An Overview of the Computational Models Dealing with the Regulatory ceRNA Mechanism and ceRNA Deregulation in Cancer

Conte, Federica; Fiscon, Giulia; Sibilio, Pasquale; Licursi, Valerio; Paci, Paola

doi:10.1007/978-1-0716-1503-4_10

Cited by 27 publications

(18 citation statements)

References 47 publications

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“…The competing endogenous RNA (ceRNA) hypothesis revealed that ceRNAs can regulate the gene expression by competitively binding miRNAs. Therefore, the lncRNA should meet the following conditions: (1) negatively correlated with miRNA and (2) positively correlated with mRNA [ 14 – 16 ].…”

Section: Methodsmentioning

confidence: 99%

ncRNA-Mediated High Expression of LPCAT1 Correlates with Poor Prognosis and Tumor Immune Infiltration of Liver Hepatocellular Carcinoma

Sun

Peng

et al. 2022

Journal of Immunology Research

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Purpose. To investigate the expression of LPCAT1 in liver hepatocellular carcinoma (LIHC) and its relationship with prognosis and immune infiltration and predict its upstream nonencoding RNAs (ncRNAs). Method. In this study, expression analysis and survival analysis for LPCAT1 in pan cancers were first performed by using The Cancer Genome Atlas (TCGA) data, which suggested that LPCAT1 might be a potential LIHC oncogene. Then, ncRNAs contributing to the overexpression of LPCAT1 were explored in starBase by a combination of expression analysis, correlation analysis, and survival analysis. Immune cell infiltration of LPCAT1 in LIHC was finally investigated via Tumor Immune Estimation Resource (TIMER). Result. SNHG3 was observed to be the most promising upstream lncRNA for the hsa-miR-139-5p/LPCAT1 axis in LIHC. In addition, the LPCAT1 level was significantly positively associated with tumor immune cell infiltration, biomarkers of immune cells, and immune checkpoint expression in LIHC. Conclusion. To summarize, the upregulation of LPCAT1 mediated by ncRNAs is associated with poor prognosis, immune infiltration, and immune checkpoint expression in LIHC.

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Section: Methodsmentioning

confidence: 99%

ncRNA-Mediated High Expression of LPCAT1 Correlates with Poor Prognosis and Tumor Immune Infiltration of Liver Hepatocellular Carcinoma

Sun

Peng

et al. 2022

Journal of Immunology Research

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“…They may share miRNA response elements with other genes, especially parental ones, and positively regulate their expression by competing for the same pool of miRNAs, acting as miRNAs sponges [20]. In this process, pseudogene transcripts inhibit miRNA-target gene binding, allowing gene expression and modulating biological processes and tumor progression [22,23]. In addition, pseudogene transcripts in sense orientation may compete for miRNAs, RNA-binding proteins, and translational machinery with the parental gene [18].…”

Section: Pseudogene Transcriptsmentioning

confidence: 99%

Pseudogene Transcripts in Head and Neck Cancer: Literature Review and In Silico Analysis

Carron

Coletta

Lourenço

2021

Genes

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Once considered nonfunctional, pseudogene transcripts are now known to provide valuable information for cancer susceptibility, including head and neck cancer (HNC), a serious health problem worldwide, with about 50% unimproved overall survival over the last decades. The present review focuses on the role of pseudogene transcripts involved in HNC risk and prognosis. We combined current literature and in silico analyses from The Cancer Genome Atlas (TCGA) database to identify the most deregulated pseudogene transcripts in HNC and their genetic variations. We then built a co-expression network and performed gene ontology enrichment analysis to better understand the pseudogenes’ interactions and pathways in HNC. In the literature, few pseudogenes have been studied in HNC. Our in silico analysis identified 370 pseudogene transcripts associated with HNC, where SPATA31D5P, HERC2P3, SPATA31C2, MAGEB6P1, SLC25A51P1, BAGE2, DNM1P47, SPATA31C1, ZNF733P and OR2W5 were found to be the most deregulated and presented several genetic alterations. NBPF25P, HSP90AB2P, ZNF658B and DPY19L2P3 pseudogenes were predicted to interact with 12 genes known to participate in HNC, DNM1P47 was predicted to interact with the TP53 gene, and HLA-H pseudogene was predicted to interact with HLA-A and HLA-B genes. The identified pseudogenes were associated with cancer biology pathways involving cell communication, response to stress, cell death, regulation of the immune system, regulation of gene expression, and Wnt signaling. Finally, we assessed the prognostic values of the pseudogenes with the Kaplan–Meier Plotter database, and found that expression of SPATA31D5P, SPATA31C2, BAGE2, SPATA31C1, ZNF733P and OR2W5 pseudogenes were associated with patients’ survival. Due to pseudogene transcripts’ potential for cancer diagnosis, progression, and as therapeutic targets, our study can guide new research to HNC understanding and development of new target therapies.

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“…A growing body of evidence suggests that circRNAs play important roles in many biological processes including cell proliferation, invasion, and cell differentiation [ 7–10 ]. In 2010, Poliseno et al first proposed the hypothesis of the interaction between protein-coding messenger RNAs (mRNAs) and ncRNAs [ 7 , 8 ] and circRNAs could act as ceRNAs [ 11 , 12 ]. Owing to the advantages of abundance, conservation, stability, and high specificity in serum, plasma, and other body fluids [ 13 , 14 ], circRNAs hold great potential as noninvasive blood-based biomarkers in cancer management [ 15 , 16 ].…”

Section: Introductionmentioning

confidence: 99%

CircMYC promotes proliferation, migration, invasion and inhibits apoptosis of small cell lung cancer by targeting miR-145/ Matrix Metallopeptidase 2 axis

Yang

Tao

et al. 2022

Bioengineered

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Circular RNAs (circRNAs) are involved in the carcinogenesis of lung cancer. Human MYC gene is highly expressed in melanoma, multiple myeloma, and nasopharyngeal carcinoma. We aimed to investigate the role of circMYC in small cell lung cancer (SCLC). The expression of cirMYC in SCLC tissues and cells were examined. Functional studies were performed to evaluate the roles of circMYC in SCLC cells. Luciferase reporter gene assay, RNA pull-down assay, and rescue experiments were performed to evaluate the regulatory relationship between circMYC and miR-145, and MiR-145 and MMP2 mRNA. We found that CirMYC was highly expressed in SCLC tissues and cells. Knockdown of circMYC could inhibit cell proliferation, migration, invasion, and induce apoptosis. CircMYC targeted miR-145 and miR-145 targeted MMP2 (Matrix Metallopeptidase 2) mRNA. Our data indicated that circMYC upregulates the expression of MMP-2 by inhibiting miR-145, which functions to promote the proliferation, migration, and invasion and inhibit the apoptosis of SCLC. These findings suggest that targeting circMYC/miR-145/MMP-2 could serve as a potential therapeutic strategy for SCLC treatment.

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An Overview of the Computational Models Dealing with the Regulatory ceRNA Mechanism and ceRNA Deregulation in Cancer

Cited by 27 publications

References 47 publications

ncRNA-Mediated High Expression of LPCAT1 Correlates with Poor Prognosis and Tumor Immune Infiltration of Liver Hepatocellular Carcinoma

ncRNA-Mediated High Expression of LPCAT1 Correlates with Poor Prognosis and Tumor Immune Infiltration of Liver Hepatocellular Carcinoma

Pseudogene Transcripts in Head and Neck Cancer: Literature Review and In Silico Analysis

CircMYC promotes proliferation, migration, invasion and inhibits apoptosis of small cell lung cancer by targeting miR-145/ Matrix Metallopeptidase 2 axis

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