Abstract
lncRNA–mRNA co-expression pairs and prognostic markers related to the development of laryngeal squamous cell carcinoma (LSCC) were investigated. The lncRNA and mRNA expression data of LSCC in GSE84957 and RNA-seq data of 112 LSCC samples from TCGA database were used. Differentially expressed genes (DEGs) and lncRNAs (DE-lncRNAs) between LSCC and para-cancer tissues were identified. Co-expression analysis of DEGs and DE-lncRNA was conducted. Protein–protein interaction network for co-expressed DEGs of top 25 DE-lncRNA was constructed, followed by survival analysis for key nodes in co-expression network. Finally, expressions of several DE-lncRNAs and DEGs were verified using qRT-PCR. The lncRNA–mRNA network showed that ANKRD20A5P, C21orf15, CYP4F35P, LOC_I2_011146, XLOC_006053, XLOC_I2_003881, and LOC100506027 were highlighted in network. Some DEGs, including FUT7, PADI1, PPL, ARHGAP40, MUC21, and CEACAM1, were co-expressed with above lncRNAs. Survival analysis showed that PLOD1, GLT25D1, and KIF22 were significantly associated with prognosis. qRT-PCR results showed that the expressions of MUC21, CEACAM1, FUT7, PADI1, PPL, ARHGAP40, ANKRD20A5P, C21orf15, CYP4F35P, XLOC_I2_003881, LOC_I2_011146, and XLOC_006053 were downregulated, whereas the expression of LOC100506027 was upregulated in LSCC tissues. PLOD1, GLT25D1, and KIF22 may be potential prognostic markers in the development of LSCC. C21orf15-MUC21/CEACAM1/FUT7/PADI1/PPL/ARHGAP40 are potential lncRNA–mRNA pairs that play significant roles in the development of LSCC.
Highlights
Squamous cell carcinoma of the head and neck is the 6th most common malignancy worldwide with nearly 177,000 new cases in 2018 [1]
Some Differentially expressed genes (DEGs) were co-expressed with these lncRNA, such as FUT7, PADI1, PPL, ARHGAP40, MUC21, and CEACAM1
The results showed that PLOD1 (p = 0.016), GLT25D1, and KIF22 (p = 0.032) were significantly associated with prognosis (Figure 5a–c)
Summary
Squamous cell carcinoma of the head and neck is the 6th most common malignancy worldwide with nearly 177,000 new cases in 2018 [1]. Laryngeal squamous cell carcinoma (LSCC) is the second common malignant tumor of the head and neck, comprising 96% of all laryngeal cancers [2]. It has been reported that the mortality rates and crude incidence of laryngeal cancer in China from 2008 to 2012 are 1.01/100,000 and 1.22/100,000, respectively, higher in men than in women [3]. Significant advances in LSCC detection and treatment have been made, the 5-year survival rate and prognosis of LSCC are still poor [5,6]. It is of great importance to clarify the molecular mechanisms of LSCC to establish more effective biomarkers or appropriate treatment targets
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