Identification And Bioinformatics Analysis Of Differentially Expressed Genes In Hypopharyngeal Carcinoma And Adjacent Tissues

Objective: Screening of differentially expressed lncRNAs,miRNAs,and mRNAs in hypopharyngeal carcinoma and adjacent tissues.Analyzing the bioinformatics functions of them.Exploring the lncRNA-miRNA-mRNA regulatory network and the key genes that may be related to the occurrence and development of hypopharyngeal carcinoma.Materials and methods:(1)RNA-seq was used to sequence the tumor tissues and normal tissues adjacent to cancer of 16 patients with hypopharyngeal squamous cell carcinoma,then screening the differentially expressed lncRNAs,miRNAs,and mRNAs in hypopharyngeal cancer tissues compared to the paired normal tissues.(2)Converting the ID of differentially expressed miRNAs in the Funrich software.Then,searching for their target-genes(target-mRNAs,target-lncRNAs)in the Starbase 3.0 database.(3)Screening the target-genes that were differentially expressed in hypopharyngeal cancer tissues and the Starbase 3.0 database by Funrich software.Based on the lnc ATLAS database analyzing the location of the differentially expressed target-lncRNAs in cells.Searching for the functions and pathways of differentially expressed target-mRNAs and miRNAs with target-genes in Funrich software.(4)Based on Funrich software and Starbase 3.0 database,the regulatory network between differentially expressed lncRNAs,miRNAs,and mRNAs related to the occurrence and development of hypopharyngeal carcinoma was constructed,and key genes that may be related to hypopharyngeal carcinoma were analyzed.Results:(1)There were 556 lncRNAs,11 miRNAs,and 1247 mRNAs that were significantly differentially expressed in hypopharyngeal cancer tissues compared with normal tissues adjacent to cancer.(2)A total of 10 miRNAs with target-genes were found in the Starbase 3.0 database,542 target-lncRNAs and 8423 target-mRNA were found.There were 4 target-lncRNAs and 381 target-mRNAs that were differentially expressed in hypopharyngeal cancer tissues and the Starbase 3.0 database.(3)Function and enrichment analysis showed that the differentially expressed target-mRNAs were mainly involved in 5 pathways that were related to the Mitotic Cell Cycle.The 5 pathways were Cell Cycle Mitotic,G1/S-Specific Transcription,E2 F mediated regulation of DNA replication,FOXM1 transcription factor network,and Aurora-B signaling.The abnormal regulation of the Mitotic Cell Cycle was related to the occurrence and development of many kinds of tumors.(4)The lncRNA-miRNA-mRNA regulatory network that might be related to the development of hypopharyngeal carcinoma was constructed based on Funrich software and Starbase 3.0 database.The network included 4 lncRNAs(VPS9D1-AS1,LINC00319,AP001065.2,LINC01018);3 miRNAs(hsa-mi R-197-3p,hsa-mi R-135a-5p,hsa-mi R-200a-3p);14 mRNAs(ESR1,ORC6,CDK1,CDC6,CDC45,TOP2 A,CDCA8,CCNE1,RRM2,NCAPG,CENPF,CENPE,CDC25,BIRC5).(5)LINC01018 regulated the expression of RRM2 in hypopharyngeal cancer through binding with hsa-mi R-197-3p,and both of them were the key genes related to the occurrence and development of hypopharyngeal carcinoma.Conclusion: We had screened out the differentially expressed lncRNAs,mRNAs,and miRNAs in hypopharyngeal cancer tissues based on the RNA-seq and we predicted and constructed the lncRNA-miRNA-mRNA regulatory network that may be related to the hypopharyngeal carcinoma.LINC01018,hsa-mi R-197-3p,and RRM2 may all be the key genes related to hypopharyngeal carcinoma's occurrence and development.