Abstract
Breast cancer, the most common cancer in women, is characterized by high morbidity and mortality worldwide. Recent evidence has shown that long non-coding RNAs (lncRNAs) play a crucial role in the development and progression of breast cancer. However, despite increasing data and evidence indicating the implication of lncRNAs in breast cancer, no web resource or database exists primarily for lncRNAs associated with only breast cancer. Therefore, we developed a manually curated, comprehensive database, “BCLncRDB,” for lncRNAs associated with breast cancer. For this, we collected, processed, and analyzed available data on breast cancer-associated lncRNAs from different sources, including previously published research articles, the Gene Expression Omnibus (GEO) Database of the National Centre for Biotechnology Information (NCBI), The Cancer Genome Atlas (TCGA), and the Ensembl database; subsequently, these data were hosted at BCLncRDB for public access. Currently, the database contains 5324 unique breast cancer-lncRNA associations and has the following features: (i) a user-friendly, easy-to-use web interface for searching and browsing about lncRNAs of the user’s interest, (ii) differentially expressed and methylated lncRNAs, (iii) stage- and subtype-specific lncRNAs, and (iv) drugs, subcellular localization, sequence, and chromosome information of these lncRNAs. Thus, the BCLncRDB provides a one-stop dedicated platform for exploring breast cancer-related lncRNAs to advance and support the ongoing research on this disease. The BCLncRDB is publicly available for use at http://sls.uohyd.ac.in/new/bclncrdb_v1.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data availability
The BCLncRDB is publicly available at http://sls.uohyd.ac.in/new/bclncrdb_v1. The downloadable information of this database is available at http://sls.uohyd.ac.in/new/bclncrdb_v1/Downloads.php.
References
Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, Yefanov A (2012) NCBI GEO: archive for functional genomics data sets—update. Nucleic Acids Res 41(D1):D991–D995. https://doi.org/10.1093/nar/gks1193
Chen G, Wang Z, Wang D, Qiu C, Liu M, Chen X, Zhang Q, Yan G, Cui Q (2012) LncRNADisease: a database for long-non-coding RNA-associated diseases. Nucleic Acids Res 41(D1):D983–D986. https://doi.org/10.1093/nar/gks1099
Chen H, Xu Z, Liu D (2019) Small non-coding RNA and colorectal cancer. J Cell Mol Med 23(5):3050–3057. https://doi.org/10.1111/jcmm.14209
He W, Li D, Zhang X (2022) LncRNA HOTAIR promotes the proliferation and invasion/metastasis of breast cancer cells by targeting the miR-130a-3p/Suv39H1 axis. Biochem Biophys Rep 30:101279. https://doi.org/10.1016/j.bbrep.2022.101279
Hozhabri H, Ghasemi Dehkohneh RS, Razavi SM, Razavi SM, Salarian F, Rasouli A, Azami J, Ghasemi Shiran M, Kardan Z, Farrokhzad N, Mikaeili Namini A (2022) Comparative analysis of protein-protein interaction networks in metastatic breast cancer. PLoS One 17(1):e0260584. https://doi.org/10.1371/journal.pone.0260584
Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R (2002) The Ensembl genome database project. Nucleic Acids Res 30(1):38–41. https://doi.org/10.1093/nar/30.1.38
Jin H, Du W, Huang W, Yan J, Tang Q, Chen Y, Zou Z (2021) lncRNA and breast cancer: progress from identifying mechanisms to challenges and opportunities of clinical treatment. Mol Ther Nucleic Acids 25:613–637. https://doi.org/10.1016/j.omtn.2021.08.005
Kopp F, Mendell JT (2018) Functional classification and experimental dissection of long non-coding RNAs. Cell 172(3):393–407. https://doi.org/10.1016/j.cell.2018.01.011
Kung JT, Colognori D, Lee JT (2013) Long noncoding RNAs: past, present, and future. Genetics 193(3):651–669. https://doi.org/10.1093/genetics/193.3.NP
Li HL, Wang CP, Zhang Y, Du JX, Han LH, Yang HY (2022) Long non-coding RNA PVT1 facilitates cell migration and invasion by regulating miR-148a-3p and ROCK1 in breast cancer. Clin Transl Oncol 24(5):882–891. https://doi.org/10.1007/s12094-021-02736-0
Li J, Xuan Z, Liu C (2013) Long non-coding RNAs and complex human diseases. Int J Mol Sci 14(9):18790–18808. https://doi.org/10.3390/ijms140918790
Li W, Zhai L, Wang H, Liu C, Zhang J, Chen W, Wei Q (2016) Downregulation of LncRNA GAS5 causes trastuzumab resistance in breast cancer. Oncotarget 7(19):27778–27786. https://doi.org/10.18632/oncotarget.8413
Lin Y, Pan X, Shen HB (2021) lncLocator 2.0: a cell-line-specific subcellular localization predictor for long non-coding RNAs with interpretable deep learning. Bioinformatics 37(16):2308–2316. https://doi.org/10.1093/bioinformatics/btab127
Liu Y, Zhao M (2016) lnCaNet: pan-cancer co-expression network for human lncRNA and cancer genes. Bioinformatics 32(10):1595–1597. https://doi.org/10.1093/bioinformatics/btw017
Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15(12):1–21
Ning S, Zhang J, Wang P, Zhi H, Wang J, Liu Y, Gao Y, Guo M, Yue M, Wang L, Li X (2016) Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers. Nucleic Acids Res 44(D1):D980–D985. https://doi.org/10.1093/nar/gkv1094
Pang B, Wang Q, Ning S, Wu J, Zhang X, Chen Y, Xu S (2019) Landscape of tumor suppressor long non-coding RNAs in breast cancer. J Exp Clin Cancer Res 38:1–18. https://doi.org/10.1186/s13046-019-1096-0
Ren C, An G, Zhao C, Ouyang Z, Bo X, Shu W (2018) Lnc2Catlas: an atlas of long non-coding RNAs associated with risk of cancers. Sci Rep 8(1):1–8. https://doi.org/10.1038/s41598-018-20232-4
Ritchie ME, Phipson B, Wu DI, Hu Y, Law CW, Shi W, Smyth GK (2015) limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 43(7):e47–e47. https://doi.org/10.1093/nar/gkv007
Silva TC, Coetzee SG, Gull N, Yao L, Hazelett DJ, Noushmehr H, Lin DC, Berman BP (2019) ELMER v. 2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles. Bioinformatics 35(11):1974–1977. https://doi.org/10.1093/bioinformatics/bty902
Su X, Malouf GG, Chen Y, Zhang J, Yao H, Valero V, Weinstein JN, Spano JP, Meric-Bernstam F, Khayat D, Esteva FJ (2014) Comprehensive analysis of long non-coding RNAs in human breast cancer clinical subtypes. Oncotarget 5(20):9864–9876. https://doi.org/10.18632/oncotarget.2454
Sun L, Li Y, Yang B (2016) Downregulated long non-coding RNA MEG3 in breast cancer regulates proliferation, migration and invasion by depending on p53’s transcriptional activity. Biochem Biophys Res Commun 478(1):323–329. https://doi.org/10.1016/j.bbrc.2016.05.031
Sun M, Gadad SS, Kim DS, Kraus WL (2015) Discovery, annotation, and functional analysis of long non-coding RNAs controlling cell-cycle gene expression and proliferation in breast cancer cells. Mol Cell 59(4):698–711. https://doi.org/10.1016/j.molcel.2015.06.023
Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F (2021) Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin 71(3):209–249. https://doi.org/10.3322/caac.21660
Weinstein JN, Collisson EA, Mills GB, Shaw KRM, Ozenberger BA, Ellrott K, Shmulevich I, Sander SJM (2013) The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet 45(10):1113–1120. https://doi.org/10.1038/ng.2764
Xue JM, Liu Y, Wan LH, Zhu YX (2020) Comprehensive analysis of differential gene expression to identify common gene signatures in multiple cancers. Med Sci Monit 26:e919953–1. https://doi.org/10.12659/MSM.919953
Zhu Y, Dai B, Zhang H, Shi G, Shen Y, Ye D (2016) Long non-coding RNA LOC572558 inhibits bladder cancer cell proliferation and tumor growth by regulating the AKT–MDM2–p53 signaling axis. Cancer Lett 380(2):369–374. https://doi.org/10.1016/j.canlet.2016.04.030
Zuo Y, Li Y, Zhou Z, Ma M, Fu K (2017) Long non-coding RNA MALAT1 promotes proliferation and invasion via targeting miR-129-5p in triple-negative breast cancer. Biomed Pharmacother 95:922–928. https://doi.org/10.1016/j.biopha.2017.09.005
Acknowledgements
Vaibhav Vindal would like to acknowledge the Indian Council of Medical Research (ICMR), GoI (ISRM/12(72)/2020, ID: 2020-2951), Institution of Eminence (IoE), University of Hyderabad (No. UoH/IoE/RC3-21-052), and Department of Biotechnology, GoI (No. BUILDER-DBT-BT/INF/22/SP41176/2020) for their financial support. Swapnil Kumar would like to acknowledge the ICMR for providing financial assistance as the Senior Research Fellowship (Grant No. 3/2/2/113/2019/NCD-III, ID: 2019-6723). The authors would like to thank Mr. Sayed Saleem Javed for his technical assistance in database hosting on the server.
Funding
This study was supported by the extramural research grant from the Indian Council of Medical Research (ICMR) New Delhi (ISRM/12(72)/2020, ID: 2020-2951).
Author information
Authors and Affiliations
Contributions
AA and SK analyzed the data. AA curated the literature and developed the database. SK wrote the original draft. SK and VV conceived this study, proofread, and edited the manuscript. VV supervised the study. All authors read and approved the final version of the manuscript.
Corresponding author
Ethics declarations
Ethics approval and consent to participate
Not applicable.
Consent to publish
Not applicable.
Competing interests
The authors declare no competing interests.
Additional information
Additional information
A preprint of this article is available at the link (https://www.biorxiv.org/content/10.1101/2022.12.05.519223).
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Kumar, S., Agrawal, A. & Vindal, V. BCLncRDB: a comprehensive database of LncRNAs associated with breast cancer. Funct Integr Genomics 23, 178 (2023). https://doi.org/10.1007/s10142-023-01112-1
Received:
Revised:
Accepted:
Published:
DOI: https://doi.org/10.1007/s10142-023-01112-1