Comprehensive Analysis of Circular RNAs in Nasopharyngeal Cancer

Overview

Journal Genes Genomics

Specialty Genetics

Date 2023 Aug 31

PMID 37651065

Authors

Si-Yu Zhu

Xiao-Yi Wang

Hui Xie

Li-Zhi Liu

Affiliations

Soon will be listed here.

Abstract

Background: Nasopharyngeal cancer (NPC) is a type of epithelial malignancy that is positive for Epstein-Barr virus (EBV) and affects several populations worldwide. Due to the high rates of relapse and metastasis following primary treatment, there is an urgent need to identify new candidates for NPC therapy. Recently, circular RNA (circRNA) has emerged as a promising target for cancer diagnosis and prevention.

Objective: This study aimed to study the circRNAs enriched in NPC patients, and further analyze potential signaling pathways involved.

Methods: A new bioinformatic tool named psirc was used to analyze RNA-sequencing datasets from NPC patients and normal specimens to study the NPC-enriched circRNAs.

Results: We identified and quantified the full-length circRNA in these samples and found the top 10 enriched circRNAs in NPC patients compared to control samples. Furthermore, we selected the most enriched circRNA, circEEF1A1_E8B1, and studied its protein coding ability, microRNA and RNA-binding protein (RBP) binding capacity. We also constructed a protein-protein interaction (PPI) network for its binding proteins and extracted hub genes. Finally, we conducted survival analysis for these hub genes in head and neck cancer patients.

Conclusions: In summary, our study has revealed the presence of previously unidentified circRNAs that are enriched in NPC patients. Through an analysis of their molecular functions, we have advanced our understanding of the potential role of circRNAs in NPC development.

Citing Articles

Roles and mechanisms of circular RNA in respiratory system cancers.

Yang N, Jiao M, Zhang Y, Mo S, Wang L, Liang J Front Oncol. 2024; 14:1430051.

PMID: 39077467 PMC: 11284073. DOI: 10.3389/fonc.2024.1430051.

An Evaluation of Treatment Outcomes and Associated Factors in Nasopharyngeal Cancer Patients at a Tertiary Cancer Center in the United Arab Emirates.

Bin Sumaida A, Shanbhag N, Aby Ali H, Jaafar N, AlKaabi K, Balaraj K Cureus. 2024; 16(2):e54344.

PMID: 38371438 PMC: 10873819. DOI: 10.7759/cureus.54344.

References

Agarwal V, Bell G, Nam J, Bartel D . Predicting effective microRNA target sites in mammalian mRNAs. Elife. 2015; 4. PMC: 4532895. DOI: 10.7554/eLife.05005. View

Ahringer J . NuRD and SIN3 histone deacetylase complexes in development. Trends Genet. 2000; 16(8):351-6. DOI: 10.1016/s0168-9525(00)02066-7. View

Arimbasseri A, Rijal K, Maraia R . Comparative overview of RNA polymerase II and III transcription cycles, with focus on RNA polymerase III termination and reinitiation. Transcription. 2015; 5(1):e27639. PMC: 4214234. DOI: 10.4161/trns.27369. View

Ayer D . Histone deacetylases: transcriptional repression with SINers and NuRDs. Trends Cell Biol. 1999; 9(5):193-8. DOI: 10.1016/s0962-8924(99)01536-6. View

Bahn J, Zhang Q, Li F, Chan T, Lin X, Kim Y . The landscape of microRNA, Piwi-interacting RNA, and circular RNA in human saliva. Clin Chem. 2014; 61(1):221-30. PMC: 4332885. DOI: 10.1373/clinchem.2014.230433. View

Bray N, Pimentel H, Melsted P, Pachter L . Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol. 2016; 34(5):525-7. DOI: 10.1038/nbt.3519. View

Chen L . The biogenesis and emerging roles of circular RNAs. Nat Rev Mol Cell Biol. 2016; 17(4):205-11. DOI: 10.1038/nrm.2015.32. View

Chen L . The expanding regulatory mechanisms and cellular functions of circular RNAs. Nat Rev Mol Cell Biol. 2020; 21(8):475-490. DOI: 10.1038/s41580-020-0243-y. View

Chen C, Cheng R, Demeter J, Chen J, Weingarten-Gabbay S, Jiang L . Structured elements drive extensive circular RNA translation. Mol Cell. 2021; 81(20):4300-4318.e13. PMC: 8567535. DOI: 10.1016/j.molcel.2021.07.042. View

10.

Enuka Y, Lauriola M, Feldman M, Sas-Chen A, Ulitsky I, Yarden Y . Circular RNAs are long-lived and display only minimal early alterations in response to a growth factor. Nucleic Acids Res. 2015; 44(3):1370-83. PMC: 4756822. DOI: 10.1093/nar/gkv1367. View

11.

Hansen T, Jensen T, Clausen B, Bramsen J, Finsen B, Damgaard C . Natural RNA circles function as efficient microRNA sponges. Nature. 2013; 495(7441):384-8. DOI: 10.1038/nature11993. View

12.

Hulo N, Bairoch A, Bulliard V, Cerutti L, de Castro E, Langendijk-Genevaux P . The PROSITE database. Nucleic Acids Res. 2005; 34(Database issue):D227-30. PMC: 1347426. DOI: 10.1093/nar/gkj063. View

13.

Lanier A, Bender T, Talbot M, Wilmeth S, Tschopp C, Henle W . Nasopharyngeal carcinoma in Alaskan Eskimos Indians, and Aleuts: a review of cases and study of Epstein-Barr virus, HLA, and environmental risk factors. Cancer. 1980; 46(9):2100-6. DOI: 10.1002/1097-0142(19801101)46:9<2100::aid-cncr2820460932>3.0.co;2-g. View

14.

Lee A, Ma B, Ng W, Chan A . Management of Nasopharyngeal Carcinoma: Current Practice and Future Perspective. J Clin Oncol. 2015; 33(29):3356-64. DOI: 10.1200/JCO.2015.60.9347. View

15.

Li Y, Zheng Q, Bao C, Li S, Guo W, Zhao J . Circular RNA is enriched and stable in exosomes: a promising biomarker for cancer diagnosis. Cell Res. 2015; 25(8):981-4. PMC: 4528056. DOI: 10.1038/cr.2015.82. View

16.

Liu C, Chen L . Expanded regulation of circular RNA translation. Mol Cell. 2021; 81(20):4111-4113. DOI: 10.1016/j.molcel.2021.09.023. View

17.

Maracci C, Rodnina M . Review: Translational GTPases. Biopolymers. 2016; 105(8):463-75. PMC: 5084732. DOI: 10.1002/bip.22832. View

18.

Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A . Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013; 495(7441):333-8. DOI: 10.1038/nature11928. View

19.

Memczak S, Papavasileiou P, Peters O, Rajewsky N . Identification and Characterization of Circular RNAs As a New Class of Putative Biomarkers in Human Blood. PLoS One. 2015; 10(10):e0141214. PMC: 4617279. DOI: 10.1371/journal.pone.0141214. View

20.

Mesri E, Feitelson M, Munger K . Human viral oncogenesis: a cancer hallmarks analysis. Cell Host Microbe. 2014; 15(3):266-82. PMC: 3992243. DOI: 10.1016/j.chom.2014.02.011. View