information were obtained from The Cancer Genome Atlas (TCGA) dataset. Results Based on Gene Set Enrichment Analysis (GSEA), we found 5 glycolysis-related gene sets that were significantly enriched in LUSC tissues. Univariate and multivariate Cox proportional regression models were performed to choose prognostic-related gene signatures. Based on a Cox proportional regression model, a risk score for a three-gene signature (HKDC1, ALDH7A1, and MDH1) was established to divide patients into high-risk and low-risk subgroups. Multivariate Cox regression analysis indicated that the risk score for this three-gene signature can be used as an independent prognostic indicator in LUSC. Additionally, based on the cBioPortal database, the rate of genomic alterations in the HKDC1, ALDH7A1, and MDH1 genes were 1.9, 1.1, and 5% in LUSC patients, respectively. Conclusion A glycolysis-based three-gene signature could serve as a novel biomarker in predicting the prognosis of patients with LUSC and it also provides additional gene targets that can be used to cure LUSC patients.

scholarly journals Prognostic Significance of PD-L1 and mTOR Expression in Oral Squamous Cell Carcinoma

2020 ◽  
Author(s):  
Nattinee Charoen ◽  
Kitti Jantharapattana ◽  
Paramee Thongsuksai
Keyword(s):  
Squamous Cell Carcinoma ◽  
Regression Analysis ◽  
Prognostic Factors ◽  
Oral Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Cox Regression ◽  
Prognostic Significance ◽  
P Value ◽  
Cox Regression Analysis

Objective: Programmed cell death ligand 1 (PD-L1) and mammalian target of rapamycin (mTOR) are key players in host immune evasion and oncogenic activation, respectively. Evidence of the prognostic role in oral squamous cell carcinoma (OSCC) is conflicting. This study examined the associations of PD-L1 and mTOR expression with 5-year overall survival in OSCC patients. Material and Methods: The expressions of PD-L1 and mTOR proteins were immunohistochemically evaluated on tissue microarrays of 191 patients with OSCC who were treated by surgery at Songklanagarind Hospital, Thailand from 2008 to 2011. Cox regression analysis was used to determine independent prognostic factors. Results: PD-L1 expression was observed in 14.1% of cases while mTOR expression was present in 74.3% of cases. Females were more likely to have tumors with PD-L1 (p-value=0.007) and mTOR expressions (p-value=0.003) than males. In addition, lower clinical stage and well differentiated tumor are more likely to have mTOR expression (p-value= 0.038 and p-value<0.001, respectively). Cox regression analysis showed that age, tumor stage, nodal stage, combined surgical treatment with radiation or chemoradiation therapy, surgical margin status, PD-L1 expression and mTOR expression are independent prognostic factors. High PD-L1 expression (hazard ratio (HR) 3.14, 95% confidence interval (CI), 1.26–7.79) and high mTOR expression (HR 1.69, 95% CI, 1.00–2.84) are strong predictors of poor outcome. Conclusion: A proportion of OSCC expressed PD-L1 and mTOR proteins. Expression of PD-L1 and mTOR proteins are strong prognostic factors of OSCC.

scholarly journals The Functionalities and Clinical Significance of Tumor-Infiltrating Immune Cells in Esophageal Squamous Cell Carcinoma

2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Jishuai Zhang ◽  
Haifeng Wang ◽  
Haitao Wu ◽  
Guangliang Qiang
Keyword(s):  
Gene Expression ◽  
Squamous Cell Carcinoma ◽  
T Cells ◽  
Esophageal Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Natural Killer ◽  
Clinical Significance ◽  
Squamous Cell ◽  
Immune Cells ◽  
Gene Set Enrichment Analysis

Tumor-infiltrating immune cells have been implicated in the tumorigenesis and progression of esophageal squamous cell carcinoma (ESCC). However, the functionalities and clinical significance of immune cells remain largely unveiled. In this study, the gene expression data from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were extracted. The relative infiltrating levels were estimated by single-sample gene set enrichment analysis. Some cytotoxic immune cells were attenuated, and resting cytotoxic immune cells were accumulated in ESCC. Remarkably, we also observed that infiltrating levels of macrophage M2 and resting natural killer (NK) cells were increased in nonresponders of CRT, and T cells that had anticancer activities such as activated memory CD4 and T helper 2 (Th2) cells were significantly reduced in ESCC tissues of the nonresponders. Moreover, the high infiltrations of the resting natural killer (NK) and dendritic cell (DC) were observed to result in a shorter overall survival in ESCC. Consistently, high expression of immune checkpoint genes, CTLA4 and HAVCR2, was associated with poor prognosis. Furthermore, STAT5B, a key transcription factor, as well as its target genes, involved in the regulation of T cells, was significantly downregulated in ESCC, especially subgroup I, indicating that downregulation of STAT5B might be associated with reduced T cell-mediated anticancer activity. In conclusion, the present study significantly improved our understanding of the regulatory roles of immune cells in ESCC.

scholarly journals Gene Expression of Cancer Stem Cell in Oral Squamous Cell Carcinoma

2012 ◽  
Vol 32 (2) ◽  
pp. 81-89
Author(s):  
Tomohide ISOBE ◽  
Gou YAMAMOTO ◽  
Tarou IRIE ◽  
Tetuhiko TACHIKAWA ◽  
Kenji MISHIMA
Keyword(s):  
Gene Expression ◽  
Squamous Cell Carcinoma ◽  
Stem Cell ◽  
Oral Squamous Cell Carcinoma ◽  
Cancer Stem Cell ◽  
Cell Carcinoma ◽  
Squamous Cell

scholarly journals AIRE is induced in oral squamous cell carcinoma and promotes cancer gene expression

PLoS ONE ◽  
2020 ◽  
Vol 15 (2) ◽  
pp. e0222689
Author(s):  
Chi Thi Kim Nguyen ◽  
Wanlada Sawangarun ◽  
Masita Mandasari ◽  
Kei-ichi Morita ◽  
Hiroyuki Harada ◽  
...  
Keyword(s):  
Gene Expression ◽  
Squamous Cell Carcinoma ◽  
Oral Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Cancer Gene
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