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Identification of key pseudogenes in nasopharyngeal carcinoma based on RNA-Seq analysis
- Source :
- BMC Cancer, Vol 21, Iss 1, Pp 1-14 (2021), BMC Cancer
- Publication Year :
- 2021
- Publisher :
- BMC, 2021.
-
Abstract
- Background Nasopharyngeal carcinoma (NPC) is a malignant head and neck tumor, and more than 70% of new cases are in East and Southeast Asia. However, association between NPC and pseudogenes playing important roles in genesis of multiple tumor types is still not clear and needs to be investigated. Methods Using RNA-Sequencing (RNA-seq) technology, we analyzed pseudogene expression in 13 primary NPC and 6 recurrent NPC samples as well as their paracancerous counterparts. Quantitative PCR was used to validate the differentially expressed pseudogenes. Results We found 251 differentially expressed pseudogenes including 73 up-regulated and 178 down-regulated ones between primary NPC and paracancerous tissues. Enrichment analysis of gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were conducted to filter out the key pseudogenes. We reported that pseudogenes from cytochrome P450 (CYP) family, such as CYP2F2P, CYP2G1P, CYP4F24P, CYP2B7P and CYP2G2P were significantly down-regulated in NPC compared to paracancerous tissues, while IGHV1OR15–2, IGHV3–11, FCGR1CP and IGHV3–69-1 belonging to Fc gamma receptors were significantly up-regulated. CYP2B7P, CYP2F2P and CYP4F26P were enriched in arachidonic acid metabolism pathway. The qRT-PCR analysis validated the lower expression of pseudogenes CYP2F2P and CYP2B7P in NPC tissues and cell lines compared to paracancerous tissues and normal human nasopharyngeal epithelial cell line. CYP2B7P overexpression weakened migratory and invasive capacity of NPC cell line. Moreover, the expression pattern of those pseudogenes in recurrent NPC tissues was different from the primary NPC. Conclusion This study suggested the role of pseudogenes in tumorigenesis and progression, potentially functioning as therapeutic targets to NPC.
- Subjects :
- Male
0301 basic medicine
Cancer Research
Fc gamma receptor
RNA-Seq
Cytochrome P450
medicine.disease_cause
0302 clinical medicine
Cytochrome P-450 Enzyme System
Cell Movement
Receptor
RC254-282
Arachidonic Acid
Neoplasms. Tumors. Oncology. Including cancer and carcinogens
Middle Aged
Up-Regulation
Real-time polymerase chain reaction
Oncology
030220 oncology & carcinogenesis
Female
Pseudogenes
Adult
Pseudogene
Down-Regulation
Biology
Real-Time Polymerase Chain Reaction
Transfection
03 medical and health sciences
Cell Line, Tumor
Genetics
medicine
otorhinolaryngologic diseases
Nasopharyngeal carcinoma
Humans
Neoplasm Invasiveness
KEGG
Cytochrome P450 Family 2
Aged
Sequence Analysis, RNA
Research
Receptors, IgG
Nasopharyngeal Neoplasms
medicine.disease
stomatognathic diseases
Gene Ontology
030104 developmental biology
Cancer research
biology.protein
Neoplasm Recurrence, Local
Carcinogenesis
Subjects
Details
- Language :
- English
- ISSN :
- 14712407
- Volume :
- 21
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- BMC Cancer
- Accession number :
- edsair.doi.dedup.....3bd424c670b4cf4419e31235897c6510