Abstract
Purpose
The aim of the study is to identify a reliable gene panel to predict the prognosis of HNSCC patients by integrated genomic analysis.
Methods
Co-expression gene networks were constructed by WGCNA using GSE113282 gene expression profile. The biological functional investigation was performed by GO and KEGG function enrichment analysis. The hub gene module was screened by PPI. The prognostic gene panel was established by Lasso regression analysis, and further progression-free survival (PFS) analysis was validated by Kaplan–Meier survival analysis using GSE102995 data.
Results
We identified 195 genes associated with the overall survival (OS) status (correlation coefficients: − 0.42, and p value: 2e−05) by WGCNA. These genes were enriched in immune-related cytokines and pathways analyzed by GO and KEGG. Among the 195 genes, the module (42 genes) with the highest score was screened by PPI. A novel seven-gene predictive panel (CD19, CD40LG, CD5, CXCR6, FPR2, NCAM1, and SELL) was established by Lasso regression analysis, and the area under ROC curve (AUC) for 3-year OS status was 0.8298 and 0.7571, respectively, in the training set and the test set. The PFS time of the low-risk patients was significantly longer than the high-risk patients (p < 0.0001; log-rank test) by further validation using GSE102995 data.
Conclusion
The seven-gene panel may serve as a reliable predictive tool for HNSCC patients treated with platinum-based radio (chemo) therapy, and may be potential therapeutic targets for HNSCC patients.
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Code availability
The data in our study are available from the corresponding author upon reasonable request.
Abbreviations
- SCC:
-
Squamous cell carcinoma
- HNSCC:
-
Head and neck squamous cell carcinoma
- NCBI:
-
National Center Biotechnology Information
- GEO:
-
Gene Expression Omnibus
- OPSCC:
-
Oropharyngeal squamous cell carcinoma
- WGCNA:
-
Weighted correlation network analysis
- OS:
-
Overall survival
- GO:
-
Gene ontology
- KEGG:
-
Kyoto Encyclopedia of Genes and Genomes
- BP:
-
Biological process
- CC:
-
Cellular component
- MF:
-
Molecular function
- STRING:
-
The Search Tool for the Retrieval of Interacting Genes/Proteins
- PPI:
-
Protein–protein interaction
- MCODE:
-
Molecular Complex Detection
- ROC:
-
Receiver operating characteristic
- Lasso:
-
Least absolute shrinkage and selection operator
- AUC:
-
Area under curve
- PFS:
-
Progression-free survival
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Funding
This work was supported by the Bei**g Natural Science Foundation Program and Scientific Research Key Program of Bei**g Municipal Commission of Education (KZ201910025034), the Bei**g Municipal Administration of Hospitals’ Ascent Plan (DFL20180202), the National Key R&D Program of China (No. 2020YFB1312805), the Capital Health Research and Development of Special (No.2018–2-2054) and Bei**g Municipal Administration of Hospitals Incubating Program” (PX2021008).
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LWW performed comparative analysis using bioinformatics tools. LWW, YFY, LF, CT, HZM, SZH, ML, RW and JGF participated in data analysis and discussion, LWW, RW and JGF interpreted data and wrote the manuscript. All authors read and approved the final manuscript.
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For human datasets mentioned in this study, please refer to the original article (PMCID: PMC6682352 and PMID: 29909889). We re-analyzed the open accessed datasets, and the study was approved by the local ethics committees.
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Wang, L., Yang, Y., Feng, L. et al. A novel seven-gene panel predicts the sensitivity and prognosis of head and neck squamous cell carcinoma treated with platinum-based radio(chemo)therapy. Eur Arch Otorhinolaryngol 278, 3523–3531 (2021). https://doi.org/10.1007/s00405-021-06717-5
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DOI: https://doi.org/10.1007/s00405-021-06717-5