Genomics

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Competing endogenous RNA analysis reveals the regulatory potency of CKAP5 in HPV+ HNSCC based on high throughput sequencing technology and clinical validation [miRNA]


ABSTRACT: Purpose: The current study used high-throughput sequencing technology and related basic experimental verification assays to evaluate new pathogenic mechanisms of Human papilloma virus HPV+ Head and neck squamous cell carcinoma (HNSCC) as well as to determine the potential therapeutic targets. Materials and methods: In this study 3 pairs of tissues were collected from patient with HPV+ and HPV- HNSCC for high-throughput sequencing analysis. After mRNA sequencing and analysis, multiple bioinformatics methods, real-time quantitative reverse transcription-quantitative polymerase chain reaction (qRT-PCR) and immunehistochemical verification assays were carried out to evaluate the potential therapeutic targets of HNSCC (CKAP5). The CKAP5 was then used to further predict the circular RNA (circRNA), long non-coding RNA (lncRNA), and microRNA (miRNA). Sequencing analysis was also performed to further evaluate the potential carcinogenic pathway. Human papilloma virus detection was carried out through Enzyme-Linked Immune Sorbent Assay (ELISA) and the RT-PCR. Results: Results of high-throughput sequencing analysis, related databases, and verification of qRT-PCR at the cell and tissue level, revealed that the expression level of CKAP5 in HPV+HNSCC was significantly higher than that in HPV-HNSCC. Further, a competitive endogenous RNA (ceRNA) network was also constructed through the analysis of Miranda, multiMiR, lncBase prediction, and sequencing technology. The constructed ceRNA consisted of 1 mRNA, 2 miRNAs, and 1 lncRNA, and 6 CircRNAs. This was verified by RNA22, whereby the relationship between miR-155-5p and CKAP5 was found to be important whereas the hsa_circ_00058495 was a key circRNA according to the binding site scores. Conclusion: In conclusion it was evident that Hsa_circ_00058495/miR-155-5p CKAP5 may be an important pathway which is involved in the occurrence and development of HPV+ HNSCC.

ORGANISM(S): Homo sapiens

PROVIDER: GSE190223 | GEO | 2021/12/08

REPOSITORIES: GEO

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