Mining TCGA database for prognostic genes in head and neck squamous cell carcinoma microenvironment
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 p...
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| Format: | Article |
| Language: | English |
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Elsevier
2021-03-01
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| Series: | Journal of Dental Sciences |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1991790220302233 |
| _version_ | 1830192176195174400 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Qiu-Chi Ran |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-17T23:52:13Z |
| format | Article |
| id | doaj.art-9d870e2ec3344e7dab24ef0c7b4c0da1 |
| institution | Directory Open Access Journal |
| issn | 1991-7902 |
| language | English |
| last_indexed | 2024-12-17T23:52:13Z |
| publishDate | 2021-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Dental Sciences |
| spelling | doaj.art-9d870e2ec3344e7dab24ef0c7b4c0da12022-12-21T21:28:10ZengElsevierJournal of Dental Sciences1991-79022021-03-01162661667Mining TCGA database for prognostic genes in head and neck squamous cell carcinoma microenvironmentQiu-Chi Ran0Sheng-Rong Long1Yan Ye2Chen Xie3Zhuo-Lin XuXiao4Yu-Song Liu5Hong-Xia Pang6Diwas Sunchuri7Nai-Chia Teng8Zhu-Ling Guo9School of Dentistry, Hainan Medical University, Hainan, China; Department of Dentistry, Stomatological Hospital Affiliated to China Medical University, Shenyang, ChinaDepartment of Neurosurgery, The First Affiliated Hospital of China Medical University, Shenyang, ChinaTechnology Section, Duoyi Network, Wuhan, ChinaSchool of Dentistry, Hainan Medical University, Hainan, ChinaSchool of Dentistry, Hainan Medical University, Hainan, ChinaSchool of Dentistry, Hainan Medical University, Hainan, ChinaDepartment of Dentistry, The First Affiliated Hospital of Hainan Medical University, Hainan, ChinaSchool of Dentistry, Hainan Medical University, Hainan, ChinaSchool of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan; Department of Dentistry, Taipei Medical University Hospital, Taipei, Taiwan; Corresponding author. School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan. Fax: +886 227362295.School of Dentistry, Hainan Medical University, Hainan, China; Department of Dentistry, The First Affiliated Hospital of Hainan Medical University, Hainan, China; Corresponding author. Department of Neurosurgery, The First Affiliated Hospital of China Medical University, Shenyang, China.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.http://www.sciencedirect.com/science/article/pii/S1991790220302233HNSCCImmune scoresTCGATumor microenvironment |
| spellingShingle | 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 Mining TCGA database for prognostic genes in head and neck squamous cell carcinoma microenvironment Journal of Dental Sciences HNSCC Immune scores TCGA Tumor microenvironment |
| title | Mining TCGA database for prognostic genes in head and neck squamous cell carcinoma microenvironment |
| title_full | Mining TCGA database for prognostic genes in head and neck squamous cell carcinoma microenvironment |
| title_fullStr | Mining TCGA database for prognostic genes in head and neck squamous cell carcinoma microenvironment |
| title_full_unstemmed | Mining TCGA database for prognostic genes in head and neck squamous cell carcinoma microenvironment |
| title_short | Mining TCGA database for prognostic genes in head and neck squamous cell carcinoma microenvironment |
| title_sort | mining tcga database for prognostic genes in head and neck squamous cell carcinoma microenvironment |
| topic | HNSCC Immune scores TCGA Tumor microenvironment |
| url | http://www.sciencedirect.com/science/article/pii/S1991790220302233 |
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