scholarly journals Identification of a Gene Prognostic Signature for Oral Squamous Cell Carcinoma by RNA Sequencing and Bioinformatics

2021 ◽  
Vol 2021 ◽  
pp. 1-14
Author(s):  
Yang-Yang Zhang ◽  
Ming-Hui Mao ◽  
Zheng-Xue Han
Keyword(s):  
Overall Survival ◽  
Squamous Cell Carcinoma ◽  
Oral Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Candidate Genes ◽  
Rna Sequencing ◽  
Squamous Cell ◽  
Risk Model ◽  
Ppi Network ◽  
Prognostic Signature

Objectives. Oral squamous cell carcinoma (OSCC) is the most common oral cancer and has a poor prognosis. We aimed to identify new biomarkers or potential therapeutic targets for OSCC. Materials and Methods. Four pairs of tumor and adjacent normal tissues were collected from OSCC patients, and differentially expressed genes (DEGs) were screened via high-throughput RNA sequencing (RNA-seq). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were used to analyze the DEGs. A protein-protein interaction (PPI) network was established with the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database and Cytoscape, and two significant clusters were found. Candidate genes were screened by analyzing head and neck squamous cell carcinoma (HNSCC) data from The Cancer Genome Atlas (TCGA). A DEG-based risk model was established to predict the overall survival (OS) of OSCC patients via Kaplan-Meier analysis and the log-rank test. Furthermore, univariate Cox regression analysis was applied to assess associations between potential biomarkers and the overall survival rate. Results. Of 720 total DEGs, fifty-two DEGs in the two subclusters of the PPI network analysis were selected. A risk model was established, and five candidate genes (SPRR2E, ICOS, CTLA4, HTR1D, and CCR4) were identified as biomarkers of OS in OSCC patients. Conclusions. We successfully constructed a prognostic signature to predict prognosis and identified five candidate genes associated with the OS of OSCC patients that are potential tumor biomarkers and targets in OSCC.

A two‐CpG‐based prognostic signature for oral squamous cell carcinoma overall survival

2018 ◽  
Vol 120 (6) ◽  
pp. 9082-9090 ◽  
Author(s):  
Yanping Chen ◽  
Naiheng Hei ◽  
Jianguang Zhao ◽  
Shixiong Peng ◽  
Kaicheng Yang ◽  
...  
Keyword(s):  
Overall Survival ◽  
Squamous Cell Carcinoma ◽  
Oral Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Prognostic Signature

scholarly journals Survival Analysis of Age-related Oral Squamous Cell Carcinoma: A Population Study Based on SEER

2021 ◽  
Author(s):  
Peipei Wang ◽  
Kaibo Guo ◽  
Anlai Zhang ◽  
Wendi Li ◽  
Shuning Ding ◽  
...  
Keyword(s):  
Overall Survival ◽  
Squamous Cell Carcinoma ◽  
Oral Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Risk Model ◽  
Survival Rates ◽  
Competing Risk ◽  
Cox Regression Analysis ◽  
Competing Risk Model

Abstract This research aimed to investigate the prognostic factors of oral squamous cell carcinoma (OSCC), especially the role of age. A total of 33619 cases of OSCC were received from the Surveillance, Epidemiology, and End Results database during 2005–2015. Kaplan-Meier curves of 5-year overall survival rates and 5-year cancer specific survival rates were performed, and univariate and multivariate Cox regression analysis as well as competing risk model were used to help understand the relationship between various factors and mortality of OSCC. Compared to 18–39 years old group, the older age was an important predictor of worse prognosis. The multivariate analysis of overall survival (OS) were 50–59 years old (HR, 1.32; 95% CI, 1.17–1.48; p ≤ .001), 60–69 years old (HR, 1.66; 95% CI, 1.42–1.87; p ≤ .001) and 70 + years old (HR, 3.21; 95% CI, 2.86–3.62; p ≤ .001) respectively, while the specific value of competing risk model were 60–69 years old (HR, 1.21; 95% CI, 1.07–1.38; p = .002) and 70 + years old (HR, 1.85; 95% CI, 1.63–2.10; p ≤ .001). In addition, female gender, unmarried, Blacks, tumor in floor of mouth, size and higher TNM classification were also other predictors that signify significant clinically deterioration of OS / CSS. Our research revealed that age was an important factor in explaining the difference of survival in the whole process of OSCC. It’s suggested that we should pay attention to the influence of age on diagnosis, treatment and prognosis in the clinical process.

scholarly journals Epigenetic Alterations Associated with the Overall Survival and Recurrence Free Survival among Oral Squamous Cell Carcinoma Patients

2020 ◽  
Vol 9 (4) ◽  
pp. 1035 ◽  
Author(s):  
Yasmen Ghantous ◽  
Aysar Nashef ◽  
Imad Abu-Elnaaj
Keyword(s):  
Overall Survival ◽  
Squamous Cell Carcinoma ◽  
Oral Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Clinical Features ◽  
Squamous Cell ◽  
Methylation Status ◽  
Recurrence Free Survival ◽  
Epigenetic Alterations ◽  
Free Survival

Oral squamous cell carcinoma (OSCC) is a fatal disease caused by complex interactions between environmental, genomic, and epigenetic alterations. In the current study, we aimed to identify clusters of genes whose promoter methylation status correlated with various tested clinical features. Molecular datasets of genetic and methylation analysis based on whole-genome sequencing of 159 OSCC patients were obtained from the The Cancer Genome Atlas (TCGA) data portal. Genes were clustered based on their methylation status and were tested for their association with demographic, pathological, and clinical features of the patients. Overall, seven clusters of genes were revealed that showed a significant association with the overall survival/recurrence free survival of patients. The top ranked genes within cluster 4, which showed the worst prognosis, primarily acted as paraneoplastic genes, while the genes within cluster 6 primarily acted as anti-tumor genes. A significant difference was found regarding the mean age in the different clusters. No significant correlation was found between the tumor staging and the different clusters. In conclusion, our result provided a proof-of-principle for the existence of phenotypic diversity among the epigenetic clusters of OSCC and demonstrated the utility of the use epigenetics alterations in devolving new prognostic and therapeutics tools for OSCC patients.

MicroRNA expression correlates with disease recurrence and overall survival in oral squamous cell carcinoma

2019 ◽  
Vol 47 (3) ◽  
pp. 523-529 ◽  
Author(s):  
Julius Moratin ◽  
Stefan Hartmann ◽  
Roman C. Brands ◽  
Dominik Horn ◽  
Andreas Fuchs ◽  
...  
Keyword(s):  
Overall Survival ◽  
Squamous Cell Carcinoma ◽  
Oral Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Disease Recurrence ◽  
Microrna Expression

scholarly journals Are Comorbidities Associated With Overall Survival in Patients With Oral Squamous Cell Carcinoma?

2019 ◽  
Vol 77 (9) ◽  
pp. 1906-1914 ◽  
Author(s):  
Úrsula M. Jariod-Ferrer ◽  
Jose M. Arbones-Mainar ◽  
Marina A. Gavin-Clavero ◽  
M. Victoria Simón-Sanz ◽  
Ignacio Moral-Saez ◽  
...  
Keyword(s):  
Overall Survival ◽  
Squamous Cell Carcinoma ◽  
Oral Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell

scholarly journals A Novel Lipid Prognostic Signature of ADCY2, LIPE, and OLR1 in Head and Neck Squamous Cell Carcinoma

2021 ◽  
Vol 11 ◽  
Author(s):  
Xiaolei Gao ◽  
Na Zhao ◽  
Liying Dong ◽  
Xuan Zheng ◽  
Yixin Zhang ◽  
...  
Keyword(s):  
Overall Survival ◽  
Squamous Cell Carcinoma ◽  
Lipid Metabolism ◽  
Cell Carcinoma ◽  
Head And Neck ◽  
Squamous Cell ◽  
Metabolic Reprogramming ◽  
Prognostic Signature ◽  
New Findings ◽  
Tp53 Status

Simple SummaryClinically, aberrant lipid metabolism is responsible for overweight and/or obesity. Overweight is considered as an independent factor of cancer risk in 2019. Therefore, lipid metabolic reprogramming is an emerging hallmark of malignancy. It is an urgent need to comprehensively understand the relationship among lipid metabolism and HNSCC and identify a valuable biomarker for predicting prognosis of HNSCC patients. Three new findings were found in this study. Firstly, we identified the lipid-related differentially expressed genes (DEGs) by using the GEO microarrays and TCGA dataset. A novel lipid-related mRNA prognostic signature (LRPS, consisting of ADCY2, LIPE and OLR1) was developed, which could predict the survival and prognosis of HNSCC patients as an independent effective prognostic factor. Secondly, we found that the LRPS could indicate the type of infiltrated immune cells in HNSCC tumor microenvironment. Thirdly, we verified that the LPPS score could interpret the TP53 status of HNSCC. Our new findings indicated that LRPS has a potential to be a promising indicator of overall survival, TP53 status, and immune characteristics in HNSCC, and perhaps can monitor and guide the treatment efficacy and prognosis of HNSCC in the future.BackgroundHead and neck squamous cell carcinoma (HNSCC) is characterized by a high frequency of lymph node metastasis and a high mortality. Lipid metabolic reprogramming is an emerging carcinogen as its role in fulfilling cancer growth and spread. However, little is known about the correlation between lipid metabolism and HNSCC.Materials and MethodsExpressions of lipid-related genes were obtained from the Cancer Genome Atlas (TCGA) and Gene expression Omnibus (GEO) databases for differential and functional analyses. A total number of 498 patients from TCGA with complete information were included to identify a lipid-related prognostic signature (LRPS), based on ADCY2, LIPE, and OLR1, by using univariate and multivariate Cox regression analyses. LRPS-high and LRPS-low groups were accordingly divided to pathway and cell enrichment analyses.ResultsLRS-low patients had a better overall survival and relapse - free survival than LRS-high ones in HNSCC. The LRPS-high group was significantly related to perineural invasion of cancer, cancer-related pathways, high TP53 mutation rate, high proportion of natural killer T cells (NKT), dendritic cells, monocytes, Treg, and M1 and M2 macrophage infiltration in HNSCC tumor tissues. Conversely, the LRPS-low group correlated with DNA damage-related and T-cell-regulated pathways, low frequency of mutated TP53, and high infiltration of B cells and CD4+ effector cells including Th1 and Th2.ConclusionLRPS has a potential to be a promising indicator of overall survival, prognosis, TP53 status, and immune characteristics in HNSCC.

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