Journal of Otolaryngology and Ophthalmology of Shandong University ›› 2023, Vol. 37 ›› Issue (1): 47-55.doi: 10.6040/j.issn.1673-3770.0.2022.012

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Bioinformatics analysis of key molecular markers for malignant transformation of laryngeal papilloma

WANG Lingwa, WANG Ru, FANG Jugao   

  1. Department of otorhinolaryngology & Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
  • Published:2023-02-06

Abstract: Objective To screen for molecular markers affecting malignant transformation and prognosis of laryngeal papilloma using bioinformatics analysis. Methods The GSE10935 gene expression profile of adult laryngeal papilloma was downloaded from the Gene Expression Omnibus database, and the transcriptome data for laryngeal squamous cell carcinoma were downloaded from The Cancer Genome Atlas. Differentially expressed genes(DEGs)in each dataset were identified using limma and DESeq2 R package. Venn diagrams analysis was conducted for identifying common DEGs. Survival analysis was performed by plotting the Kaplan-Meier curves in the Gene Expression Profiling Interactive Analysis(GEPIA)database to screen for candidate genes. Protein expression in the Human Protein Atlas database was analyzed to identify key genes. Univariate/multivariate Cox regression analysis and functional enrichment analyses were performed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. Results A total of 112 DEGs were related to the occurrence and development of laryngeal papilloma, and 1817 DEGs were related to laryngeal squamous cell carcinoma. Twenty-four common DEGs were identified using Venn diagram analysis. GEPIA revealed that the expression of FSCN1, MMP1, and IFI27 was upregulated, while that of ALDH3A1, HLF, and MMRN1 was downregulated in head and neck squamous cell carcinoma(HNSCC)samples compared with that in normal tissue samples; all differences were significant(FSCN1:P=0.002 9, MMP1:P=0.047, IFI27:P=0.035, ALDH3A1:P=0.024, HLF:P=0.008, MMRN1:P=0.036). Survival analysis revealed that the overexpression of FSCN1, MMP1, and IFI27 and low expression of ALDH3A1, HLF, and MMRN1 affected overall survival. Immunohistochemical analysis showed high FSCN1 expression and low ALDH3A1 expression in HNSCC samples. Further survival analysis showed that the expression levels of FSCN1 and ALDH3A1 were independent risk factors affecting the prognosis of human papillomavirus-related HNSCC. Conclusion FSCN1 and ALDH3A1 are plausible key genes in the malignant transformation of laryngeal papilloma. High FSCN1 expression and low ALDH3A1 expression affect the prognosis of human papillomavirus-related HNSCC and are potential molecular targets for suppressing malignant transformation.

Key words: Laryngeal papilloma, Fascin actin-binding protein 1, Aldehyde Dehydrogenase 3 Family Member A1, Bioinformatics, Molecular markers

CLC Number: 

  • R739.65
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[1] QI Wenwen, CHEN Luqiu, JIA Tao, CHEN Xuemei, ZHANG Jie, ZHANG Hao, JIN Peng, ZHANG Hu. Potential biomarkers and bioinformatics analysis of differentially expressed genes in recurrent laryngeal papilloma [J]. Journal of Otolaryngology and Ophthalmology of Shandong University, 2021, 35(5): 75-84.
[2] NIU Zijie, XIAO Yang,WANG Jun,MA Lijinng. Progress in the surgical treatment of recurrent laryngeal papillomatosis [J]. Journal of Otolaryngology and Ophthalmology of Shandong University, 2021, 35(4): 96-100.
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[4] HU Wenliang, ZHENG Yanqiu, CUI Xiaobo, CUI Yanru, SUN Yuanhao. Bioinformatic screening of differentially expressed protein kinases and their inhibitors in hypopharyngeal cancer. [J]. JOURNAL OF SHANDONG UNIVERSITY (OTOLARYNGOLOGY AND OPHTHALMOLOGY), 2016, 30(3): 24-28.
[5] CHEN Yong, XIE Xiu-fang, LIU Fang, JIANG Yi, LI Rui-yu. Treatment of laryngeal papilloma with bone marrow mesenchymal stem cells transfected with the IFN-γ gene [J]. JOURNAL OF SHANDONG UNIVERSITY (OTOLARYNGOLOGY AND OPHTHALMOLOGY), 2012, 26(3): 24-27.
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