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Evolution of the Mir-155 Family and Possible Targets in Cancers and the Immune System

  • Published : 2014.10.11

Abstract

The mir-155 family is not only involved in a diversity of cancers, but also as a regulator of the immune system. However, the evolutionary history of this family is still unclear. The present study indicates that mir-155 evolved independently with lineage-specific gain of miRNAs. In addition, arm switching has occurred in the mir-155 family, and alternative splicing could produce two different lengths of ancestral sequences, implying the alternative splicing can also drive evolution for intragenic miRNAs. Here we screened validated target genes and immunity-related proteins, followed by analyzation of the mir-155 family function by high-throughput methods like the gene ontology (GO) and Kyoto Eneyclopedin of Genes and Genemes (KEGG) pathway enrichment analysis. The high-throughput analysis showed that the CCND1 and EGFR genes were outstanding in being significantly enriched, and the target genes cebpb and VCAM1 and the protein SMAD2 were also vital in mir-155-related immune reponse activities. Therefore, we conclude that the mir-155 family is highly conserved in evolution, and CCND1 and EGFR genes might be potential targets of mir-155 with regard to progress of cancers, while the cebpb and VCAM1 genes and the protein SMAD2 might be key factors in the mir-155 regulated immune activities.

Keywords

References

  1. Babar IA, Cheng CJ, Booth CJ, et al (2012). Nanoparticle-based therapy in an in vivo microRNA-155 (miR-155)-dependent mouse model of lymphoma. Proc Natl Acad Sci USA, 109, 1695-704. https://doi.org/10.1073/pnas.1201516109
  2. Bartel DP (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281-97. https://doi.org/10.1016/S0092-8674(04)00045-5
  3. Bartel DP (2009). MicroRNAs: target recognition and regulatory functions. Cell, 136, 215-33. https://doi.org/10.1016/j.cell.2009.01.002
  4. Blow MJ, Grocock RJ, van Dongen S, et al (2006). RNA editing of human microRNAs. Genome biology, 7, 27. https://doi.org/10.1186/gb-2006-7-4-r27
  5. Concepcion CP, Bonetti C, Ventura A (2012). The microRNA-17-92 family of microRNA clusters in development and disease. Cancer J, 18, 262-7. https://doi.org/10.1097/PPO.0b013e318258b60a
  6. Corsten MF, Papageorgiou A, Verhesen W, et al (2012). MicroRNA profiling identifies microRNA-155 as an adverse mediator of cardiac injury and dysfunction during acute viral myocarditis. Circulation Res, 111, 415-25. https://doi.org/10.1161/CIRCRESAHA.112.267443
  7. Croce CM (2008). Oncogenes and cancer. N Engl J Med, 358, 502-11. https://doi.org/10.1056/NEJMra072367
  8. Darty K, Denise A, Ponty Y (2009). VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics, 25, 1974. https://doi.org/10.1093/bioinformatics/btp250
  9. Das R, Xu S, Quan X, et al (2014). Upregulation of mitochondrial Nox4 mediates TGF-$\beta$-induced apoptosis in cultured mouse podocytes. Am J Physiol Renal Physio, 306, 155-67. https://doi.org/10.1152/ajprenal.00438.2013
  10. de Wit E, Linsen SE, Cuppen E, Berezikov E (2009). Repertoire and evolution of miRNA genes in four divergent nematode species. Genome Res, 19, 2064-74. https://doi.org/10.1101/gr.093781.109
  11. Elton TS, Selemon H, Elton SM, Parinandi NL (2013). Regulation of the MIR155 host gene in physiological and pathological processes. Gene, 532, 1-12. https://doi.org/10.1016/j.gene.2012.12.009
  12. Farooqi AA, Qureshi MZ, Coskunpinar E, et al (2014). miR-421, miR-155 and miR-650: emerging trends of regulation of cancer and apoptosis. Asian Pac J Cancer Prev, 15, 1909-12. https://doi.org/10.7314/APJCP.2014.15.5.1909
  13. Griffiths-Jones S, Hui JH, Marco A, Ronshaugen M (2011). MicroRNA evolution by arm switching. EMBO Rep, 12, 172-7. https://doi.org/10.1038/embor.2010.191
  14. Grimson A, Srivastava M, Fahey B, et al (2008). Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature, 455, 1193-7. https://doi.org/10.1038/nature07415
  15. Guddeti S, De Chun ZHANG ALL, LESEBERG C H, et al (2005). Molecular evolution of the rice miR395 gene family. Cell Res, 15, 631-8. https://doi.org/10.1038/sj.cr.7290333
  16. Hertel J, Bartschat S, Wintsche A, et al (2012). Evolution of the let-7 microRNA Family. RNA biology, 9, 231-41. https://doi.org/10.4161/rna.18974
  17. Hsu SD, Lin FM, Wu WY, et al (2011). miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res, 39, 163-9. https://doi.org/10.1093/nar/gkq1107
  18. Hu H Y, He L, Fominykh K, et al (2012). Evolution of the humanspecific microRNA miR-941. Nature Communications, 3, 1145. https://doi.org/10.1038/ncomms2146
  19. Kinsella RJ, Kähäri A, Haider S, et al (2011). Ensembl BioMarts:a hub for data retrieval across taxonomic space. Database, 2011, 30.
  20. Kozomara A, Griffiths-Jones S (2011). miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res, 39, 152-7.
  21. Landthaler M, Yalcin A, Tuschl T (2004). The human DiGeorge syndrome critical region gene 8 and its D. melanogaster homolog are required for miRNA biogenesis. Curr Biol, 14, 2162-7. https://doi.org/10.1016/j.cub.2004.11.001
  22. Larkin M, Blackshields G, Brown N, et al (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-8. https://doi.org/10.1093/bioinformatics/btm404
  23. Lewis BP, Shih IH, Jones-Rhoades MW, et al (2003). Prediction of mammalian microRNA targets. Cell, 115, 787-98. https://doi.org/10.1016/S0092-8674(03)01018-3
  24. Liang T, Guo L, Liu C (2012). Genome-wide analysis of mir-548 gene family reveals evolutionary and functional implications. J Biomed Biotechnol, 2012, 679563
  25. Louafi F, Martinez-Nunez RT, Sanchez-Elsner T (2010). MicroRNA-155 targets SMAD2 and modulates the response of macrophages to transforming growth factor-$\beta$. J Biol Chem, 285, 41328-36. https://doi.org/10.1074/jbc.M110.146852
  26. MacRae IJ, Zhou K, Li F, et al (2006). Structural basis for doublestranded RNA processing by Dicer. Science, 311, 195-8. https://doi.org/10.1126/science.1121638
  27. Maher C, Stein L, Ware D (2006). Evolution of Arabidopsis microRNA families through duplication events. Genome research, 16, 510-9. https://doi.org/10.1101/gr.4680506
  28. Marco A, Hooks K, Griffiths-Jones S (2012a). Evolution and function of the extended miR-2 microRNA family. RNA biology, 9, 242-8. https://doi.org/10.4161/rna.19160
  29. Marco A, Hui JH, Ronshaugen M, Griffiths-Jones S (2010). Functional shifts in insect microRNA evolution. Genome Biol Evol, 2, 686.
  30. Marco A, MacPherson JI, Ronshaugen M, Griffiths-Jones S (2012b). MicroRNAs from the same precursor have different targeting properties. Silence, 3, 8-. https://doi.org/10.1186/1758-907X-3-8
  31. Marco A, Ninova M, Ronshaugen M, Griffiths-Jones S (2013). Clusters of microRNAs emerge by new hairpins in existing transcripts. Nucleic Acids Res, 41, 7745-52. https://doi.org/10.1093/nar/gkt534
  32. Mattiske S, Suetani RJ, Neilsen PM, Callen DF (2012). The oncogenic role of miR-155 in breast cancer. Cancer Epidemiol Biomarkers Prev, 21, 1236-43. https://doi.org/10.1158/1055-9965.EPI-12-0173
  33. Nahvi A, Shoemaker CJ, Green R (2009). An expanded seed sequence definition accounts for full regulation of the hid 3' UTR by bantam miRNA. RNA, 15, 814-22. https://doi.org/10.1261/rna.1565109
  34. O'Connell RM, Chaudhuri AA, Rao D S, Baltimore D (2009). Inositol phosphatase SHIP1 is a primary target of miR-155. Proc Natl Acad Sci USA, 106, 7113-8. https://doi.org/10.1073/pnas.0902636106
  35. O'Connell RM, Rao DS, Baltimore D (2012). microRNA regulation of inflammatory responses. Annu Rev Immuno 30, 295-312. https://doi.org/10.1146/annurev-immunol-020711-075013
  36. Prasad TK, Goel R, Kandasamy K, et al (2009). Human protein reference database-2009 update. Nucleic Acids res, 37, 767-72. https://doi.org/10.1093/nar/gkn892
  37. Price N, Cartwright RA, Sabath N, et al (2011). Neutral evolution of robustness in Drosophila microRNA precursors. Mol Biol Evol, 28, 2115-23. https://doi.org/10.1093/molbev/msr029
  38. Pritchard CC, Cheng HH, Tewari M (2012). MicroRNA profiling: approaches and considerations. Nat Rev Gene, 13, 358-69. https://doi.org/10.1038/nrg3198
  39. Schwarz D S, Hutvagner G, Du T, et al (2003). Asymmetry in the assembly of the RNAi enzyme complex. Cell, 115, 199-208. https://doi.org/10.1016/S0092-8674(03)00759-1
  40. Smoot ME, Ono K, Ruscheinski J, et al (2011). Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics, 27, 431-2. https://doi.org/10.1093/bioinformatics/btq675
  41. Tamura K, Dudley J, Nei M, Kumar S (2007). MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol, 24, 1596-9. https://doi.org/10.1093/molbev/msm092
  42. Vargova K, Curik N, Burda P, et al (2011). MYB transcriptionally regulates the miR-155 host gene in chronic lymphocytic leukemia. Blood, 117, 3816-25. https://doi.org/10.1182/blood-2010-05-285064
  43. Vigorito E, Kohlhaas S, Lu D, Leyland R (2013). miR-155: an ancient regulator of the immune system. Immunological reviews, 253, 146-57. https://doi.org/10.1111/imr.12057
  44. Wang L, Toomey N L, Diaz L A, et al (2011). Oncogenic IRFs provide a survival advantage for Epstein-Barr virus-or human T-cell leukemia virus type 1-transformed cells through induction of BIC expression. J Virol, 85, 8328-37. https://doi.org/10.1128/JVI.00570-11
  45. Wang X (2008). miRDB: a microRNA target prediction and functional annotation database with a wiki interface. Rna, 14, 1012-7. https://doi.org/10.1261/rna.965408
  46. Wheeler BM, Heimberg AM, Moy VN, et al (2009). The deep evolution of metazoan microRNAs. Evol Dev, 11, 50-68. https://doi.org/10.1111/j.1525-142X.2008.00302.x
  47. Wienholds E, Kloosterman WP, Miska E, et al (2005). MicroRNA expression in zebrafish embryonic development. Science, 309, 310-1. https://doi.org/10.1126/science.1114519
  48. Xiao F, Zuo Z, Cai G, et al (2009). miRecords: an integrated resource for microRNA–target interactions. Nucleic Acids Res, 37, 105-10.
  49. Xu L, Dai WQ, Xu XF, et al (2012). Effects of multiple-target antimicroRNA antisense oligodeoxyribonucleotides on proliferation and migration of gastric cancer cells. Asian Pac J Cancer Prev, 13, 3203-7. https://doi.org/10.7314/APJCP.2012.13.7.3203
  50. Yi R, Qin Y, Macara I G, Cullen B R (2003). Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev, 17, 3011-6. https://doi.org/10.1101/gad.1158803
  51. Zhang H, Kolb F A, Jaskiewicz L, et al (2004). Single processing center models for human Dicer and bacterial RNase III. Cell, 118, 57-68. https://doi.org/10.1016/j.cell.2004.06.017
  52. Zhang J, Haider S, Baran J, et al (2011). BioMart: a data federation framework for large collaborative projects. Database, 2011, 38.
  53. Zheng SR, Guo GL, Zhai Q, et al (2013). Effects of miR-155 antisense oligonucleotide on breast carcinoma cell line MDA-MB-157 and implanted tumors. Asian Pac J Cancer Prev, 14, 2361-6. https://doi.org/10.7314/APJCP.2013.14.4.2361
  54. Liu ZY, Zhang GL, Wang MM, Xiong YN, Cui HQ (2011). MicroRNA-663 targets TGFB1 and regulates lung cancer proliferation. Asian Pac J Cancer Pre, 12, 2819-23.
  55. Zuker M (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res, 31, 3406-15. https://doi.org/10.1093/nar/gkg595

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