The Identification and Analysis of MRNA-lncRNA-miRNA Cliques From the Integrative Network of Ovarian Cancer

Overview

Journal Front Genet

Date 2019 Sep 10

PMID 31497032

Citations 18

Authors

You Zhou

Xiao Zheng

Bin Xu

Wenwei Hu

Tao Huang

Jingting Jiang

Affiliations

Soon will be listed here.

Abstract

Ovarian cancer is one of the leading causes of cancer mortality in women. Since little clinical symptoms were shown in the early period of ovarian cancer, most patients were found in phases III-IV or with abdominal metastasis when diagnosed. The lack of effective early diagnosis biomarkers makes ovarian cancer difficult to screen. However, in essence, the fundamental problem is we know very little about the regulatory mechanisms during tumorigenesis of ovarian cancer. There are emerging regulatory factors, such as long noncoding RNAs (lncRNAs) and microRNAs (miRNAs), which have played important roles in cancers. Therefore, we analyzed the RNA-seq profiles of 407 ovarian cancer patients. An integrative network of 20,424 coding RNAs (mRNAs), 10,412 lncRNAs, and 742 miRNAs were construed with variance inflation factor (VIF) regression method. The mRNA-lncRNA-miRNA cliques were identified from the network and analyzed. Such promising cliques showed significant correlations with survival and stage of ovarian cancer and characterized the complex sponge regulatory mechanism, suggesting their contributions to tumorigenicity. Our results provided novel insights of the regulatory mechanisms among mRNAs, lncRNAs, and miRNAs and highlighted several promising regulators for ovarian cancer detection and treatment.

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References

Yamamoto K, Okamoto A, Isonishi S, Ochiai K, Ohtake Y . A novel gene, CRR9, which was up-regulated in CDDP-resistant ovarian tumor cell line, was associated with apoptosis. Biochem Biophys Res Commun. 2001; 280(4):1148-54. DOI: 10.1006/bbrc.2001.4250. View

Yang Y, Hentati A, Deng H, Dabbagh O, Sasaki T, Hirano M . The gene encoding alsin, a protein with three guanine-nucleotide exchange factor domains, is mutated in a form of recessive amyotrophic lateral sclerosis. Nat Genet. 2001; 29(2):160-5. DOI: 10.1038/ng1001-160. View

Rogers M, Winter H, Langbein L, Wollschlager A, Praetzel-Wunder S, Jave-Suarez L . Characterization of human KAP24.1, a cuticular hair keratin-associated protein with unusual amino-acid composition and repeat structure. J Invest Dermatol. 2007; 127(5):1197-204. DOI: 10.1038/sj.jid.5700702. View

Koldehoff M, Zakrzewski J, Klein-Hitpass L, Beelen D, Elmaagacli A . Gene profiling of growth factor independence 1B gene (Gfi-1B) in leukemic cells. Int J Hematol. 2008; 87(1):39-47. DOI: 10.1007/s12185-007-0013-z. View

Baldwin E, May L, Justice A, Martin C, Ledbetter D . Mechanisms and consequences of small supernumerary marker chromosomes: from Barbara McClintock to modern genetic-counseling issues. Am J Hum Genet. 2008; 82(2):398-410. PMC: 2427313. DOI: 10.1016/j.ajhg.2007.10.013. View

Crawford N, Walker R, Lukes L, Officewala J, Williams R, Hunter K . The Diasporin Pathway: a tumor progression-related transcriptional network that predicts breast cancer survival. Clin Exp Metastasis. 2008; 25(4):357-69. PMC: 2410042. DOI: 10.1007/s10585-008-9146-6. View

Moll R, Divo M, Langbein L . The human keratins: biology and pathology. Histochem Cell Biol. 2008; 129(6):705-33. PMC: 2386534. DOI: 10.1007/s00418-008-0435-6. View

Wyman S, Parkin R, Mitchell P, Fritz B, OBriant K, Godwin A . Repertoire of microRNAs in epithelial ovarian cancer as determined by next generation sequencing of small RNA cDNA libraries. PLoS One. 2009; 4(4):e5311. PMC: 2668797. DOI: 10.1371/journal.pone.0005311. View

Ramakrishna M, Williams L, Boyle S, Bearfoot J, Sridhar A, Speed T . Identification of candidate growth promoting genes in ovarian cancer through integrated copy number and expression analysis. PLoS One. 2010; 5(4):e9983. PMC: 2851616. DOI: 10.1371/journal.pone.0009983. View

10.

Goitre L, Balzac F, Degani S, Degan P, Marchi S, Pinton P . KRIT1 regulates the homeostasis of intracellular reactive oxygen species. PLoS One. 2010; 5(7):e11786. PMC: 2910502. DOI: 10.1371/journal.pone.0011786. View

11.

Karantza V . Keratins in health and cancer: more than mere epithelial cell markers. Oncogene. 2010; 30(2):127-38. PMC: 3155291. DOI: 10.1038/onc.2010.456. View

12.

Kim Y, Hwan J, Bae S, Bae D, Shick W . Identification of differentially expressed genes using an annealing control primer system in stage III serous ovarian carcinoma. BMC Cancer. 2010; 10:576. PMC: 2974737. DOI: 10.1186/1471-2407-10-576. View

13.

Nguyen C, Mansfield R, Leung W, Vaz P, Loughlin F, Grant R . Characterization of a family of RanBP2-type zinc fingers that can recognize single-stranded RNA. J Mol Biol. 2011; 407(2):273-83. DOI: 10.1016/j.jmb.2010.12.041. View

14.

Braconi C, Kogure T, Valeri N, Huang N, Nuovo G, Costinean S . microRNA-29 can regulate expression of the long non-coding RNA gene MEG3 in hepatocellular cancer. Oncogene. 2011; 30(47):4750-6. PMC: 4292930. DOI: 10.1038/onc.2011.193. View

15.

Cesana M, Cacchiarelli D, Legnini I, Santini T, Sthandier O, Chinappi M . A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell. 2011; 147(2):358-69. PMC: 3234495. DOI: 10.1016/j.cell.2011.09.028. View

16.

Yang C, Cai J, Wang Q, Tang H, Cao J, Wu L . Epigenetic silencing of miR-130b in ovarian cancer promotes the development of multidrug resistance by targeting colony-stimulating factor 1. Gynecol Oncol. 2011; 124(2):325-34. DOI: 10.1016/j.ygyno.2011.10.013. View

17.

Farina B, Fattorusso R, Pellecchia M . Targeting zinc finger domains with small molecules: solution structure and binding studies of the RanBP2-type zinc finger of RBM5. Chembiochem. 2011; 12(18):2837-45. PMC: 3408030. DOI: 10.1002/cbic.201100582. View

18.

James M, Wen W, Wang Y, Byers L, Heymach J, Coombes K . Functional characterization of CLPTM1L as a lung cancer risk candidate gene in the 5p15.33 locus. PLoS One. 2012; 7(6):e36116. PMC: 3366984. DOI: 10.1371/journal.pone.0036116. View

19.

Garipov A, Li H, Bitler B, Thapa R, Balachandran S, Zhang R . NF-YA underlies EZH2 upregulation and is essential for proliferation of human epithelial ovarian cancer cells. Mol Cancer Res. 2013; 11(4):360-9. PMC: 3631279. DOI: 10.1158/1541-7786.MCR-12-0661. View

20.

Yamamoto N, Kinoshita T, Nohata N, Itesako T, Yoshino H, Enokida H . Tumor suppressive microRNA-218 inhibits cancer cell migration and invasion by targeting focal adhesion pathways in cervical squamous cell carcinoma. Int J Oncol. 2013; 42(5):1523-32. PMC: 3661225. DOI: 10.3892/ijo.2013.1851. View