Emerging role of transcription factor‑microRNA‑target gene feed‑forward loops in cancer (Review)
- Authors:
- Qian Wu
- Hua Qin
- Qiu Zhao
- Xing‑Xing He
-
Affiliations: Institute of Liver Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China - Published online on: June 11, 2015 https://doi.org/10.3892/br.2015.477
- Pages: 611-616
This article is mentioned in:
Abstract
 |
|
Siegel R, Naishadham D and Jemal A: Cancer statistics, 2012. CA Cancer J Clin. 62:10–29. 2012. View Article : Google Scholar : PubMed/NCBI | |
|
Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D and Alon U: Network motifs: Simple building blocks of complex networks. Science. 298:824–827. 2002. View Article : Google Scholar : PubMed/NCBI | |
|
Widder S, Solé R and Macía J: Evolvability of feed-forward loop architecture biases its abundance in transcription networks. BMC Syst Biol. 6:72012. View Article : Google Scholar : PubMed/NCBI | |
|
Shen-Orr SS, Milo R, Mangan S and Alon U: Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet. 31:64–68. 2002. View Article : Google Scholar : PubMed/NCBI | |
|
Re A, Corá D, Taverna D and Caselle M: Genome-wide survey of microRNA-transcription factor feed-forward regulatory circuits in human. Mol Biosyst. 5:854–867. 2009. View Article : Google Scholar : PubMed/NCBI | |
|
Ma HW, Kumar B, Ditges U, Gunzer F, Buer J and Zeng AP: An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs. Nucleic Acids Res. 32:6643–6649. 2004. View Article : Google Scholar : PubMed/NCBI | |
|
Mangan S and Alon U: Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci USA. 100:11980–11985. 2003. View Article : Google Scholar : PubMed/NCBI | |
|
He XX, Guo AY, Xu CR, et al: Bioinformatics analysis identifies miR-221 as a core regulator in hepatocellular carcinoma and its silencing suppresses tumor properties. Oncol Rep. 32:1200–1210. 2014.PubMed/NCBI | |
|
Yan JW, Lin JS and He XX: The emerging role of miR-375 in cancer. Int J Cancer. 135:1011–1018. 2014. View Article : Google Scholar : PubMed/NCBI | |
|
Li Y, Liang C, Easterbrook S, Luo J and Zhang Z: Investigating the functional implications of reinforcing feedback loops in transcriptional regulatory networks. Mol Biosys. 10:3238–3248. 2014. View Article : Google Scholar | |
|
Fujita Y, Komatsu N, Matsuda M and Aoki K: Fluorescence resonance energy transfer based quantitative analysis of feedforward and feedback loops in epidermal growth factor receptor signaling and the sensitivity to molecular targeting drugs. FEBS J. 281:3177–3192. 2014. View Article : Google Scholar : PubMed/NCBI | |
|
Hsieh WT, Tzeng KR, Ciou JS, Tsai JJ, Kurubanjerdjit N, Huang CH, et al: Transcription factor and microRNA-regulated network motifs for cancer and signal transduction networks. BMC Syst Biol. 9:(Suppl 1). S52015. View Article : Google Scholar : PubMed/NCBI | |
|
Latchman DS: Transcription factors: An overview. Int J Biochem Cell Biol. 29:1305–1312. 1997. View Article : Google Scholar : PubMed/NCBI | |
|
Mitchell PJ and Tjian R: Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins. Science. 245:371–378. 1989. View Article : Google Scholar : PubMed/NCBI | |
|
Ptashne M and Gann A: Transcriptional activation by recruitment. Nature. 386:569–577. 1997. View Article : Google Scholar : PubMed/NCBI | |
|
van Nimwegen E: Scaling laws in the functional content of genomes. Trends Genet. 19:479–484. 2003. View Article : Google Scholar : PubMed/NCBI | |
|
Lane D and Levine A: p53 Research: The past thirty years and the next thirty years. Cold Spring Harb Perspect Biol. 2:a0008932010. View Article : Google Scholar : PubMed/NCBI | |
|
Hainaut P and Wiman KG: 30 years and a long way into p53 research. Lancet Oncol. 10:913–919. 2009. View Article : Google Scholar : PubMed/NCBI | |
|
Hermeking H: p53 enters the microRNA world. Cancer Cell. 12:414–418. 2007. View Article : Google Scholar : PubMed/NCBI | |
|
Brosh R, Shalgi R, Liran A, Landan G, Korotayev K, Nguyen GH, Enerly E, Johnsen H, Buganim Y, Solomon H, et al: p53-Repressed miRNAs are involved with E2F in a feed-forward loop promoting proliferation. Mol Syst Biol. 4:2292008. View Article : Google Scholar : PubMed/NCBI | |
|
Altshuler ML, Severin SE and Glukhov AI: The tumor cell and telomerase. Biochemistry (Mosc). 68:1275–1283. 2003. View Article : Google Scholar : PubMed/NCBI | |
|
Sanda T, Lawton LN, Barrasa MI, Fan ZP, Kohlhammer H, Gutierrez A, Ma W, Tatarek J, Ahn Y, Kelliher MA, et al: Core transcriptional regulatory circuit controlled by the TAL1 complex in human T cell acute lymphoblastic leukemia. Cancer Cell. 22:209–221. 2012. View Article : Google Scholar : PubMed/NCBI | |
|
Bartel DP: MicroRNAs: Target recognition and regulatory functions. Cell. 136:215–233. 2009. View Article : Google Scholar : PubMed/NCBI | |
|
Lujambio A and Lowe SW: The microcosmos of cancer. Nature. 482:347–355. 2012. View Article : Google Scholar : PubMed/NCBI | |
|
Calin GA and Croce CM: MicroRNA-cancer connection: The beginning of a new tale. Cancer Res. 66:7390–7394. 2006. View Article : Google Scholar : PubMed/NCBI | |
|
Lewis BP, Burge CB and Bartel DP: Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 120:15–20. 2005. View Article : Google Scholar : PubMed/NCBI | |
|
Eiring AM, Harb JG, Neviani P, Garton C, Oaks JJ, Spizzo R, Liu S, Schwind S, Santhanam R, Hickey CJ, et al: miR-328 functions as an RNA decoy to modulate hnRNP E2 regulation of mRNA translation in leukemic blasts. Cell. 140:652–665. 2010. View Article : Google Scholar : PubMed/NCBI | |
|
Moretti F, Thermann R and Hentze MW: Mechanism of translational regulation by miR-2 from sites in the 5′ untranslated region or the open reading frame. RNA. 16:2493–2502. 2010. View Article : Google Scholar : PubMed/NCBI | |
|
Shalgi R, Brosh R, Oren M, Pilpel Y and Rotter V: Coupling transcriptional and post-transcriptional miRNA regulation in the control of cell fate. Aging (Albany NY). 1:762–770. 2009.PubMed/NCBI | |
|
Johnson SM, Grosshans H, Shingara J, Byrom M, Jarvis R, Cheng A, Labourier E, Reinert KL, Brown D and Slack FJ: RAS is regulated by the let-7 microRNA family. Cell. 120:635–647. 2005. View Article : Google Scholar : PubMed/NCBI | |
|
Burk U, Schubert J, Wellner U, Schmalhofer O, Vincan E, Spaderna S and Brabletz T: A reciprocal repression between ZEB1 and members of the miR-200 family promotes EMT and invasion in cancer cells. EMBO Rep. 9:582–589. 2008. View Article : Google Scholar : PubMed/NCBI | |
|
Hwang CI, Choi J, Zhou Z, Flesken-Nikitin A, Tarakhovsky A and Nikitin AY: MET-dependent cancer invasion may be preprogrammed by early alterations of p53-regulated feedforward loop and triggered by stromal cell-derived HGF. Cell Cycle. 10:3834–3840. 2011. View Article : Google Scholar : PubMed/NCBI | |
|
Avraham R and Yarden Y: Regulation of signalling by microRNAs. Biochem Soc Trans. 40:26–30. 2012. View Article : Google Scholar : PubMed/NCBI | |
|
Kobayashi K, Sakurai K, Hiramatsu H, Inada K, Shiogama K, Nakamura S, et al: The miR-199a/Brm/EGR1 axis is a determinant of anchorage-independent growth in epithelial tumor cell lines. Sci Rep. 5:84282015. View Article : Google Scholar : PubMed/NCBI | |
|
He L, Thomson JM, Hemann MT, Hernando-Monge E, Mu D, Goodson S, Powers S, Cordon-Cardo C, Lowe SW, Hannon GJ, et al: A microRNA polycistron as a potential human oncogene. Nature. 435:828–833. 2005. View Article : Google Scholar : PubMed/NCBI | |
|
Garzon R, Marcucci G and Croce CM: Targeting microRNAs in cancer: Rationale, strategies and challenges. Nat Rev Drug Discov. 9:775–789. 2010. View Article : Google Scholar : PubMed/NCBI | |
|
Song S and Ajani JA: The role of microRNAs in cancers of the upper gastrointestinal tract. Nat Rev Gastroenterol Hepatol. 10:109–118. 2013. View Article : Google Scholar : PubMed/NCBI | |
|
Chang TC, Yu D, Lee YS, Wentzel EA, Arking DE, West KM, Dang CV, Thomas-Tikhonenko A and Mendell JT: Widespread microRNA repression by Myc contributes to tumorigenesis. Nat Genet. 40:43–50. 2008. View Article : Google Scholar : PubMed/NCBI | |
|
Jiang X, Huang H, Li Z, Li Y, Wang X, Gurbuxani S, et al: Blockade of miR-150 maturation by MLL-fusion/MYC/LIN-28 is required for MLL-associated leukemia. Cancer Cell. 22:524–535. 2012. View Article : Google Scholar : PubMed/NCBI | |
|
Musilova K and Mraz M: MicroRNAs in B-cell lymphomas: How a complex biology gets more complex. Leukemia. 29:1004–1017. 2015. View Article : Google Scholar : PubMed/NCBI | |
|
Zhao X, Lwin T, Zhang X, Huang A, Wang J, Marquez VE, Chen-Kiang S, Dalton WS, Sotomayor E and Tao J: Disruption of the MYC-miRNA-EZH2 loop to suppress aggressive B-cell lymphoma survival and clonogenicity. Leukemia. 27:2341–2350. 2013. View Article : Google Scholar : PubMed/NCBI | |
|
O'Donnell KA, Wentzel EA, Zeller KI, Dang CV and Mendell JT: c-Myc-regulated microRNAs modulate E2F1 expression. Nature. 435:839–843. 2005. View Article : Google Scholar : PubMed/NCBI | |
|
Ning Z, Wang A, Liang J, et al: USP22 promotes epithelial-mesenchymal transition via the FAK pathway in pancreatic cancer cells. Oncol Rep. 32:1451–1458. 2014.PubMed/NCBI | |
|
Kent OA, Chivukula RR, Mullendore M, Wentzel EA, Feldmann G, Lee KH, Liu S, Leach SD, Maitra A and Mendell JT: Repression of the miR-143/145 cluster by oncogenic Ras initiates a tumor-promoting feed-forward pathway. Genes Dev. 24:2754–2759. 2010. View Article : Google Scholar : PubMed/NCBI | |
|
El Baroudi M, Corà D, Bosia C, Osella M and Caselle M: A curated database of miRNA mediated feed-forward loops involving MYC as master regulator. PLoS One. 6:e147422011. View Article : Google Scholar : PubMed/NCBI | |
|
Polioudakis D, Bhinge AA, Killion PJ, Lee BK, Abell NS and Iyer VR: A Myc-microRNA network promotes exit from quiescence by suppressing the interferon response and cell-cycle arrest genes. Nucleic Acids Res. 41:2239–2254. 2013. View Article : Google Scholar : PubMed/NCBI | |
|
He L, He X, Lim LP, de Stanchina E, Xuan Z, Liang Y, Xue W, Zender L, Magnus J, Ridzon D, et al: A microRNA component of the p53 tumour suppressor network. Nature. 447:1130–1134. 2007. View Article : Google Scholar : PubMed/NCBI | |
|
Lin CJ, Cencic R, Mills JR, Robert F and Pelletier J: c-Myc and eIF4F are components of a feedforward loop that links transcription and translation. Cancer Res. 68:5326–5334. 2008. View Article : Google Scholar : PubMed/NCBI | |
|
Lin CJ, Malina A and Pelletier J: c-Myc and eIF4F constitute a feedforward loop that regulates cell growth: Implications for anticancer therapy. Cancer Res. 69:7491–7494. 2009. View Article : Google Scholar : PubMed/NCBI | |
|
Cohen EE and Rosner MR: MicroRNA-regulated feed forward loop network. Cell Cycle. 8:2477–2478. 2009. View Article : Google Scholar : PubMed/NCBI | |
|
Cohen EE, Zhu H, Lingen MW, Martin LE, Kuo WL, Choi EA, Kocherginsky M, Parker JS, Chung CH and Rosner MR: A feed-forward loop involving protein kinase Calpha and microRNAs regulates tumor cell cycle. Cancer Res. 69:65–74. 2009. View Article : Google Scholar : PubMed/NCBI | |
|
Rokavec M, Wu W and Luo J-L: IL6-mediated suppression of miR-200c directs constitutive activation of inflammatory signaling circuit driving transformation and tumorigenesis. Mol Cell. 45:777–789. 2012. View Article : Google Scholar : PubMed/NCBI | |
|
Alexiou P, Maragkakis M, Papadopoulos GL, Reczko M and Hatzigeorgiou AG: Lost in translation: An assessment and perspective for computational microRNA target identification. Bioinformatics. 25:3049–3055. 2009. View Article : Google Scholar : PubMed/NCBI | |
|
Reyes-Herrera PH and Ficarra E: One decade of development and evolution of microRNA target prediction algorithms. Genomics Proteomics Bioinformatics. 10:254–263. 2012. View Article : Google Scholar : PubMed/NCBI | |
|
Mendes ND, Freitas AT and Sagot MF: Current tools for the identification of miRNA genes and their targets. Nucleic Acids Res. 37:2419–2433. 2009. View Article : Google Scholar : PubMed/NCBI | |
|
Nazarov PV, Reinsbach SE, Muller A, Nicot N, Philippidou D, Vallar L and Kreis S: Interplay of microRNAs, transcription factors and target genes: Linking dynamic expression changes to function. Nucleic Acids Res. 41:2817–2831. 2013. View Article : Google Scholar : PubMed/NCBI | |
|
Dubchak I, Munoz M, Poliakov A, Salomonis N, Minovitsky S, Bodmer R and Zambon AC: Whole-Genome rVISTA: A tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data. Bioinformatics. 29:2059–2061. 2013. View Article : Google Scholar : PubMed/NCBI | |
|
Krystkowiak I, Lenart J, Debski K, Kuterba P, Petas M, Kaminska B and Dabrowski M: Nencki Genomics Database - Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs. Database (Oxford). 2013:bat0692013. View Article : Google Scholar : PubMed/NCBI | |
|
Jiang C, Xuan Z, Zhao F and Zhang MQ: TRED: A transcriptional regulatory element database, new entries and other development. Nucleic Acids Res. 35:(Database). D137–D140. 2007. View Article : Google Scholar : PubMed/NCBI | |
|
Yamashita R, Sugano S, Suzuki Y and Nakai K: DBTSS: DataBase of Transcriptional Start Sites progress report in 2012. Nucleic Acids Res. 40:(D1). D150–D154. 2012. View Article : Google Scholar : PubMed/NCBI | |
|
Kolchanov NA, Podkolodnaia OA, Anan'ko EA, Ignat'eva EV, Podkolodnyĭ NL, Merkulov VM, Stepanenko IL, Pozdniakov MA, Belova OE, Grigorovich DA, et al: Regulation of eukaryotic gene transcription: Description in the TRRD database. Mol Biol (Mosk). 35:934–942. 2001.(In Russian). PubMed/NCBI | |
|
Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, et al: Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods. 4:651–657. 2007. View Article : Google Scholar : PubMed/NCBI | |
|
Perez-Pinera P, Ousterout DG, Brunger JM, Farin AM, Glass KA, Guilak F, Crawford GE, Hartemink AJ and Gersbach CA: Synergistic and tunable human gene activation by combinations of synthetic transcription factors. Nat Methods. 10:239–242. 2013. View Article : Google Scholar : PubMed/NCBI | |
|
Hesselberth JR, Chen X, Zhang Z, Sabo PJ, Sandstrom R, Reynolds AP, Thurman RE, Neph S, Kuehn MS, Noble WS, et al: Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods. 6:283–289. 2009. View Article : Google Scholar : PubMed/NCBI | |
|
Hellman LM and Fried MG: Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions. Nat Protoc. 2:1849–1861. 2007. View Article : Google Scholar : PubMed/NCBI | |
|
Fernandez PC, Frank SR, Wang L, Schroeder M, Liu S, Greene J, Cocito A and Amati B: Genomic targets of the human c-Myc protein. Genes Dev. 17:1115–1129. 2003. View Article : Google Scholar : PubMed/NCBI | |
|
Wang J, Lu M, Qiu C and Cui Q: TransmiR: A transcription factor-microRNA regulation database. Nucleic Acids Res. 38:(Database). D119–D122. 2010. View Article : Google Scholar : PubMed/NCBI | |
|
Yan Z, Shah PK, Amin SB, Samur MK, Huang N, Wang X, Misra V, Ji H, Gabuzda D and Li C: Integrative analysis of gene and miRNA expression profiles with transcription factor-miRNA feed-forward loops identifies regulators in human cancers. Nucleic Acids Res. 40:e1352012. View Article : Google Scholar : PubMed/NCBI | |
|
Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ and Pandolfi PP: A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature. 465:1033–1038. 2010. View Article : Google Scholar : PubMed/NCBI |
