Whole Exome Sequencing And Transcriptome-wide Profiling Identify Potentially Subtype-relevant Genes Of Nasopharyngeal Carcinoma

Purpose:In this study,patients with newly treated nasopharyngeal carcinoma were used as the research object,using exon sequencing technology and bioinformatics analysis technology to identify gene changes and signal pathways involved in the occurrence and development of nasopharyngeal carcinoma,in order to provide a theoretical basis for exploring the mechanism of the occurrence and development of nasopharyngeal carcinoma and finding new therapeutic targets.Methods:Fourteen patients with nasopharyngeal carcinoma who were treated for the first time in the Department of Oncology and Radiotherapy of Qingdao University Affiliated Hospital from September 2017 to September 2019 were included in the study.All patients underwent nasopharyngeal biopsy.Obtain FFEP slices and corresponding peripheral blood of all patients,and perform exon gene sequencing.Downloaded the cancer chip expression data named GSE12452 from the GEO database,and used R language to obtain differentially expressed genes of different histological subtypes,and performed GEO and KEGG pathway enrichment analysis on them,and constructed a PPI network to obtain the key Genes,expression analysis of key genes and co-expressed genes,candidate genes were obtained.Finally,perform GSEA analysis on candidate genes to obtain potential subtyperelated genes.Results:1.Fourteen patients with nasopharyngeal carcinoma were included in the study,including 6 cases of non-keratinizing differentiated cancer and 8 cases of non-keratinizing undifferentiated cancer.No correlation between subtype and gender,age,and stage was found.2.A total of 80 gene mutations in 37 genes were identified in 14 patients with nasopharyngeal carcinoma,with an average of 5.7 per patient,of which 58 were clinically relevant mutations,with an average of 4.1 per patient.On average,4.9 per NPC-IIB patient and 3.2 per NPC-IIA patient.In this study,the mutation frequency of CDKN2 A was the highest.Co-mutations of CCND1,FGF3,FGF4,and FGF19 were found in 3 patients with NPC-IIB,but not in patients with NPC-IIA.The most common form of mutation is a singlenucleotide mutation,and the most frequently occurring base pair substitution is C:G>A:T.3.TMB has nothing to do with the subtypes of nasopharyngeal carcinoma.CDKN2 A and PI3 KA mutations occurred more often in the TMB-H group,but no significant correlation between CDKN2 A and PI3 KA and TMB values was found(P=0.095,0.505).4.The infectivity of NPC-IIB EBV was significantly higher than that of NPC-IIA,but no statistical difference was observed(P=0.138).There was a significant correlation between EBV infection and CDKN2 A and PIK3CA(P=0.025,0.015).5.71.4% of samples have genetic mutations related to PI3K-Akt signaling pathway,64.3% of samples have gene mutations related to JAK-STAT signaling pathway,and 57.1%of samples have c AMP signaling pathway,MAPK signaling pathway,and Ras signaling pathway related mutations.Gene mutations,50% of the samples have gene mutations related to the cell cycle pathway,35.7% of the samples have gene mutations related to the Notch signaling pathway,28.6% of the samples have gene mutations related to the Wnt signaling pathway,and 14.3% of the samples have NF-κB Pathway-related gene mutations.6.The GSE12452 chip obtained a total of 1395 differentially expressed genes,including 587 up-regulated genes and 808 down-regulated genes.There were 1139 patients with NPC-IIA type and 1232 patients with NPC-IIB type.7.There is no significant difference between the two subtypes in GO enrichment.The up-regulated differentially expressed genes are mainly enriched in chromosomes and spindles in terms of cellular components,and in molecular functions are mainly enriched in the structural components of extracellular matrix and catalytic activity on DNA,and in biological processes,they are mainly enriched in nuclear division and organelles.Fission.The down-regulated differentially expressed genes are mainly enriched in the ciliary part and active cilia in terms of cellular components,in the molecular functions are mainly enriched in locomotor activity and microscopic locomotor activity,and in biological processes,they are mainly enriched in cilia and cilia assembly.8.There is no significant difference between the two subtypes in the enrichment analysis of KEGG pathway,mainly enriched in PI3K-Akt signaling pathway,human papillomavirus infection pathway,cell cycle pathway,focal adhesion pathway and extracellular matrix-receptor signaling pathway.PI3K-Akt signaling pathway is an important pathway related to the occurrence and development of nasopharyngeal carcinoma.9.Screen 7 potential subtype-related genes: COL4A1,ASB9,RDH10,TNFRSF21,BACE2,EVA1 C and LHX2.Conclusion:Different subtypes of nasopharyngeal carcinoma have different genetic changes.COL4A1,ASB9,RDH10,TNFRSF21,BACE2,EVA1 C and LHX2 are potential subtyperelated genes,which may be potential targets for the diagnosis and treatment of nasopharyngeal carcinoma,and we can develop individualized treatment plans based on these.