| Objective:To identify somatic mutations,copy number variations and structural variations of cervical adenocarcinoma and depict a genomic mutational landscape by whole genome sequencing(WGS)and whole exome sequencing(WES).To explore the integration of human papilloma virus(HPV)in cervical adenocarcinoma and related genomics changes.To explore the differential gene expression and compare the transcriptional regulation network between cervical adenocarcinoma and cervical squamous cell carcinoma at the transcriptome level by whole transcriptome sequencing.Method:1.Twenty pairs of tumor samples and adjacent normal samples from patients with cervical adenocarcinoma were collected and genomic DNA was extracted for further WGS and WES.After quality control of sequencing data,bioinformatics analysis was carried out to identify somatic single nucleotide variations,small fragment insertions and deletions,copy number changes,structural variations and other genomic variations in cervical adenocarcinoma,and to clear the functions and signal pathways of specific significantly mutated genes(SMGs).Moreover,integration of HPV and related genomic changes were identified.2.Eight pairs of tumor samples and adjacent normal cervical samples from four patients with cervical adenocarcinoma and four patients with cervical squamous cell carcinoma were collected and total RNA was extracted for further whole transcriptome sequencing.After quality control of sequencing data,bioinformatics analysis was carried out to identify the differential expression results of miRNA.IncRNA,mRNA and circRNA in the cervical adenocarcinoma and squamous cell carcinoma groups.Results:1.WGS identified 2,916 CNVs in 20 cases of cervical adenocarcinoma.By CISTIC analysis,the most significant chromosomal regions with increased copy number were 3q27.1(30%),12q11(30%),19q11(35%),19q13.11(20%)and 3p11.1(20%),while the regions with decreased copy number were 12p13.31(10%),1p36.22(5%),2q37.1(10%),9q34.3(10%),12p12.3(5%),19q13.2(10%)and 20p11.1(15%).734 times of structural variations were identified with most breakpoints in intergenic regions.WES identified 6,113 somatic mutations with a mutational load of 2.4 mutaions/Mb.There were 3 kinds of mutational signatures confirmed in adenocarcinoma,corresponding to signature 2,5,and 6 from COSMIC database.6 genes were predicted as driver genes including PIK3CA,KRAS,TRAPPC12,NDN,GOLGA6L4 and BAIAP3.And PIK3CA,NDN,GOLGA6L4 and BAIAP3 were recognized as SMGs.HPV were detected in 95%(19/20)of patients with cervical adenocarcinoma and 7 cases were identified with HPV integration.1,036 somatic mutational genes were confirmed in the group with HPV-integration compared to 289 mutational genes in the group without HPV integration.97.4%of mutational genes in HPV-integration group and 90.7%in the no-HPV-integration group were not the same.In group with HPV integration,GOLGA6L4 and BAIAP3 were confirmed as SMG,while PIK3CA,NDN,KRAS,FUT1 and GOLGA6L64 were identified in the other group.2.30 iniRNAs,595 IncRNAs,3,500 mRNAs,173 circRNAs were identified with significantly differential expressions in the cases with cervical squamous cell carcinoma after whole transcriptome sequencing compared to 190 miRNAs,1,337 IncRNAs,6,233 mRNAs,424 circRNAs in cases with cervical adenocarcinoma.In the adenocarcinoma group,93.7%of differentially expressed miRNAs,85%of differentially expressed IncRNAs,83.8%of differentially expressed mRNAs,89.9%of differentially expressed circRNAs were not included in the squamous cell cancers.Similarly,60%of differentially expressed miRNAs,66.4%of differentially expressed lncRNAs,71.2%of differentially expressed mRNAs,75.1%of differentially expressed circRNAs in squamous cell cancers were not included in the adneocarcinomas.Conclusion:Cervical adenocarcinoma has its unique genomic and transcriptome characteristies,which may be different from cervical squamous cell carcinoma in the molecular mechanism.HPV integration results in different genomic changes of cervical adenocarcinoma. |
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