Differentially expressed AC077690.1, AL049874.3 and AP001037.1 lncRNAs in prostate cancer

Authors

  • Hexin Li Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P. R. China
  • Xiaokun Tang Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P. R. China
  • Gaoyuan Sun Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P. R. China
  • Siyuan Xu Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P. R. China
  • Luyao Wang Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P. R. China
  • Lanxin Zhang Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P. R. China
  • Yaqun Zhang Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P. R. China
  • Fei Su Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P. R. China
  • Lili Zhang Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P. R. China
  • Wei Zhang Department of Pathology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, P. R. China

DOI:

https://doi.org/10.2298/ABS221025034L

Keywords:

Prostate cancer, Long non-coding RNA, Biomarker, Signaling pathway, Candidate therapeutic targets

Abstract

Paper description:

  • Three long non-coding RNAs (lncRNAs) in prostate cancer were filtered out by high-throughput sequencing data and bioinformatics analysis as follows: AC077690.1, AL049874.3 and AP001037.1.
  • A lncRNA regulatory network was constructed and differentially expressed mRNA interactions were used to predict the function of the selected lncRNAs.
  • Functional enrichment analysis and PCR verification of these three lncRNAs revealed that they were closely associated with the PI3K-Akt-mTOR and forkhead box protein (FOXO) signaling pathways involved in prostate cancer.
  • These lncRNAs are potential therapeutic targets in prostate cancer.

Abstract: Prostate cancer (PCa) is a common type of cancer worldwide. The incidence of PCa increases with age and it is the most common malignant tumor in men. Tissue biopsy and the serum prostate-specific antigen are still the standards for diagnosing suspected PCa. Long non-coding RNA (lncRNA) contributes to the progression of PCa by recruiting transcriptional regulators. We utilized high-throughput sequencing data and bioinformatics analysis to identify specifically expressed lncRNAs in PCa and filtered out three specific lncRNAs for further analysis: AC077690.1, AL049874.3 and AP001037.1. We constructed a lncRNA regulatory network and used differentially expressed mRNA interactions to predict the functions of the selected lncRNAs. Functional enrichment analysis and PCR verification of these three lncRNAs revealed that they were closely related to well-known PI3K-Akt-mTOR and the forkhead box protein (FOXO) signaling pathways involved in PCa. By understanding the related interactions between these molecules and signaling pathways, the lncRNAs could be potential candidates for therapeutic targets in PCa.

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References

Fujita K, Nonomura N. Role of Androgen Receptor in Prostate Cancer: A Review. World J Mens Health. 2019;37(3):288-95. https://doi.org/10.5534/wjmh.180040

Tamura K, Makino A, Hullin-Matsuda F, Kobayashi T, Furihata M, Chung S, Ashida S, Miki T, Fujioka T, Shuin T, Nakamura Y, Nakagawa H. Novel lipogenic enzyme ELOVL7 is involved in prostate cancer growth through saturated long-chain fatty acid metabolism. Cancer Res. 2009;69(20):8133-40. https://doi.org/10.1158/0008-5472.CAN-09-0775

Vellky JE, Ricke WA. Development and prevalence of castration-resistant prostate cancer subtypes. Neoplasia. 2020;22(11):566-75. https://doi.org/10.1016/j.neo.2020.09.002

Kirby M, Hirst C, Crawford ED. Characterising the castration-resistant prostate cancer population: a systematic review. Int J Clin Pract. 2011;65(11):1180-92. https://doi.org/10.1111/j.1742-1241.2011.02799.x

Heinrich D, Bektic J, Bergman AM, Caffo O, Cathomas R, Chi KN, Daugaard G, Keizman D, Kindblom J, Kramer G, Olmos D, Omlin A, Sridhar SS, Tucci M, van Oort I, Nilsson S. The Contemporary Use of Radium-223 in Metastatic Castration-resistant Prostate Cancer. Clin Genitourin Cancer. 2018;16(1):E223-31. https://doi.org/10.1016/j.clgc.2017.08.020

Edlind MP, Hsieh AC. PI3K-AKT-mTOR signaling in prostate cancer progression and androgen deprivation therapy resistance. Asian J Androl. 2014;16(3):378-86. https://doi.org/10.4103/1008-682X.122876

Shorning BY, Dass MS, Smalley MJ, Pearson HB. The PI3K-AKT-mTOR Pathway and Prostate Cancer: At the Crossroads of AR, MAPK, and WNT Signaling. Int J Mol Sci. 2020;21(12). https://doi.org/10.3390/ijms21124507

Farhan M, Wang H, Gaur U, Little PJ, Xu J, Zheng W. FOXO Signaling Pathways as Therapeutic Targets in Cancer. Int J Biol Sci. 2017;13(7):815-27. https://doi.org/10.7150/ijbs.20052

Ponting CP, Oliver PL, Reik W. Evolution and functions of long noncoding RNAs. Cell. 2009;136(4):629-41. https://doi.org/10.1016/j.cell.2009.02.006

Hao Y, Zhang L, Niu Y, Cai T, Luo J, He S, Zhang B, Zhang D, Qin Y, Yang F, Chen R. SmProt: a database of small proteins encoded by annotated coding and non-coding RNA loci. Brief Bioinform. 2018;19(4):636-43. https://doi.org/10.1093/bib/bbx005

Mitobe Y, Takayama KI, Horie-Inoue K, Inoue S. Prostate cancer-associated lncRNAs. Cancer Lett. 2018;418:159-66. https://doi.org/10.1016/j.canlet.2018.01.012

Chung S, Nakagawa H, Uemura M, Piao L, Ashikawa K, Hosono N, Takata R, Akamatsu S, Kawaguchi T, Morizono T, Tsunoda T, Daigo Y, Matsuda K, Kamatani N, Nakamura Y, Kubo M. Association of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility. Cancer Sci. 2011;102(1):245-52. https://doi.org/10.1111/j.1349-7006.2010.01737.x

Ramnarine VR, Kobelev M, Gibb EA, Nouri M, Lin D, Wang Y, Buttyan R, Davicioni E, Zoubeidi A, Collins CC. The evolution of long noncoding RNA acceptance in prostate cancer initiation, progression, and its clinical utility in disease management. Eur Urol. 2019;76(5):546-59. https://doi.org/10.1016/j.eururo.2019.07.040

Hua JT, Ahmed M, Guo H, Zhang Y, Chen S, Soares F, Lu J, Zhou S, Wang M, Li H, Larson NB, McDonnell SK, Patel PS, Liang Y, Yao CQ, van der Kwast T, Lupien M, Feng FY, Zoubeidi A, Tsao MS, Thibodeau SN, Boutros PC, He HH. Risk SNP-Mediated Promoter-Enhancer Switching Drives Prostate Cancer through lncRNA PCAT19. Cell. 2018;174(3):564-75. https://doi.org/10.1016/j.cell.2018.06.014

Zheng P, Li H, Xu P, Wang X, Shi Z, Han Q, Li Z. High lncRNA HULC expression is associated with poor prognosis and promotes tumor progression by regulating epithelial-mesenchymal transition in prostate cancer. Arch Med Sci. 2018;14(3):679-86. https://doi.org/10.5114/aoms.2017.69147

Zhang L, Zhang W, Li H, Tang X, Xu S, Wu M, Wan L, Su F, Zhang Y. Five Circular RNAs in Metabolism Pathways Related to Prostate Cancer. Front Genet. 2021;12:636419. https://doi.org/10.3389/fgene.2021.636419

Bian XJ, Zhang GM, Gu CY, Cai Y, Wang CF, Shen YJ, Zhu Y, Zhang HL, Dai B, Ye DW. Down-regulation of Dicer and Ago2 is associated with cell proliferation and apoptosis in prostate cancer. Tumour Biol. 2014;35(11):11571-8. https://doi.org/10.1007/s13277-014-2462-3

Santanam U, Banach-Petrosky W, Abate-Shen C, Shen MM, White E, DiPaola RS. Atg7 cooperates with Pten loss to drive prostate cancer tumor growth. Genes Dev. 2016;30(4):399-407. https://doi.org/10.1101/gad.274134.115

Mekhail SM, Yousef PG, Jackinsky SW, Pasic M, Yousef GM. miRNA in Prostate Cancer: New Prospects for Old Challenges. EJIFCC. 2014;25(1):79-98.

Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114-20. https://doi.org/10.1093/bioinformatics/btu170

Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blocker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J, International Human Genome Sequencing C. Initial sequencing and analysis of the human genome. Nature. 2001;409(6822):860-921.https://doi.org/10.1038/35057062

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15-21. https://doi.org/10.1093/bioinformatics/bts635

Teng X, Chen X, Xue H, Tang Y, Zhang P, Kang Q, Hao Y, Chen R, Zhao Y, He S. NPInter v4.0: an integrated database of ncRNA interactions. Nucleic Acids Res. 2020;48(D1):D160-5. https://doi.org/10.1093/nar/gkz969

Gong J, Shao D, Xu K, Lu Z, Lu ZJ, Yang YT, Zhang QC. RISE: a database of RNA interactome from sequencing experiments. Nucleic Acids Res. 2018;46(D1):D194-201. https://doi.org/10.1093/nar/gkx864

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498-504. https://doi.org/10.1101/gr.1239303

Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30(7):923-30. https://doi.org/10.1093/bioinformatics/btt656

Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139-40. https://doi.org/10.1093/bioinformatics/btp616

Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44-57. https://doi.org/10.1038/nprot.2008.211

Sun Y, Hu B, Wang Y, Li Z, Wu J, Yang Y, Wei Y, Peng X, Chen H, Chen R, Jiang P, Fang S, Yu Z, Guo L. miR-216a-5p inhibits malignant progression in small cell lung cancer: involvement of the Bcl-2 family proteins. Cancer Manag Res. 2018;10:4735-45. https://doi.org/10.2147/CMAR.S178380

Xing Z, Li S, Liu Z, Zhang C, Bai Z. CircSERPINA3 regulates SERPINA3-mediated apoptosis, autophagy and aerobic glycolysis of prostate cancer cells by competitively binding to MiR-653-5p and recruiting BUD13. J Transl Med. 2021;19(1):492. https://doi.org/10.1186/s12967-021-03063-2

Zhang J, Yang G, Li Q, Xie F. Increased fibrillarin expression is associated with tumor progression and an unfavorable prognosis in hepatocellular carcinoma. Oncol Lett. 2021;21(2):92. https://doi.org/10.3892/ol.2020.12353

Muller S, Glass M, Singh AK, Haase J, Bley N, Fuchs T, Lederer M, Dahl A, Huang H, Chen J, Posern G, Huttelmaier S. IGF2BP1 promotes SRF-dependent transcription in cancer in a m6A- and miRNA-dependent manner. Nucleic Acids Res. 2019;47(1):375-90. https://doi.org/10.1093/nar/gky1012

Ali A, Kulik G. Signaling Pathways That Control Apoptosis in Prostate Cancer. Cancers (Basel). 2021;13(5):937. https://doi.org/10.3390/cancers13050937

Murillo-Garzon V, Kypta R. WNT signalling in prostate cancer. Nat Rev Urol. 2017;14(11):683-96. https://doi.org/10.1038/nrurol.2017.144

Mirzaei S, Paskeh MDA, Okina E, Gholami MH, Hushmandi K, Hashemi M, Kalu A, Zarrabi A, Nabavi N, Rabiee N, Sharifi E, Karimi-Maleh H, Ashrafizadeh M, Kumar AP, Wang Y. Molecular Landscape of LncRNAs in Prostate Cancer: A focus on pathways and therapeutic targets for intervention. J Exp Clin Cancer Res. 2022;41(1):214. https://doi.org/10.1186/s13046-022-02406-1

Jiang G, Su Z, Liang X, Huang Y, Lan Z, Jiang X. Long non-coding RNAs in prostate tumorigenesis and therapy (Review). Mol Clin Oncol. 2020;13(6):76. https://doi.org/10.3892/mco.2020.2146

Ramnarine VR, Kobelev M, Gibb EA, Nouri M, Lin D, Wang Y, Buttyan R, Davicioni E, Zoubeidi A, Collins CC. The evolution of long noncoding RNA acceptance in prostate cancer initiation, progression, and its clinical utility in disease management. Eur Urol. 2019;76(5):546-59. https://doi.org/10.1016/j.eururo.2019.07.040

Chandra Gupta S, Nandan Tripathi Y. Potential of long non-coding RNAs in cancer patients: From biomarkers to therapeutic targets. Int J Cancer. 2017;140(9):1955-67. https://doi.org/10.1002/ijc.30546

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Published

2022-12-21

How to Cite

1.
Li H, Tang X, Sun G, Xu S, Wang L, Zhang L, Zhang Y, Su F, Zhang L, Zhang W. Differentially expressed AC077690.1, AL049874.3 and AP001037.1 lncRNAs in prostate cancer. Arch Biol Sci [Internet]. 2022Dec.21 [cited 2024Nov.22];74(4):359-66. Available from: https://serbiosoc.org.rs/arch/index.php/abs/article/view/8115

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Vol. 74 No. 4 (2022)

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Copyright (c) 2022 Li Hexin, Tang Xiaokun, Sun Gaoyuan, Xu Siyuan, Wang Luyao, Zhang Yaqun, Su Fei, Zhang Lili, Zhang Wei

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