RNA Binding Protein FXR1-miR301a-3p axis contributes to p21WAF1 degradation in oral cancer
Autoři:
Mrinmoyee Majumder aff001; Viswanathan Palanisamy aff001
Působiště autorů:
Department of Biochemistry and Molecular Biology, College of Medicine, Medical University of South Carolina, Charleston, SC, United States of America
aff001
Vyšlo v časopise:
RNA Binding Protein FXR1-miR301a-3p axis contributes to p21WAF1 degradation in oral cancer. PLoS Genet 16(1): e32767. doi:10.1371/journal.pgen.1008580
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pgen.1008580
Souhrn
RNA-binding proteins (RBPs) associate with the primary, precursor, and mature microRNAs, which in turn control post-transcriptional gene regulation. Here, by small RNAseq, we show that RBP FXR1 controls the expression of a subset of mature miRNAs, including highly expressed miR301a-3p in oral cancer cells. We also confirm that FXR1 controls the stability of miR301a-3p. Exoribonuclease PNPT1 degrades miR301a-3p in the absence of FXR1 in oral cancer cells, and the degradation is rescued in the FXR1 and PNPT1 co-knockdown cells. In vitro, we show that PNPT1 is unable to bind and degrade the miRNA once the FXR1-miRNA complex forms. Both miR301a-3p and FXR1 cooperatively target the 3'-UTR of p21 mRNA to promote its degradation. Thus, our work illustrates the unique role of FXR1 that is critical for the stability of a subset of mature miRNAs or at least miR301a-3p to target p21 in oral cancer.
Klíčová slova:
Actins – Cancer treatment – Head and neck squamous cell carcinoma – Luciferase – Messenger RNA – MicroRNAs – Recombinant proteins – RNA-binding proteins
Zdroje
1. Bechara E, Davidovic L, Melko M, Bensaid M, Tremblay S, Grosgeorge J, et al. Fragile X related protein 1 isoforms differentially modulate the affinity of fragile X mental retardation protein for G-quartet RNA structure. Nucleic acids research. 2007;35(1):299–306. doi: 10.1093/nar/gkl1021 17170008; PubMed Central PMCID: PMC1802556.
2. Schaeffer C, Bardoni B, Mandel JL, Ehresmann B, Ehresmann C, Moine H. The fragile X mental retardation protein binds specifically to its mRNA via a purine quartet motif. The EMBO journal. 2001;20(17):4803–13. Epub 2001/09/05. doi: 10.1093/emboj/20.17.4803 11532944; PubMed Central PMCID: PMC125594.
3. Vasudevan S, Steitz JA. AU-rich-element-mediated upregulation of translation by FXR1 and Argonaute 2. Cell. 2007;128(6):1105–18. doi: 10.1016/j.cell.2007.01.038 17382880; PubMed Central PMCID: PMC3430382.
4. Tamanini F, Willemsen R, van Unen L, Bontekoe C, Galjaard H, Oostra BA, et al. Differential expression of FMR1, FXR1 and FXR2 proteins in human brain and testis. Human molecular genetics. 1997;6(8):1315–22. doi: 10.1093/hmg/6.8.1315 9259278.
5. Adams-Cioaba MA, Guo Y, Bian C, Amaya MF, Lam R, Wasney GA, et al. Structural studies of the tandem Tudor domains of fragile X mental retardation related proteins FXR1 and FXR2. PloS one. 2010;5(11):e13559. Epub 2010/11/13. doi: 10.1371/journal.pone.0013559 21072162; PubMed Central PMCID: PMC2970552.
6. Darnell JC, Fraser CE, Mostovetsky O, Darnell RB. Discrimination of common and unique RNA-binding activities among Fragile X mental retardation protein paralogs. Human molecular genetics. 2009;18(17):3164–77. Epub 2009/06/03. doi: 10.1093/hmg/ddp255 19487368; PubMed Central PMCID: PMC2722981.
7. Zarnescu DC, Gregorio CC. Fragile hearts: new insights into translational control in cardiac muscle. Trends in cardiovascular medicine. 2013;23(8):275–81. doi: 10.1016/j.tcm.2013.03.003 23582851; PubMed Central PMCID: PMC4142197.
8. Ambros V. microRNAs: tiny regulators with great potential. Cell. 2001;107(7):823–6. doi: 10.1016/s0092-8674(01)00616-x 11779458.
9. Macfarlane LA, Murphy PR. MicroRNA: Biogenesis, Function and Role in Cancer. Current genomics. 2010;11(7):537–61. doi: 10.2174/138920210793175895 21532838; PubMed Central PMCID: PMC3048316.
10. Pratt AJ, MacRae IJ. The RNA-induced silencing complex: a versatile gene-silencing machine. The Journal of biological chemistry. 2009;284(27):17897–901. doi: 10.1074/jbc.R900012200 19342379; PubMed Central PMCID: PMC2709356.
11. Ciafre SA, Galardi S. microRNAs and RNA-binding proteins: a complex network of interactions and reciprocal regulations in cancer. RNA biology. 2013;10(6):935–42. doi: 10.4161/rna.24641 23696003; PubMed Central PMCID: PMC4111733.
12. Loffreda A, Rigamonti A, Barabino SM, Lenzken SC. RNA-Binding Proteins in the Regulation of miRNA Activity: A Focus on Neuronal Functions. Biomolecules. 2015;5(4):2363–87. doi: 10.3390/biom5042363 26437437; PubMed Central PMCID: PMC4693239.
13. Nussbacher JK, Yeo GW. Systematic Discovery of RNA Binding Proteins that Regulate MicroRNA Levels. Molecular cell. 2018;69(6):1005–16 e7. doi: 10.1016/j.molcel.2018.02.012 29547715.
14. van Kouwenhove M, Kedde M, Agami R. MicroRNA regulation by RNA-binding proteins and its implications for cancer. Nature reviews Cancer. 2011;11(9):644–56. Epub 2011/08/09. doi: 10.1038/nrc3107 21822212.
15. Winter J, Jung S, Keller S, Gregory RI, Diederichs S. Many roads to maturity: microRNA biogenesis pathways and their regulation. Nature cell biology. 2009;11(3):228–34. doi: 10.1038/ncb0309-228 19255566.
16. Cheever A, Ceman S. Translation regulation of mRNAs by the fragile X family of proteins through the microRNA pathway. RNA biology. 2009;6(2):175–8. doi: 10.4161/rna.6.2.8196 19276651; PubMed Central PMCID: PMC4337776.
17. Gantier MP, McCoy CE, Rusinova I, Saulep D, Wang D, Xu D, et al. Analysis of microRNA turnover in mammalian cells following Dicer1 ablation. Nucleic acids research. 2011;39(13):5692–703. doi: 10.1093/nar/gkr148 21447562; PubMed Central PMCID: PMC3141258.
18. Guo Y, Liu J, Elfenbein SJ, Ma Y, Zhong M, Qiu C, et al. Characterization of the mammalian miRNA turnover landscape. Nucleic acids research. 2015;43(4):2326–41. doi: 10.1093/nar/gkv057 25653157; PubMed Central PMCID: PMC4344502.
19. Ha M, Kim VN. Regulation of microRNA biogenesis. Nat Rev Mol Cell Biol. 2014;15(8):509–24. Epub 2014/07/17. doi: 10.1038/nrm3838 25027649.
20. Krol J, Busskamp V, Markiewicz I, Stadler MB, Ribi S, Richter J, et al. Characterizing light-regulated retinal microRNAs reveals rapid turnover as a common property of neuronal microRNAs. Cell. 2010;141(4):618–31. doi: 10.1016/j.cell.2010.03.039 20478254.
21. Frixa T, Donzelli S, Blandino G. Oncogenic MicroRNAs: Key Players in Malignant Transformation. Cancers. 2015;7(4):2466–85. doi: 10.3390/cancers7040904 26694467; PubMed Central PMCID: PMC4695904.
22. Park JK, Henry JC, Jiang J, Esau C, Gusev Y, Lerner MR, et al. miR-132 and miR-212 are increased in pancreatic cancer and target the retinoblastoma tumor suppressor. Biochemical and biophysical research communications. 2011;406(4):518–23. doi: 10.1016/j.bbrc.2011.02.065 21329664; PubMed Central PMCID: PMC3069485.
23. Baumhoer D, Zillmer S, Unger K, Rosemann M, Atkinson MJ, Irmler M, et al. MicroRNA profiling with correlation to gene expression revealed the oncogenic miR-17-92 cluster to be up-regulated in osteosarcoma. Cancer genetics. 2012;205(5):212–9. doi: 10.1016/j.cancergen.2012.03.001 22682620.
24. Pallante P, Visone R, Ferracin M, Ferraro A, Berlingieri MT, Troncone G, et al. MicroRNA deregulation in human thyroid papillary carcinomas. Endocrine-related cancer. 2006;13(2):497–508. doi: 10.1677/erc.1.01209 16728577.
25. Ciafre SA, Galardi S, Mangiola A, Ferracin M, Liu CG, Sabatino G, et al. Extensive modulation of a set of microRNAs in primary glioblastoma. Biochemical and biophysical research communications. 2005;334(4):1351–8. doi: 10.1016/j.bbrc.2005.07.030 16039986.
26. Caudy AA, Myers M, Hannon GJ, Hammond SM. Fragile X-related protein and VIG associate with the RNA interference machinery. Genes & development. 2002;16(19):2491–6. doi: 10.1101/gad.1025202 12368260; PubMed Central PMCID: PMC187452.
27. Edbauer D, Neilson JR, Foster KA, Wang CF, Seeburg DP, Batterton MN, et al. Regulation of synaptic structure and function by FMRP-associated microRNAs miR-125b and miR-132. Neuron. 2010;65(3):373–84. doi: 10.1016/j.neuron.2010.01.005 20159450; PubMed Central PMCID: PMC5018398.
28. Gessert S, Bugner V, Tecza A, Pinker M, Kuhl M. FMR1/FXR1 and the miRNA pathway are required for eye and neural crest development. Developmental biology. 2010;341(1):222–35. doi: 10.1016/j.ydbio.2010.02.031 20197067.
29. Jin P, Alisch RS, Warren ST. RNA and microRNAs in fragile X mental retardation. Nature cell biology. 2004;6(11):1048–53. doi: 10.1038/ncb1104-1048 15516998.
30. Wan RP, Zhou LT, Yang HX, Zhou YT, Ye SH, Zhao QH, et al. Involvement of FMRP in Primary MicroRNA Processing via Enhancing Drosha Translation. Molecular neurobiology. 2017;54(4):2585–94. doi: 10.1007/s12035-016-9855-9 26993298.
31. Liu T, Wan RP, Tang LJ, Liu SJ, Li HJ, Zhao QH, et al. A MicroRNA Profile in Fmr1 Knockout Mice Reveals MicroRNA Expression Alterations with Possible Roles in Fragile X Syndrome. Molecular neurobiology. 2015;51(3):1053–63. Epub 2014/06/08. doi: 10.1007/s12035-014-8770-1 24906954.
32. Bukhari SIA, Truesdell SS, Lee S, Kollu S, Classon A, Boukhali M, et al. A Specialized Mechanism of Translation Mediated by FXR1a-Associated MicroRNP in Cellular Quiescence. Molecular cell. 2016;61(5):760–73. doi: 10.1016/j.molcel.2016.02.013 26942679; PubMed Central PMCID: PMC4811377.
33. Jin P, Zarnescu DC, Ceman S, Nakamoto M, Mowrey J, Jongens TA, et al. Biochemical and genetic interaction between the fragile X mental retardation protein and the microRNA pathway. Nature neuroscience. 2004;7(2):113–7. doi: 10.1038/nn1174 14703574.
34. Majumder M, House R, Palanisamy N, Qie S, Day TA, Neskey D, et al. RNA-Binding Protein FXR1 Regulates p21 and TERC RNA to Bypass p53-Mediated Cellular Senescence in OSCC. PLoS genetics. 2016;12(9):e1006306. Epub 2016/09/09. doi: 10.1371/journal.pgen.1006306 27606879; PubMed Central PMCID: PMC5015924.
35. Qian J, Hassanein M, Hoeksema MD, Harris BK, Zou Y, Chen H, et al. The RNA binding protein FXR1 is a new driver in the 3q26-29 amplicon and predicts poor prognosis in human cancers. Proc Natl Acad Sci U S A. 2015;112(11):3469–74. Epub 2015/03/04. doi: 10.1073/pnas.1421975112 25733852; PubMed Central PMCID: PMC4371932.
36. Goldman M, Craft B, Kamath A, Brooks AN, Zhu J, Haussler D. The UCSC Xena Platform for cancer genomics data visualization and interpretation. BioRxiv. 2018:326470.
37. Li Y, Lin L, Jin P. The microRNA pathway and fragile X mental retardation protein. Biochim Biophys Acta. 2008;1779(11):702–5. Epub 2008/08/09. doi: 10.1016/j.bbagrm.2008.07.003 18687414; PubMed Central PMCID: PMC2607293.
38. Tian H, Cao YX, Zhang XS, Liao WP, Yi YH, Lian J, et al. The targeting and functions of miRNA-383 are mediated by FMRP during spermatogenesis. Cell Death Dis. 2013;4:e617. Epub 2013/05/04. doi: 10.1038/cddis.2013.138 23640459; PubMed Central PMCID: PMC3674347.
39. Bail S, Swerdel M, Liu H, Jiao X, Goff LA, Hart RP, et al. Differential regulation of microRNA stability. Rna. 2010;16(5):1032–9. doi: 10.1261/rna.1851510 20348442; PubMed Central PMCID: PMC2856875.
40. Winter J, Diederichs S. Argonaute proteins regulate microRNA stability: Increased microRNA abundance by Argonaute proteins is due to microRNA stabilization. RNA biology. 2011;8(6):1149–57. Epub 2011/09/24. doi: 10.4161/rna.8.6.17665 21941127.
41. Hasan A, Cotobal C, Duncan CD, Mata J. Systematic analysis of the role of RNA-binding proteins in the regulation of RNA stability. PLoS genetics. 2014;10(11):e1004684. doi: 10.1371/journal.pgen.1004684 25375137; PubMed Central PMCID: PMC4222612.
42. Ruegger S, Grosshans H. MicroRNA turnover: when, how, and why. Trends in biochemical sciences. 2012;37(10):436–46. doi: 10.1016/j.tibs.2012.07.002 22921610.
43. Zhang Z, Qin YW, Brewer G, Jing Q. MicroRNA degradation and turnover: regulating the regulators. Wiley interdisciplinary reviews RNA. 2012;3(4):593–600. doi: 10.1002/wrna.1114 22461385; PubMed Central PMCID: PMC3635675.
44. Das SK, Sokhi UK, Bhutia SK, Azab B, Su ZZ, Sarkar D, et al. Human polynucleotide phosphorylase selectively and preferentially degrades microRNA-221 in human melanoma cells. Proceedings of the National Academy of Sciences of the United States of America. 2010;107(26):11948–53. Epub 2010/06/16. doi: 10.1073/pnas.0914143107 20547861; PubMed Central PMCID: PMC2900648.
45. Li X, Li J, Cai Y, Peng S, Wang J, Xiao Z, et al. Hyperglycaemia-induced miR-301a promotes cell proliferation by repressing p21 and Smad4 in prostate cancer. Cancer Lett. 2018;418:211–20. Epub 2018/01/15. doi: 10.1016/j.canlet.2018.01.031 29331421.
46. Fillies T, Woltering M, Brandt B, Van Diest JP, Werkmeister R, Joos U, et al. Cell cycle regulating proteins p21 and p27 in prognosis of oral squamous cell carcinomas. Oncol Rep. 2007;17(2):355–9. Epub 2007/01/05. 17203174.
47. Chen AJ, Paik JH, Zhang H, Shukla SA, Mortensen R, Hu J, et al. STAR RNA-binding protein Quaking suppresses cancer via stabilization of specific miRNA. Genes & development. 2012;26(13):1459–72. doi: 10.1101/gad.189001.112 22751500; PubMed Central PMCID: PMC3403014.
48. Lu Y, Gao W, Zhang C, Wen S, Huangfu H, Kang J, et al. Hsa-miR-301a-3p Acts as an Oncogene in Laryngeal Squamous Cell Carcinoma via Target Regulation of Smad4. J Cancer. 2015;6(12):1260–75. Epub 2015/12/08. doi: 10.7150/jca.12659 26640587; PubMed Central PMCID: PMC4643083.
49. Zhang L, Zhang Y, Zhu H, Sun X, Wang X, Wu P, et al. Overexpression of miR-301a-3p promotes colorectal cancer cell proliferation and metastasis by targeting deleted in liver cancer-1 and runt-related transcription factor 3. J Cell Biochem. 2019;120(4):6078–89. Epub 2018/10/27. doi: 10.1002/jcb.27894 30362160.
50. Zheng JZ, Huang YN, Yao L, Liu YR, Liu S, Hu X, et al. Elevated miR-301a expression indicates a poor prognosis for breast cancer patients. Sci Rep. 2018;8(1):2225. Epub 2018/02/06. doi: 10.1038/s41598-018-20680-y 29396508; PubMed Central PMCID: PMC5797194.
51. Stoecklin G, Mayo T, Anderson P. ARE-mRNA degradation requires the 5'-3' decay pathway. EMBO reports. 2006;7(1):72–7. doi: 10.1038/sj.embor.7400572 16299471; PubMed Central PMCID: PMC1369226.
52. Behm-Ansmant I, Rehwinkel J, Doerks T, Stark A, Bork P, Izaurralde E. mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes. Genes & development. 2006;20(14):1885–98. doi: 10.1101/gad.1424106 16815998; PubMed Central PMCID: PMC1522082.
53. Lykke-Andersen J, Wagner E. Recruitment and activation of mRNA decay enzymes by two ARE-mediated decay activation domains in the proteins TTP and BRF-1. Genes & development. 2005;19(3):351–61. doi: 10.1101/gad.1282305 15687258; PubMed Central PMCID: PMC546513.
54. Jiang P, Coller H. Functional interactions between microRNAs and RNA binding proteins. MicroRNA. 2012;1(1):70–9. doi: 10.2174/2211536611201010070 25048093; PubMed Central PMCID: PMC5123774.
55. Galardi S, Mercatelli N, Giorda E, Massalini S, Frajese GV, Ciafre SA, et al. miR-221 and miR-222 expression affects the proliferation potential of human prostate carcinoma cell lines by targeting p27Kip1. The Journal of biological chemistry. 2007;282(32):23716–24. doi: 10.1074/jbc.M701805200 17569667.
56. Liu X, Fu R, Pan Y, Meza-Sosa KF, Zhang Z, Lieberman J. PNPT1 Release from Mitochondria during Apoptosis Triggers Decay of Poly(A) RNAs. Cell. 2018;174(1):187–201 e12. Epub 2018/05/22. doi: 10.1016/j.cell.2018.04.017 29779946.
57. el-Deiry WS, Tokino T, Velculescu VE, Levy DB, Parsons R, Trent JM, et al. WAF1, a potential mediator of p53 tumor suppression. Cell. 1993;75(4):817–25. Epub 1993/11/19. doi: 10.1016/0092-8674(93)90500-p 8242752.
58. Davis-Turak J, Courtney SM, Hazard ES, Glen WB Jr., da Silveira WA, Wesselman T, et al. Genomics pipelines and data integration: challenges and opportunities in the research setting. Expert Rev Mol Diagn. 2017;17(3):225–37. Epub 2017/01/17. doi: 10.1080/14737159.2017.1282822 28092471; PubMed Central PMCID: PMC5580401.
59. Andrews S. FASTQC A JAVA-based quality control tool for high throughput sequence data. 2010. Available from: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
60. Martin M. Cutadapt removes adapter sequences from high-throughput seqeunceing reads. EMBnetjournal. 17.1:3. doi: 10.14806/ej.17.1.200
61. Sun Z, Evans J, Bhagwate A, Middha S, Bockol M, Yan H, et al. CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data. BMC Genomics. 2014;15:423. Epub 2014/06/05. doi: 10.1186/1471-2164-15-423 24894665; PubMed Central PMCID: PMC4070549.
62. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25. Epub 2009/03/06. doi: 10.1186/gb-2009-10-3-r25 19261174; PubMed Central PMCID: PMC2690996.
63. Anders S, Reyes A, Huber W. Detecting differential usage of exons from RNA-seq data. Genome Res. 2012;22(10):2008–17. Epub 2012/06/23. doi: 10.1101/gr.133744.111 22722343; PubMed Central PMCID: PMC3460195.
64. Walker MA, Pedamallu CS, Ojesina AI, Bullman S, Sharpe T, Whelan CW, et al. GATK PathSeq: A customizable computational tool for the discovery and identification of microbial sequences in libraries from eukaryotic hosts. Bioinformatics. 2018. Epub 2018/07/10. doi: 10.1093/bioinformatics/bty501 29982281.
65. Friedlander MR, Mackowiak SD, Li N, Chen W, Rajewsky N. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic acids research. 2012;40(1):37–52. Epub 2011/09/14. doi: 10.1093/nar/gkr688 21911355; PubMed Central PMCID: PMC3245920.
66. Nikolayeva O, Robinson MD. edgeR for differential RNA-seq and ChIP-seq analysis: an application to stem cell biology. Methods Mol Biol. 2014;1150:45–79. Epub 2014/04/20. doi: 10.1007/978-1-4939-0512-6_3 24743990.
67. Talwar S, Jin J, Carroll B, Liu A, Gillespie MB, Palanisamy V. Caspase-mediated cleavage of RNA-binding protein HuR regulates c-Myc protein expression after hypoxic stress. The Journal of biological chemistry. 2011;286(37):32333–43. doi: 10.1074/jbc.M111.255927 21795698; PubMed Central PMCID: PMC3173192.
68. Han J, Lee Y, Yeom KH, Kim YK, Jin H, Kim VN. The Drosha-DGCR8 complex in primary microRNA processing. Genes & development. 2004;18(24):3016–27. doi: 10.1101/gad.1262504 15574589; PubMed Central PMCID: PMC535913.
69. Evans TL, Mihailescu MR. Recombinant bacterial expression and purification of human fragile X mental retardation protein isoform 1. Protein Expr Purif. 2010;74(2):242–7. Epub 2010/06/15. doi: 10.1016/j.pep.2010.06.002 20541608; PubMed Central PMCID: PMC2952666.
Štítky
Genetika Reprodukční medicínaČlánek vyšel v časopise
PLOS Genetics
2020 Číslo 1
Nejčtenější v tomto čísle
- Autophagy gene haploinsufficiency drives chromosome instability, increases migration, and promotes early ovarian tumors
- Genomic profiling of human vascular cells identifies TWIST1 as a causal gene for common vascular diseases
- Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing
- Ligand dependent gene regulation by transient ERα clustered enhancers