Gene-expression profiles of primary and metastatic lesions in head and neck squamous cell carcinoma

Abstract Background: Head and neck squamous cell carcinoma (HNSCC) is one of the most prevalent malignancy worldwide with high incidence and mortality. Recently, it has been well established that tumor microenvironment (TME) is intimately associated with cancer progression, in which the infiltration of immune and stromal cells could be exploited as effective biomarkers for cancer diagnosis and prognosis. In this study, we aimed to investigate HNSCC microenvironment to identify significant genes involved in carcinogenesis. Methods: The ESTIMATE algorithm was applied to calculate immune scores and stromal scores based on the gene expression profiles downloaded from The Cancer Genome Atlas (TCGA) database and the correlation of these scores with clinical parameters and prognosis was further analyzed. Differential expression analysis and functional enrichment analysis were performed by R software. Results: Immune scores and stromal scores were calculated by ESTIMATE algorithm and their correlations with clinicopathological characteristics of HNSCC patients were identified. Differentially expressed genes (DEGs) based on two scores were identified and subjected to functional analysis, demonstrating their close associations with tumor immunity. Hub genes were selected from which CCR2, CCR4, CCR8 and P2RY14 were found to be significantly associated with the survival rate of HNSCC patients. Conclusions: In summary, we made a comprehensive analysis of HNSCC microenvironment and illustrated several key immune-related genes, which may provide evidences for the development of precision immunotherapy.

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Bioinformatics analysis of DNMT1 expression and its role in head and neck squamous cell carcinoma prognosis

Scientific Reports ◽

10.1038/s41598-021-81971-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jili Cui ◽

Lian Zheng ◽

Yuanyuan Zhang ◽

Miaomiao Xue

Keyword(s):

Gene Expression ◽

Squamous Cell Carcinoma ◽

Cell Carcinoma ◽

Head And Neck ◽

Squamous Cell ◽

Immune Cell ◽

Neck Squamous Cell Carcinoma ◽

Hub Genes ◽

Significant Difference ◽

Dnmt1 Expression

AbstractHead and neck squamous cell carcinoma (HNSCC) is the sixth most common type of malignancy in the world. DNA cytosine-5-methyltransferase 1 (DNMT1) play key roles in carcinogenesis and regulation of the immune micro-environment, but the gene expression and the role of DNMT1 in HNSCC is unknown. In this study, we utilized online tools and databases for pan-cancer and HNSCC analysis of DNMT1 expression and its association with clinical cancer characteristics. We also identified genes that positively and negatively correlated with DNMT1 expression and identified eight hub genes based on protein–protein interaction (PPI) network analysis. Enrichment analyses were performed to explore the biological functions related with of DNMT1. The Tumor Immune Estimation Resource (TIMER) database was performed to explore the relationship between DNMT1 expression and immune-cell infiltration. We demonstrated that DNMT1 gene expression was upregulated in HNSCC and associated with poor prognosis. Based on analysis of the eight hub genes, we determined that DNMT1 may be involved in cell cycle, proliferation and metabolic related pathways. We also found that significant difference of B cells infiltration based on TP 53 mutation. These findings suggest that DNMT1 related epigenetic alterations have close relationship with HNSCC progression, and DNMT1 could be a novel diagnostic biomarker and a promising therapeutic target for HNSCC.

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MicroRNA expression profiles of cancer stem cells in head and neck squamous cell carcinoma

International Journal of Oncology ◽

10.3892/ijo.2015.3145 ◽

2015 ◽

Vol 47 (4) ◽

pp. 1249-1256 ◽

Cited By ~ 8

Author(s):

KAZUYA YATA ◽

LEVENT BEKIR BEDER ◽

SHUNJI TAMAGAWA ◽

MUNEKI HOTOMI ◽

YOSHIHIKO HIROHASHI ◽

...

Keyword(s):

Stem Cells ◽

Squamous Cell Carcinoma ◽

Cancer Stem Cells ◽

Cell Carcinoma ◽

Head And Neck ◽

Squamous Cell ◽

Expression Profiles ◽

Microrna Expression ◽

Neck Squamous Cell Carcinoma

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Two subclasses of lung squamous cell carcinoma with different gene expression profiles and prognosis identified by hierarchical clustering and non-negative matrix factorization

Oncogene ◽

10.1038/sj.onc.1208858 ◽

2005 ◽

Vol 24 (47) ◽

pp. 7105-7113 ◽

Cited By ~ 57

Author(s):

Kentaro Inamura ◽

Takeshi Fujiwara ◽

Yujin Hoshida ◽

Takayuki Isagawa ◽

Michael H Jones ◽

...

Keyword(s):

Gene Expression ◽

Squamous Cell Carcinoma ◽

Cell Carcinoma ◽

Hierarchical Clustering ◽

Squamous Cell ◽

Matrix Factorization ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Lung Squamous Cell Carcinoma ◽

Non Negative Matrix Factorization

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Salivary MicroRNAs for Early Detection of Head and Neck Squamous Cell Carcinoma: A Case-Control Study in the High Altitude Mestizo Ecuadorian Population

BioMed Research International ◽

10.1155/2018/9792730 ◽

2018 ◽

Vol 2018 ◽

pp. 1-9 ◽

Cited By ~ 9

Author(s):

Carolina Salazar-Ruales ◽

Jessica-Viviana Arguello ◽

Andrés López-Cortés ◽

Alejandro Cabrera-Andrade ◽

Jennyfer M. García-Cárdenas ◽

...

Keyword(s):

Squamous Cell Carcinoma ◽

High Altitude ◽

Cell Carcinoma ◽

Head And Neck ◽

Squamous Cell ◽

Expression Profiles ◽

Neck Squamous Cell Carcinoma ◽

Altered Expression ◽

Mortality And Morbidity ◽

Tumor Stages

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer with the highest incidence worldwide. HNSCC is often diagnosed at advanced stages, incurring significant high mortality and morbidity. The use of saliva, as a noninvasive tool for the diagnosis of cancer, has recently increased. Salivary microRNAs (miRNAs) have emerged as a promising molecular tool for early diagnosis of HNSCC. The aim was to identify the differential expression of salivary miRNAs associated with HNSCC in the high altitude mestizo Ecuadorian population. Using PCR Arrays, miR-122-5p, miR-92a-3p, miR-124-3p, miR-205-5p, and miR-146a-5p were found as the most representative ones. Subsequently, miRNAs expression was confirmed in saliva samples from 108 cases and 108 controls. miR-122-5p, miR-92a-3p, miR-124-3p, and miR-146a-5p showed significant statistical difference between cases and controls with areas under the curve (AUC) of 0.73 (p < 0.001), 0.70 (p < 0.001), 0.71 (p = 0.002), and 0.66 (p = 0.008), respectively. miRNAs were also deregulated in between HNSCC localizations. A differentiated expression of miR-122-5p between oral cancer and oropharynx cancer (AUC of 0.96 p = 0.01) was found: miR-124-3p between larynx and pharynx (AUC = 0.97, p < 0.01) and miR-146a-5p between larynx, oropharynx, and oral cavity (AUC = 0.96, p = 0.01). Moreover, miR-122-5p, miR-124-3p, miR-205-5p, and miR-146a-5p could differentiate between HPV+ and HPV- (p=0.004). Finally, the expression profiles of the five miRNAs were evaluated to discriminate HNSCC patient’s tumor stages (TNM 2-4). miR-122-5p differentiates TNM 2 and 3 (p = 0.002, AUC = 0.92), miR-124-3p TNM 2, 3, and 4 (p < 0.001, AUC = 98), miR-146a-5p TNM 2 and 3 (p < 0.001, AUC = 0.97), and miR-92a-3p TNM 3 (p < 0.001, AUC = 0.99). Taken together, these findings show that altered expression of miRNAs could be used as biomarkers for HNSCC diagnosis in the high altitude mestizo Ecuadorian population.

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