In Silico Analyses Identify LncRNAs: WDFY3-AS2, BDNF-AS and AFAP1-AS1 As Potential Prognostic Factors for Patients with Triple-negative Breast Tumors

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2020 May 14

PMID 32401758

Citations 12

Authors

Daniel Rodrigues de Bastos

Maria A Nagai

Affiliations

Soon will be listed here.

Abstract

Background: Long non-coding RNAs (lncRNAs) are characterized as having 200 nucleotides or more and not coding any protein, and several been identified as differentially expressed in several human malignancies, including breast cancer.

Methods: Here, we evaluated lncRNAs differentially expressed in triple-negative breast cancer (TNBC) from a cDNA microarray data set obtained in a previous study from our group. Using in silico analyses in combination with a review of the current literature, we identify three lncRNAs as potential prognostic factors for TNBC patients.

Results: We found that the expression of WDFY3-AS2, BDNF-AS, and AFAP1-AS1 was associated with poor survival in patients with TNBCs. WDFY3-AS2 and BDNF-AS are lncRNAs known to play an important role in tumor suppression of different types of cancer, while AFAP1-AS1 exerts oncogenic activity.

Conclusion: Our findings provided evidence that WDFY3-AS2, BDNF-AS, and AFAP1-AS1 may be potential prognostic factors in TNBC development.

Citing Articles

Long Non-Coding RNAs as Determinants of Thyroid Cancer Phenotypes: Investigating Differential Gene Expression Patterns and Novel Biomarker Discovery.

DeSouza N, Jarboe T, Carnazza M, Quaranto D, Islam H, Tiwari R Biology (Basel). 2024; 13(5).

PMID: 38785786 PMC: 11118935. DOI: 10.3390/biology13050304.

Roles of AFAP1-AS1 in Gynecology and Urogenital System.

Qiu X, Huang Y, Jin L, Yang C, Wang J Curr Pharm Des. 2024; 30(8):639-647.

PMID: 38347771 DOI: 10.2174/0113816128286229240129090915.

SP1-Induced Upregulation of LncRNA AFAP1-AS1 Promotes Tumor Progression in Triple-Negative Breast Cancer by Regulating mTOR Pathway.

Li F, Xian D, Huang J, Nie L, Xie T, Sun Q Int J Mol Sci. 2023; 24(17).

PMID: 37686205 PMC: 10563082. DOI: 10.3390/ijms241713401.

Comprehensive analysis of cuproptosis-related long non-coding RNA signature and personalized therapeutic strategy of breast cancer patients.

Guo Q, Qiu P, Pan K, Lin J Front Oncol. 2023; 12:1081089.

PMID: 36620596 PMC: 9815178. DOI: 10.3389/fonc.2022.1081089.

lncRNA pair as candidate diagnostic signature for colorectal cancer based on the within-sample relative expression levels.

Wang O, Shi D, Li Y, Zhou X, Yan H, Yao Q Front Oncol. 2022; 12:912882.

PMID: 36059706 PMC: 9428707. DOI: 10.3389/fonc.2022.912882.

References

Zhang T, Hu H, Yan G, Wu T, Liu S, Chen W . Long Non-Coding RNA and Breast Cancer. Technol Cancer Res Treat. 2019; 18:1533033819843889. PMC: 6466467. DOI: 10.1177/1533033819843889. View

Shang M, Chang C, Pei Y, Guan Y, Chang J, Li H . Potential Management of Circulating Tumor DNA as a Biomarker in Triple-Negative Breast Cancer. J Cancer. 2018; 9(24):4627-4634. PMC: 6299380. DOI: 10.7150/jca.28458. View

Zhi H, Lian J . LncRNA BDNF-AS suppresses colorectal cancer cell proliferation and migration by epigenetically repressing GSK-3β expression. Cell Biochem Funct. 2019; 37(5):340-347. DOI: 10.1002/cbf.3403. View

Li W, Ma S, Bai X, Pan W, Ai L, Tan W . Long noncoding RNA WDFY3-AS2 suppresses tumor progression by acting as a competing endogenous RNA of microRNA-18a in ovarian cancer. J Cell Physiol. 2019; 235(2):1141-1154. DOI: 10.1002/jcp.29028. View

Zhang Z, Wang S, Liu W . EMT-related long non-coding RNA in hepatocellular carcinoma: A study with TCGA database. Biochem Biophys Res Commun. 2018; 503(3):1530-1536. DOI: 10.1016/j.bbrc.2018.07.075. View

Chen W, Xu X, Li J, Kong K, Li H, Chen C . MALAT1 is a prognostic factor in glioblastoma multiforme and induces chemoresistance to temozolomide through suppressing miR-203 and promoting thymidylate synthase expression. Oncotarget. 2017; 8(14):22783-22799. PMC: 5410262. DOI: 10.18632/oncotarget.15199. View

Rao A, Patel K, Korivi Jyothiraj S, Meenakumari B, Sundersingh S, Sridevi V . Identification of lncRNAs associated with early-stage breast cancer and their prognostic implications. Mol Oncol. 2019; 13(6):1342-1355. PMC: 6547626. DOI: 10.1002/1878-0261.12489. View

Szklarczyk D, Gable A, Lyon D, Junge A, Wyder S, Huerta-Cepas J . STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2018; 47(D1):D607-D613. PMC: 6323986. DOI: 10.1093/nar/gky1131. View

Sorlie T, Perou C, Tibshirani R, Aas T, Geisler S, Johnsen H . Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci U S A. 2001; 98(19):10869-74. PMC: 58566. DOI: 10.1073/pnas.191367098. View

10.

Gao H, Hao G, Sun Y, Li L, Wang Y . Long noncoding RNA H19 mediated the chemosensitivity of breast cancer cells via Wnt pathway and EMT process. Onco Targets Ther. 2018; 11:8001-8012. PMC: 6235328. DOI: 10.2147/OTT.S172379. View

11.

Collignon J, Lousberg L, Schroeder H, Jerusalem G . Triple-negative breast cancer: treatment challenges and solutions. Breast Cancer (Dove Med Press). 2016; 8:93-107. PMC: 4881925. DOI: 10.2147/BCTT.S69488. View

12.

Youness R, Gad M . Long non-coding RNAs: Functional regulatory players in breast cancer. Noncoding RNA Res. 2019; 4(1):36-44. PMC: 6404363. DOI: 10.1016/j.ncrna.2019.01.003. View

13.

Xu S, Xu J, Zheng Z, Zhao Q, Zeng X, Cheng S . Long non-coding RNA ANRIL promotes carcinogenesis via sponging miR-199a in triple-negative breast cancer. Biomed Pharmacother. 2017; 96:14-21. DOI: 10.1016/j.biopha.2017.09.107. View

14.

Liang H, Huang W, Wang Y, Ding L, Zeng L . Overexpression of MiR-146a-5p Upregulates lncRNA HOTAIR in Triple-Negative Breast Cancer Cells and Predicts Poor Prognosis. Technol Cancer Res Treat. 2019; 18:1533033819882949. PMC: 6826924. DOI: 10.1177/1533033819882949. View

15.

Yu F, Wang L, Zhang B . Long non-coding RNA DRHC inhibits the proliferation of cancer cells in triple negative breast cancer by downregulating long non-coding RNA HOTAIR. Oncol Lett. 2019; 18(4):3817-3822. PMC: 6733000. DOI: 10.3892/ol.2019.10683. View

16.

Arnold S, Brekken R . SPARC: a matricellular regulator of tumorigenesis. J Cell Commun Signal. 2009; 3(3-4):255-73. PMC: 2778590. DOI: 10.1007/s12079-009-0072-4. View

17.

Neophytou C, Boutsikos P, Papageorgis P . Molecular Mechanisms and Emerging Therapeutic Targets of Triple-Negative Breast Cancer Metastasis. Front Oncol. 2018; 8:31. PMC: 5827095. DOI: 10.3389/fonc.2018.00031. View

18.

Wang J, Li B, Wang C, Luo Y, Zhao M, Chen P . Long noncoding RNA FOXD2-AS1 promotes glioma cell cycle progression and proliferation through the FOXD2-AS1/miR-31/CDK1 pathway. J Cell Biochem. 2019; 120(12):19784-19795. DOI: 10.1002/jcb.29284. View

19.

Yang R, Xing L, Wang M, Chi H, Zhang L, Chen J . Comprehensive Analysis of Differentially Expressed Profiles of lncRNAs/mRNAs and miRNAs with Associated ceRNA Networks in Triple-Negative Breast Cancer. Cell Physiol Biochem. 2018; 50(2):473-488. DOI: 10.1159/000494162. View

20.

Vikas P, Borcherding N, Zhang W . The clinical promise of immunotherapy in triple-negative breast cancer. Cancer Manag Res. 2018; 10:6823-6833. PMC: 6292225. DOI: 10.2147/CMAR.S185176. View