Biomolecules & Therapeutics

The Korean Society of Applied Pharmacology (한국응용약물학회)
권호 표지
DOI QR코드

DOI QR Code

Isolation of MLL1 Inhibitory RNA Aptamers

  • Ul-Haq, Asad (Gachon Institute of Pharmaceutical Sciences, College of Pharmacy, Gachon University) ;
  • Jin, Ming Li (Gachon Institute of Pharmaceutical Sciences, College of Pharmacy, Gachon University) ;
  • Jeong, Kwang Won (Gachon Institute of Pharmaceutical Sciences, College of Pharmacy, Gachon University) ;
  • Kim, Hwan-Mook (Gachon Institute of Pharmaceutical Sciences, College of Pharmacy, Gachon University) ;
  • Chun, Kwang-Hoon (Gachon Institute of Pharmaceutical Sciences, College of Pharmacy, Gachon University)
  • Received : 2018.08.09
  • Accepted : 2018.09.18
  • Published : 2019.03.01
Download PDF
⟨ Previous Next ⟩

Abstract

Mixed lineage leukemia proteins (MLL) are the key histone lysine methyltransferases that regulate expression of diverse genes. Aberrant activation of MLL promotes leukemia as well as solid tumors in humans, highlighting the urgent need for the development of an MLL inhibitor. We screened and isolated MLL1-binding ssRNAs using SELEX (${\underline{S}}ystemic$ ${\underline{E}}volution$ of ${\underline{L}}igands$ by ${\underline{E}}xponential$ enrichment) technology. When sequences in sub-libraries were obtained using next-generation sequencing (NGS), the most enriched aptamers-APT1 and APT2-represented about 30% and 26% of sub-library populations, respectively. Motif analysis of the top 50 sequences provided a highly conserved sequence: 5'-A[A/C][C/G][G/U][U/A]ACAGAGGG[U/A]GG[A/C] GAGUGGGU-3'. APT1, APT2, and APT5 embracing this motif generated secondary structures with similar topological characteristics. We found that APT1 and APT2 have a good binding activity and the analysis using mutated aptamer variants showed that the site information in the central region was critical for binding. In vitro enzyme activity assay showed that APT1 and APT2 had MLL1 inhibitory activity. Three-dimensional structure prediction of APT1-MLL1 complex indicates multiple weak interactions formed between MLL1 SET domain and APT1. Our study confirmed that NGS-assisted SELEX is an efficient tool for aptamer screening and that aptamers could be useful in diagnosis and treatment of MLL1-mediated diseases.

Keywords

References

  1. Agostini, F., Zanzoni, A., Klus, P., Marchese, D., Cirillo, D. and Tartaglia, G. G. (2013) catRAPID omics: a web server for large-scale prediction of protein-RNA interactions. Bioinformatics 29, 2928-2930. https://doi.org/10.1093/bioinformatics/btt495
  2. Ansari, K. I., Kasiri, S. and Mandal, S. S. (2013) Histone methylase MLL1 has critical roles in tumor growth and angiogenesis and its knockdown suppresses tumor growth in vivo. Oncogene 32, 3359-3370. https://doi.org/10.1038/onc.2012.352
  3. Bailey, T. L., Boden, M., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., Ren, J., Li, W. W. and Noble, W. S. (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37, W202-W208. https://doi.org/10.1093/nar/gkp335
  4. Bolshan, Y., Getlik, M., Kuznetsova, E., Wasney, G. A., Hajian, T., Poda, G., Nguyen, K. T., Wu, H., Dombrovski, L., Dong, A., Senisterra, G., Schapira, M., Arrowsmith, C. H., Brown, P. J., Al-Awar, R., Vedadi, M. and Smil, D. (2013) Synthesis, Optimization, and Evaluation of Novel Small Molecules as Antagonists of WDR5-MLL Interaction. ACS Med. Chem. Lett. 4, 353-357. https://doi.org/10.1021/ml300467n
  5. Borkin, D., He, S., Miao, H., Kempinska, K., Pollock, J., Chase, J., Purohit, T., Malik, B., Zhao, T., Wang, J., Wen, B., Zong, H., Jones, M., Danet-Desnoyers, G., Guzman, M. L., Talpaz, M., Bixby, D. L., Sun, D., Hess, J. L., Muntean, A. G., Maillard, I., Cierpicki, T. and Grembecka, J. (2015) Pharmacologic inhibition of the Menin-MLL interaction blocks progression of MLL leukemia in vivo. Cancer Cell 27, 589-602. https://doi.org/10.1016/j.ccell.2015.02.016
  6. Cao, F., Townsend, E. C., Karatas, H., Xu, J., Li, L., Lee, S., Liu, L., Chen, Y., Ouillette, P., Zhu, J., Hess, J. L., Atadja, P., Lei, M., Qin, Z. S., Malek, S., Wang, S. and Dou, Y. (2014) Targeting MLL1 H3K4 methyltransferase activity in mixed-lineage leukemia. Mol. Cell 53, 247-261. https://doi.org/10.1016/j.molcel.2013.12.001
  7. Cho, M., Xiao, Y., Nie, J., Stewart, R., Csordas, A. T., Oh, S. S., Thomson, J. A. and Soh, H. T. (2010) Quantitative selection of DNA aptamers through microfluidic selection and high-throughput sequencing. Proc. Natl. Acad. Sci. U.S.A. 107, 15373-15378. https://doi.org/10.1073/pnas.1009331107
  8. Cosgrove, M. S. and Patel, A. (2010) Mixed lineage leukemia: a structure-function perspective of the MLL1 protein. FEBS J. 277, 1832-1842. https://doi.org/10.1111/j.1742-4658.2010.07609.x
  9. Dou, Y. and Hess, J. L. (2008) Mechanisms of transcriptional regulation by MLL and its disruption in acute leukemia. Int. J. Hematol. 87, 10-18. https://doi.org/10.1007/s12185-007-0009-8
  10. Dou, Y., Milne, T. A., Ruthenburg, A. J., Lee, S., Lee, J. W., Verdine, G. L., Allis, C. D. and Roeder, R. G. (2006) Regulation of MLL1 H3K4 methyltransferase activity by its core components. Nat. Struct. Mol. Biol. 13, 713-719. https://doi.org/10.1038/nsmb1128
  11. Ellington, A. D. and Szostak, J. W. (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818-822. https://doi.org/10.1038/346818a0
  12. Frith, M. C., Saunders, N. F., Kobe, B. and Bailey, T. L. (2008) Discovering sequence motifs with arbitrary insertions and deletions. PLoS Comput. Biol. 4, e1000071. https://doi.org/10.1371/journal.pcbi.1000071
  13. Hess, J. L. (2004) MLL: a histone methyltransferase disrupted in leukemia. Trends Mol. Med. 10, 500-507. https://doi.org/10.1016/j.molmed.2004.08.005
  14. Hoon, S., Zhou, B., Janda, K. D., Brenner, S. and Scolnick, J. (2011) Aptamer selection by high-throughput sequencing and informatic analysis. Biotechniques 51, 413-416.
  15. Hsieh, J. J., Ernst, P., Erdjument-Bromage, H., Tempst, P. and Korsmeyer, S. J. (2003) Proteolytic cleavage of MLL generates a complex of N- and C-terminal fragments that confers protein stability and subnuclear localization. Mol. Cell. Biol. 23, 186-194. https://doi.org/10.1128/MCB.23.1.186-194.2003
  16. Jeong, K. W., Andreu-Vieyra, C., You, J. S., Jones, P. A. and Stallcup, M. R. (2014) Establishment of active chromatin structure at enhancer elements by mixed-lineage leukemia 1 to initiate estrogendependent gene expression. Nucleic Acids Res. 42, 2245-2256. https://doi.org/10.1093/nar/gkt1236
  17. Karatas, H., Townsend, E. C., Cao, F., Chen, Y., Bernard, D., Liu, L., Lei, M., Dou, Y. and Wang, S. (2013) High-affinity, small-molecule peptidomimetic inhibitors of MLL1/WDR5 protein-protein interaction. J. Am. Chem. Soc. 135, 669-682. https://doi.org/10.1021/ja306028q
  18. Marschalek, R. (2010) Mixed lineage leukemia: roles in human malignancies and potential therapy. FEBS J. 277, 1822-1831. https://doi.org/10.1111/j.1742-4658.2010.07608.x
  19. Milne, T. A., Briggs, S. D., Brock, H. W., Martin, M. E., Gibbs, D., Allis, C. D. and Hess, J. L. (2002) MLL targets SET domain methyltransferase activity to Hox gene promoters. Mol. Cell 10, 1107-1117. https://doi.org/10.1016/S1097-2765(02)00741-4
  20. Milne, T. A., Dou, Y., Martin, M. E., Brock, H. W., Roeder, R. G. and Hess, J. L. (2005) MLL associates specifically with a subset of transcriptionally active target genes. Proc. Natl. Acad. Sci. U.S.A. 102, 14765-14770. https://doi.org/10.1073/pnas.0503630102
  21. Morillon, A., Karabetsou, N., Nair, A. and Mellor, J. (2005) Dynamic lysine methylation on histone H3 defines the regulatory phase of gene transcription. Mol. Cell 18, 723-734. https://doi.org/10.1016/j.molcel.2005.05.009
  22. Nieuwlandt, D. (2000) In vitro selection of functional nucleic acid sequences. Curr. Issues Mol. Biol. 2, 9-16.
  23. Patel, A., Dharmarajan, V., Vought, V. E. and Cosgrove, M. S. (2009) On the mechanism of multiple lysine methylation by the human mixed lineage leukemia protein-1 (MLL1) core complex. J. Biol. Chem. 284, 24242-24256. https://doi.org/10.1074/jbc.M109.014498
  24. Popenda, M., Szachniuk, M., Antczak, M., Purzycka, K. J., Lukasiak, P., Bartol, N., Blazewicz, J. and Adamiak, R. W. (2012) Automated 3D structure composition for large RNAs. Nucleic Acids Res. 40, e112. https://doi.org/10.1093/nar/gks339
  25. Schutze, T., Wilhelm, B., Greiner, N., Braun, H., Peter, F., Morl, M., Erdmann, V. A., Lehrach, H., Konthur, Z., Menger, M., Arndt, P. F. and Glokler, J. (2011) Probing the SELEX process with next-generation sequencing. PLoS ONE 6, e29604. https://doi.org/10.1371/journal.pone.0029604
  26. Southall, S. M., Wong, P. S., Odho, Z., Roe, S. M. and Wilson, J. R. (2009) Structural basis for the requirement of additional factors for MLL1 SET domain activity and recognition of epigenetic marks. Mol. Cell 33, 181-191. https://doi.org/10.1016/j.molcel.2008.12.029
  27. Terranova, R., Agherbi, H., Boned, A., Meresse, S. and Djabali, M. (2006) Histone and DNA methylation defects at Hox genes in mice expressing a SET domain-truncated form of Mll. Proc. Natl. Acad. Sci. U.S.A. 103, 6629-6634. https://doi.org/10.1073/pnas.0507425103
  28. Thiel, A. T., Blessington, P., Zou, T., Feather, D., Wu, X., Yan, J., Zhang, H., Liu, Z., Ernst, P., Koretzky, G. A. and Hua, X. (2010) MLL-AF9-induced leukemogenesis requires coexpression of the wild-type Mll allele. Cancer Cell 17, 148-159. https://doi.org/10.1016/j.ccr.2009.12.034
  29. Tuerk, C. and Gold, L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510. https://doi.org/10.1126/science.2200121
  30. Tuszynska, I., Magnus, M., Jonak, K., Dawson, W. and Bujnicki, J. M. (2015) NPDock: a web server for protein-nucleic acid docking. Nucleic Acids Res. 43, W425-430. https://doi.org/10.1093/nar/gkv493
  31. Yokoyama, A., Kitabayashi, I., Ayton, P. M., Cleary, M. L. and Ohki, M. (2002) Leukemia proto-oncoprotein MLL is proteolytically processed into 2 fragments with opposite transcriptional properties. Blood 100, 3710-3718. https://doi.org/10.1182/blood-2002-04-1015
  32. Yu, B. D., Hess, J. L., Horning, S. E., Brown, G. A. and Korsmeyer, S. J. (1995) Altered Hox expression and segmental identity in Mllmutant mice. Nature 378, 505-508. https://doi.org/10.1038/378505a0
  33. Ziemin-van der Poel, S., McCabe, N. R., Gill, H. J., Espinosa, R., 3rd, Patel, Y., Harden, A., Rubinelli, P., Smith, S. D., LeBeau, M. M., Rowley, J. D. and Diaz, M. O. (1991) Identification of a gene, MLL, that spans the breakpoint in 11q23 translocations associated with human leukemias. Proc. Natl. Acad. Sci. U.S.A. 88, 10735-10739. https://doi.org/10.1073/pnas.88.23.10735
  34. Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406-3415. https://doi.org/10.1093/nar/gkg595