Mining TCGA database for prognostic genes in head and neck squamous cell carcinoma microenvironment

Qiu-Chi Ran; Sheng-Rong Long; Yan Ye; Chen Xie; Zhuo-Lin XuXiao; Yu-Song Liu; Hong-Xia Pang; Diwas Sunchuri; Nai-Chia Teng; Zhu-Ling Guo

doi:10.1016/j.jds.2020.09.017

Mining TCGA database for prognostic genes in head and neck squamous cell carcinoma microenvironment

J Dent Sci. 2021 Mar;16(2):661-667. doi: 10.1016/j.jds.2020.09.017. Epub 2020 Oct 16.

Authors

Qiu-Chi Ran^{1

2}, Sheng-Rong Long³, Yan Ye⁴, Chen Xie¹, Zhuo-Lin XuXiao¹, Yu-Song Liu¹, Hong-Xia Pang⁵, Diwas Sunchuri¹, Nai-Chia Teng^{6

7}, Zhu-Ling Guo^{1

5}

Affiliations

¹ School of Dentistry, Hainan Medical University, Hainan, China.
² Department of Dentistry, Stomatological Hospital Affiliated to China Medical University, Shenyang, China.
³ Department of Neurosurgery, The First Affiliated Hospital of China Medical University, Shenyang, China.
⁴ Technology Section, Duoyi Network, Wuhan, China.
⁵ Department of Dentistry, The First Affiliated Hospital of Hainan Medical University, Hainan, China.
⁶ School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan.
⁷ Department of Dentistry, Taipei Medical University Hospital, Taipei, Taiwan.

Abstract

Background/purpose: Head and neck squamous cell carcinoma (HNSCC) is one of the most common malignant tumors. The aim of this study was to elucidate the effect of tumor microenvironment-related genes on the prognosis of HNSCC and to obtain tumor microenvironment-related genes that can predict poor prognosis in HNSCC patients.

Materials and methods: The ESTIMATE algorithm was applied to the HNSCC transcriptomic data downloaded from the TCGA (The cancer genome atlas), and then the samples were divided into two groups: high and low immune scoring groups, and high and low basal scoring groups to screen for differentially expressed genes (DEGs) associated with poor patient outcomes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was performed to explore the potential functions of DEGs, and then to explore the potential prognostic value of individual DEGs. The results of survival analysis between DEGs and overall survival (OS) to explore tumor microenvironment-related genes relevant to the prognosis of HNSCC patients.

Results: Fifty-nine tumor microenvironment-related genes were screened for association of OS with HNSCC (P < 0.05). The GO and KEGG enrichment analysis showed that the selected DEGs may mediate immune response, extracellular matrix, and immunoglobulin binding via neutrophil activation in HNSCC. Six of these DEGs, GIMAP6, SELL, TIFAB, KCNA3, P2RY8 and CCR4 were most significantly associated with OS (P < 0.001).

Conclusion: We identified six tumor microenvironment-related genes that were significantly associated with poor prognosis in HNSCC. These genes may inspire researchers to discover new targets and approaches for HNSCC treatment.

Keywords: HNSCC; Immune scores; TCGA; Tumor microenvironment.