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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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE190224 | GEO | 2021/12/08

REPOSITORIES: GEO

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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]

Project description: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.

2021-12-08 | GSE190223 | GEO

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

2021-12-08 | GSE190222 | GEO

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

Project description:Competing endogenous RNA analysis reveals the regulatory potency of CKAP5 in HPV+ HNSCC based on high throughput sequencing technology and clinical validation

| PRJNA786457 | ENA

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

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

| PRJNA786459 | ENA

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

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

| PRJNA786460 | ENA

Competing endogenous RNA analysis reveals the regulatory potency of circRNA_036186 in HNSCC.

Project description:This study aimed to characterize circular RNA (circRNA) expression profiles and biological functions in head and neck squamous cell carcinoma (HNSCC). Differentially expressed circRNAs were screened using an Arraystar Human CircRNA Array and verified by reverse transcription-quantitative polymerase chain reaction. Multiple bioinformatics methods and a hypergeometric test were employed to predict the interactions between RNAs and the functional circRNA?microRNA (miRNA)-mRNA axes in HNSCC. As a result, 287 circRNAs and 1,053 mRNAs were determined to be differentially expressed in HNSCC compared with the adjacent tissue. In addition, the expression levels of circRNA_036186 and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, ? polypeptide (14?3?3?) were identified to be significantly different. A competing endogenous RNA (ceRNA) network was constructed, consisting of 5 circRNAs, 385 miRNAs and 96 mRNAs. Furthermore, we predicted that miR?193b?3p exerts a significant effect on 14?3?3?, and was significantly associated with the Hippo signaling pathway in HNSCC. On the whole, these findings suggest that circRNA_036186 likely regulates 14?3?3? expression by functioning as a ceRNA in the development and progression of HNSCC.

| S-EPMC6086620 | biostudies-literature

Competing endogenous RNA networks in human cancer: hypothesis, validation, and perspectives.

Project description:Non-coding RNAs represent a majority of the human transcriptome. However, less is known about the functions and regulatory mechanisms of most non-coding species. Moreover, little is known about the potential non-coding functions of coding RNAs. The competing endogenous RNAs (ceRNAs) hypothesis is proposed recently. This hypothesis describes potential communication networks among all transcript RNA species mediated by miRNAs and miRNA-recognizing elements (MREs) within RNA transcripts. Here we review the evolution of the ceRNA hypothesis, summarize the validation experiments and discusses the significance and perspectives of this hypothesis in human cancer.

| S-EPMC4924655 | biostudies-other

FF and FFPE HPV+ and HPV- HNSCC and HNSCC cell lines

Project description:This SuperSeries is composed of the SubSeries listed below.

2012-11-30 | GSE38271 | GEO

FF and FFPE HPV+ and HPV- HNSCC and HNSCC cell lines

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2012-11-30 | E-GEOD-38271 | biostudies-arrayexpress

HPV infection related immune infiltration gene associated therapeutic strategy and clinical outcome in HNSCC.

Project description:BackgroundHead and neck squamous cell carcinoma (HNSCC) is the sixth most common tumor in human. Research has shown that HPV status HNSCC is a unique prognosis factor, which may due to its immune infiltration landscape. But the underlying mechanism is unclear.MethodsIn this study, we used a combination of several bioinformatics tools, including WCGNA, ssGSEA, CIBERSORT, TIDE,etc., to explore significant genes both related to HPV infection status and immune cell infiltration in HNSCC patients.ResultsCombined with several bioinformatics algorithms, eight hub genes were identified, including LTB, CD19, CD3D, SKAP1, KLRB1, CCL19, TBC1D10C and ARHGAP4. In HNSCC population, the hub genes had a stable co-expression, which was related to immune cell infiltration, especially CD8+ T cells, and the infiltrative immune cells were in a dysfunctional status. Samples with high hub genes expression presented with better response to immune check point block (ICB) therapy and sensitivity to bleomycin and methotrexate.ConclusionsThe eight hub genes we found presented with a stable co-expression in immune cell infiltration of HPV?+?ve HNSCC population. The co-expression of hub genes related to an immune microenvironment featuring an increase in immune cells but high degree of immune dysfunction status. Patients with high hub gene expression had a better response to ICB treatment, bleomycin and methotrexate. The co-expression of hub genes may be related to immune infiltration status in patients. The concrete molecular mechanism of hub genes function demands further exploration.

| S-EPMC7444264 | biostudies-literature

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