Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Original Article
  • Published:

Chronic Lymphocytic Leukemia

Small RNAs analysis in CLL reveals a deregulation of miRNA expression and novel miRNA candidates of putative relevance in CLL pathogenesis

Leukemia volume 22, pages 330–338 (2008)Cite this article

Abstract

MicroRNAs (miRNAs) are a novel class of small noncoding RNA molecules that regulate gene expression by inducing degradation or translational inhibition of target mRNAs. There are more than 500 miRNA genes reported in the human genome, constituting one of the largest classes of regulatory genes. Increasing experimental evidence supports the idea of aberrant miRNA expression in cancer pathogenesis. We analyzed the pattern of miRNA expression in chronic lymphocytic leukemia (CLL) cells and our results showed a global reduction in miRNA expression levels in CLL cells associated to a consistent underexpression of miR-181a, let-7a and miR-30d. We observed overexpression of miR-155 and a set of five miRNAs that are differentially expressed between patients with different clinical outcomes. Five novel miRNA candidates cloned from leukemic cells are reported. Surprisingly, predicted mRNA targets for these novel miRNA revealed a high proportion of targets located in a small region of chromosome 1, which is frequently altered in human cancer. Additionally, several targets were shared by at least two of miRNA candidates. Predicted targets included several genes recently described as tumor suppressors. These data could afford new avenues for exploring innovative pathways in CLL biology and therapy.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1
Figure 2

Similar content being viewed by others

References

  1. Montserrat E, Rozman C . Chronic lymphocytic leukemia: present status. Ann Oncol 1995; 6: 219–235.

    Article  CAS  Google Scholar 

  2. Dighiero G, Kipps T, Schroeder HW, Chiorazzi N, Stevenson F, Silberstein LE et al. What is the CLL B-lymphocyte? Leuk Lymphoma 1996; 22 (Suppl 2): 13–39.

    Article  Google Scholar 

  3. Dameshek W . Chronic lymphocytic leukemia—an accumulative disease of immunologically incompetent lymphocytes. Blood 1967; 29 (Suppl 4): 566–584.

    Google Scholar 

  4. Caligaris-Cappio F, Hamblin TJ . B-cell chronic lymphocytic leukemia: a bird of a different feather. J Clin Oncol 1999; 17: 399–408.

    Article  CAS  Google Scholar 

  5. Chiorazzi N, Rai KR, Ferrarini M . Chronic lymphocytic leukemia. N Engl J Med 2005; 352: 804–815.

    Article  CAS  Google Scholar 

  6. Kitada S, Andersen J, Akar S, Zapata JM, Takayama S, Krajewski S et al. Expression of apoptosis-regulating proteins in chronic lymphocytic leukemia: correlations with in vitro and in vivo chemoresponses. Blood 1998; 91: 3379–3389.

    CAS  Google Scholar 

  7. Messmer BT, Messmer D, Allen SL, Kolitz JE, Kudalkar P, Cesar D et al. In vivo measurements document the dynamic cellular kinetics of chronic lymphocytic leukemia B cells. J Clin Invest 2005; 115: 755–764.

    Article  CAS  Google Scholar 

  8. Maloum K, Davi F, Magnac C, Pritsch O, McIntyre E, Valensi F et al. Analysis of VH gene expression in CD5+ and CD5− B-cell chronic lymphocytic leukemia. Blood 1995; 86: 3883–3890.

    CAS  Google Scholar 

  9. Hamblin TJ, Davis Z, Gardiner A, Oscier DG, Stevenson FK . Unmutated Ig V(H) genes are associated with a more aggressive form of chronic lymphocytic leukemia. Blood 1999; 94: 1848–1854.

    CAS  Google Scholar 

  10. Orchard JA, Ibbotson RE, Davis Z, Wiestner A, Rosenwald A, Thomas PW et al. ZAP-70 expression and prognosis in chronic lymphocytic leukaemia. Lancet 2004; 363: 105–111.

    Article  CAS  Google Scholar 

  11. Damle RN, Wasil T, Fais F, Ghiotto F, Valetto A, Allen SL et al. Ig V gene mutation status and CD38 expression as novel prognostic indicators in chronic lymphocytic leukemia. Blood 1999; 94: 1840–1847.

    CAS  Google Scholar 

  12. Dohner H, Stilgenbauer S, Benner A, Leupolt E, Krober A, Bullinger L et al. Genomic aberrations and survival in chronic lymphocytic leukemia. N Engl J Med 2000; 343: 1910–1916.

    Article  CAS  Google Scholar 

  13. Bartel DP . MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004; 116: 281–297.

    Article  CAS  Google Scholar 

  14. Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP . MicroRNAs in plants. Genes Dev 2002; 16: 1616–1626.

    Article  CAS  Google Scholar 

  15. Valencia-Sanchez MA, Liu J, Hannon GJ, Parker R . Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev 2006; 20: 515–524.

    Article  CAS  Google Scholar 

  16. Carrington JC, Ambros V . Role of microRNAs in plant and animal development. Science 2003; 301: 336–338.

    Article  CAS  Google Scholar 

  17. Calin GA, Sevignani C, Dumitru CD, Hyslop T, Noch E, Yendamuri S et al. Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc Natl Acad Sci USA 2004; 101: 2999–3004.

    Article  CAS  Google Scholar 

  18. Metzler M, Wilda M, Busch K, Viehmann S, Borkhardt A . High expression of precursor microRNA-155/BIC RNA in children with Burkitt lymphoma. Genes Chromosomes Cancer 2004; 39: 167–169.

    Article  CAS  Google Scholar 

  19. Michael MZ, SM OC, van Holst Pellekaan NG, Young GP, James RJ . Reduced accumulation of specific microRNAs in colorectal neoplasia. Mol Cancer Res 2003; 1: 882–891.

    CAS  Google Scholar 

  20. Takamizawa J, Konishi H, Yanagisawa K, Tomida S, Osada H, Endoh H et al. Reduced expression of the let-7 microRNAs in human lung cancers in association with shortened postoperative survival. Cancer Res 2004; 64: 3753–3756.

    Article  CAS  Google Scholar 

  21. Iorio MV, Ferracin M, Liu CG, Veronese A, Spizzo R, Sabbioni S et al. MicroRNA gene expression deregulation in human breast cancer. Cancer Res 2005; 65: 7065–7070.

    Article  CAS  Google Scholar 

  22. Chan JA, Krichevsky AM, Kosik KS . MicroRNA-21 is an antiapoptotic factor in human glioblastoma cells. Cancer Res 2005; 65: 6029–6033.

    Article  CAS  Google Scholar 

  23. Esquela-Kerscher A, Slack FJ . Oncomirs—microRNAs with a role in cancer. Nat Rev Cancer 2006; 6: 259–269.

    Article  CAS  Google Scholar 

  24. He L, Thomson JM, Hemann MT, Hernando-Monge E, Mu D, Goodson S et al. A microRNA polycistron as a potential human oncogene. Nature 2005; 435: 828–833.

    Article  CAS  Google Scholar 

  25. Johnson SM, Grosshans H, Shingara J, Byrom M, Jarvis R, Cheng A et al. RAS is regulated by the let-7 microRNA family. Cell 2005; 120: 635–647.

    Article  CAS  Google Scholar 

  26. Voorhoeve PM, le Sage C, Schrier M, Gillis AJ, Stoop H, Nagel R et al. A genetic screen implicates miRNA-372 and miRNA-373 as oncogenes in testicular germ cell tumors. Cell 2006; 124: 1169–1181.

    Article  CAS  Google Scholar 

  27. Calin GA, Ferracin M, Cimmino A, Di Leva G, Shimizu M, Wojcik SE et al. A microRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. N Engl J Med 2005; 353: 1793–1801.

    Article  CAS  Google Scholar 

  28. Fulci V, Chiaretti S, Goldoni M, Azzalin G, Carucci N, Tavolaro S et al. Quantitative technologies establish a novel microRNA profile of chronic lymphocytic leukemia. Blood 2007; 109: 4944–4951.

    Article  CAS  Google Scholar 

  29. Calin GA, Liu CG, Sevignani C, Ferracin M, Felli N, Dumitru CD et al. MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias. Proc Natl Acad Sci USA 2004; 101: 11755–11760.

    Article  CAS  Google Scholar 

  30. Cimmino A, Calin GA, Fabbri M, Iorio MV, Ferracin M, Shimizu M et al. miR-15 and miR-16 induce apoptosis by targeting BCL2. Proc Natl Acad Sci USA 2005; 102: 13944–13949.

    Article  CAS  Google Scholar 

  31. Pfeffer S, Lagos-Quintana M, Tuschl T . Cloning of small RNA molecules. In: Ausubel FM, Brent R, Kingston RE, Moore DD, Seidmann JG, Smith JA, Struhl K (eds). Current Protocols in Molecular Biology. New York: Wiley, 2003, pp 26.4.1–26.4.18.

    Google Scholar 

  32. Pfaffl MW . A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 2001; 29: e45.

    Article  CAS  Google Scholar 

  33. Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS . MicroRNA targets in Drosophila. Genome Biol 2003; 5: R1.

    Article  Google Scholar 

  34. Lewis BP, Burge CB, Bartel DP . Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005; 120: 15–20.

    Article  CAS  Google Scholar 

  35. Chen CZ, Li L, Lodish HF, Bartel DP . MicroRNAs modulate hematopoietic lineage differentiation. Science 2004; 303: 83–86.

    Article  CAS  Google Scholar 

  36. Neilson JR, Zheng GX, Burge CB, Sharp PA . Dynamic regulation of miRNA expression in ordered stages of cellular development. Genes Dev 2007; 21: 578–589.

    Article  CAS  Google Scholar 

  37. Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B et al. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 2000; 408: 86–89.

    Article  CAS  Google Scholar 

  38. Bohnsack MT, Czaplinski K, Gorlich D . Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs. RNA 2004; 10: 185–191.

    Article  CAS  Google Scholar 

  39. Ritchie W, Legendre M, Gautheret D . RNA stem-loops: to be or not to be cleaved by RNAse III. RNA 2007; 13: 457–462.

    Article  CAS  Google Scholar 

  40. Bagchi A, Papazoglu C, Wu Y, Capurso D, Brodt M, Francis D et al. CHD5 is a tumor suppressor at human 1p36. Cell 2007; 128: 459–475.

    Article  CAS  Google Scholar 

  41. Takada S, Berezikov E, Yamashita Y, Lagos-Quintana M, Kloosterman WP, Enomoto M et al. Mouse microRNA profiles determined with a new and sensitive cloning method. Nucleic Acids Res 2006; 34: e115.

    Article  Google Scholar 

  42. Karube Y, Tanaka H, Osada H, Tomida S, Tatematsu Y, Yanagisawa K et al. Reduced expression of Dicer associated with poor prognosis in lung cancer patients. Cancer Sci 2005; 96: 111–115.

    Article  CAS  Google Scholar 

  43. Obernosterer G, Leuschner PJ, Alenius M, Martinez J . Post-transcriptional regulation of microRNA expression. RNA 2006; 12: 1161–1167.

    Article  CAS  Google Scholar 

  44. Thomson JM, Newman M, Parker JS, Morin-Kensicki EM, Wright T, Hammond SM . Extensive post-transcriptional regulation of microRNAs and its implications for cancer. Genes Dev 2006; 20: 2202–2207.

    Article  CAS  Google Scholar 

  45. Yue J, Tigyi G . MicroRNA trafficking and human cancer. Cancer Biol Ther 2006; 5: 573–578.

    Article  CAS  Google Scholar 

  46. Eis PS, Tam W, Sun L, Chadburn A, Li Z, Gomez MF et al. Accumulation of miR-155 and BIC RNA in human B cell lymphomas. Proc Natl Acad Sci USA 2005; 102: 3627–3632.

    Article  CAS  Google Scholar 

  47. Dostie J, Mourelatos Z, Yang M, Sharma A, Dreyfuss G . Numerous microRNPs in neuronal cells containing novel microRNAs. RNA 2003; 9: 180–186.

    Article  CAS  Google Scholar 

  48. Naguibneva I, Ameyar-Zazoua M, Polesskaya A, Ait-Si-Ali S, Groisman R, Souidi M et al. The microRNA miR-181 targets the homeobox protein Hox-A11 during mammalian myoblast differentiation. Nat Cell Biol 2006; 8: 278–284.

    Article  CAS  Google Scholar 

  49. Ambros V . The functions of animal microRNAs. Nature 2004; 431: 350–355.

    Article  CAS  Google Scholar 

  50. Thomson JM, Parker J, Perou CM, Hammond SM . A custom microarray platform for analysis of microRNA gene expression. Nat Methods 2004; 1: 47–53.

    Article  CAS  Google Scholar 

  51. Brodeur GM, Sekhon G, Goldstein MN . Chromosomal aberrations in human neuroblastomas. Cancer 1977; 40: 2256–2263.

    Article  CAS  Google Scholar 

  52. Mori N, Morosetti R, Mizoguchi H, Koeffler HP . Progression of myelodysplastic syndrome: allelic loss on chromosomal arm 1p. Br J Haematol 2003; 122: 226–230.

    Article  Google Scholar 

  53. Mori N, Morosetti R, Spira S, Lee S, Ben-Yehuda D, Schiller G et al. Chromosome band 1p36 contains a putative tumor suppressor gene important in the evolution of chronic myelocytic leukemia. Blood 1998; 92: 3405–3409.

    CAS  Google Scholar 

  54. Melendez B, Cuadros M, Robledo M, Rivas C, Fernandez-Piqueras J, Martinez-Delgado B et al. Coincidental LOH regions in mouse and humans: evidence for novel tumor suppressor loci at 9q22-q34 in non-Hodgkin's lymphomas. Leuk Res 2003; 27: 627–633.

    Article  CAS  Google Scholar 

  55. Okawa ER, Gotoh T, Manne J, Igarashi J, Fujita T, Silverman KA et al. Expression and sequence analysis of candidates for the 1p36.31 tumor suppressor gene deleted in neuroblastomas. Oncogene advance online publication, July 30, 2007; doi:10.1038/sj.onc.1210675.

    Article  Google Scholar 

  56. Thompson PM, Gotoh T, Kok M, White PS, Brodeur GM . CHD5, a new member of the chromodomain gene family, is preferentially expressed in the nervous system. Oncogene 2003; 22: 1002–1011.

    Article  CAS  Google Scholar 

  57. Jiang GL, Huang S . The yin-yang of PR-domain family genes in tumorigenesis. Histol Histopathol 2000; 15: 109–117.

    CAS  Google Scholar 

  58. Mochizuki N, Shimizu S, Nagasawa T, Tanaka H, Taniwaki M, Yokota J et al. A novel gene, MEL1, mapped to 1p36.3 is highly homologous to the MDS1/EVI1 gene and is transcriptionally activated in t(1;3)(p36;q21)-positive leukemia cells. Blood 2000; 96: 3209–3214.

    CAS  Google Scholar 

  59. Rosenwald A, Alizadeh AA, Widhopf G, Simon R, Davis RE, Yu X et al. Relation of gene expression phenotype to immunoglobulin mutation genotype in B cell chronic lymphocytic leukemia. J Exp Med 2001; 194: 1639–1647.

    Article  CAS  Google Scholar 

  60. Vasconcelos Y, De Vos J, Vallat L, Reme T, Lalanne AI, Wanherdrick K et al. Gene expression profiling of chronic lymphocytic leukemia can discriminate cases with stable disease and mutated Ig genes from those with progressive disease and unmutated Ig genes. Leukemia 2005; 19: 2002–2005.

    Article  CAS  Google Scholar 

  61. Lu D, Zhao Y, Tawatao R, Cottam HB, Sen M, Leoni LM et al. Activation of the Wnt signaling pathway in chronic lymphocytic leukemia. Proc Natl Acad Sci USA 2004; 101: 3118–3123.

    Article  CAS  Google Scholar 

  62. Reya T . Regulation of hematopoietic stem cell self-renewal. Recent Prog Horm Res 2003; 58: 283–295.

    Article  CAS  Google Scholar 

  63. Sasai Y, Kageyama R, Tagawa Y, Shigemoto R, Nakanishi S . Two mammalian helix-loop-helix factors structurally related to Drosophila hairy and Enhancer of split. Genes Dev 1992; 6: 2620–2634.

    Article  CAS  Google Scholar 

  64. Hatakeyama J, Bessho Y, Katoh K, Ookawara S, Fujioka M, Guillemot F et al. Hes genes regulate size, shape and histogenesis of the nervous system by control of the timing of neural stem cell differentiation. Development 2004; 131: 5539–5550.

    Article  CAS  Google Scholar 

  65. Katoh M, Katoh M . Integrative genomic analyses on HES/HEY family: Notch-independent HES1, HES3 transcription in undifferentiated ES cells, and Notch-dependent HES1, HES5, HEY1, HEY2, HEYL transcription in fetal tissues, adult tissues, or cancer. Int J Oncol 2007; 31: 461–466.

    CAS  Google Scholar 

  66. Tracey WD, Speck NA . Potential roles for RUNX1 and its orthologs in determining hematopoietic cell fate. Semin Cell Dev Biol 2000; 11: 337–342.

    Article  CAS  Google Scholar 

  67. Ito Y . Oncogenic potential of the RUNX gene family: ‘overview’. Oncogene 2004; 23: 4198–4208.

    Article  CAS  Google Scholar 

  68. van Wijnen AJ, Stein GS, Gergen JP, Groner Y, Hiebert SW, Ito Y et al. Nomenclature for Runt-related (RUNX) proteins. Oncogene 2004; 23: 4209–4210.

    Article  CAS  Google Scholar 

  69. Bae SC, Lee YH . Phosphorylation, acetylation and ubiquitination: the molecular basis of RUNX regulation. Gene 2006; 366: 58–66.

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank Alvaro Pena for suggestions and for bioinformatic support. This work was supported by a grant assigned to AC from ‘Comisión Honoraria de Lucha Contra el Cáncer-FMP’ Montevideo, Uruguay. Part of this work was supported by “Fondo Clemente Estable” (Dicyt-MEC), Montevideo, Uruguay.

Author information

Authors and Affiliations

  1. Molecular Oncology Unit, Institut Pasteur, Montevideo, Uruguay

    S Marton, M R Garcia, G Dighiero & A Cayota

  2. Molecular Biology Unit, Institut Pasteur, Montevideo, Uruguay

    C Robello

  3. Department of Oncology, Lund University, Lund, Sweden

    H Persson & C Rovira

  4. Structural Biology Unit, Institut Pasteur, Montevideo, Uruguay

    F Trajtenberg

  5. Protein Biophysics Unit, Institut Pasteur, Montevideo, Uruguay

    O Pritsch

  6. Bioinformatics Unit, Institut Pasteur, Montevideo, Uruguay

    H Naya

Authors
  1. S Marton
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. M R Garcia
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. C Robello
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. H Persson
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. F Trajtenberg
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. O Pritsch
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. C Rovira
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. H Naya
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. G Dighiero
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. A Cayota
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to A Cayota.

Additional information

Supplementary Information accompanies the paper on the Leukemia website (http://www.nature.com/leu)

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Cite this article

Marton, S., Garcia, M., Robello, C. et al. Small RNAs analysis in CLL reveals a deregulation of miRNA expression and novel miRNA candidates of putative relevance in CLL pathogenesis. Leukemia 22, 330–338 (2008). https://doi.org/10.1038/sj.leu.2405022

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/sj.leu.2405022

Keywords

This article is cited by

Search

Advanced search

Quick links