Abstract
MicroRNAs (miRNAs) play important roles in development, differentiation, homeostasis, and also in diseases such as lymphoma. This chapter describes methods to study the role of miRNAs in lymphoma. First, we describe a multiplex RT reaction followed by qPCR that can be used to determine differential expression of candidate miRNAs. Second, we provide a protocol for stable overexpression of miRNAs using lentiviral-based ectopic expression systems. Third, we describe a straightforward assay to determine whether the candidate miRNA may function as an oncogene or a tumor suppressor gene in lymphomagenesis.
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References
Chendrimada TP, Gregory RI, Kumaraswamy E et al (2005) TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 436:740–744
Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120:15–20
Sandhu SK, Croce CM, Garzon R (2011) Micro-RNA expression and function in lymphomas. Adv Hematol 2011:347137
Eis PS, Tam W, Sun L et al (2005) Accumulation of miR-155 and BIC RNA in human B cell lymphomas. Proc Natl Acad Sci USA 102:3627–3632
Kluiver J, Poppema S, de Jong D et al (2005) BIC and miR-155 are highly expressed in Hodgkin, primary mediastinal and diffuse large B cell lymphomas. J Pathol 207:243–249
Costinean S, Zanesi N, Pekarsky Y et al (2006) Pre-B cell proliferation and lymphoblastic leukemia/high-grade lymphoma in E(mu)-miR155 transgenic mice. Proc Natl Acad Sci USA 103:7024–7029
Robertus JL, Kluiver J, Weggemans C et al (2010) MiRNA profiling in B non-Hodgkin lymphoma: a MYC-related miRNA profile characterizes Burkitt lymphoma. Br J Haematol 149:896–899
Ota A, Tagawa H, Karnan S et al (2004) Identification and characterization of a novel gene, C13orf25, as a target for 13q31-q32 amplification in malignant lymphoma. Cancer Res 64:3087–3095
Scholtysik R, Kreuz M, Klapper W et al (2010) Detection of genomic aberrations in molecularly defined Burkitt’s lymphoma by array-based, high resolution, single nucleotide polymorphism analysis. Haematologica 95:2047–2055
Ventura A, Young AG, Winslow MM et al (2008) Targeted deletion reveals essential and overlapping functions of the miR-17 through 92 family of miRNA clusters. Cell 132:875–886
Xiao C, Srinivasan L, Calado DP et al (2008) Lymphoproliferative disease and autoimmunity in mice with increased miR-17-92 expression in lymphocytes. Nat Immunol 9:405–414
He L, Thomson J.M., Hemann M.T., et al. A microRNA polycistron as a potential human oncogene. Nature 2005; 435: 828–33.
Mu P, Han YC, Betel D et al (2009) Genetic dissection of the miR-17 92 cluster of microRNAs in Myc-induced B-cell lymphomas. Genes Dev 23:2806–2811
Olive V, Bennett MJ, Walker JC et al (2009) miR-19 is a key oncogenic component of mir-17-92. Genes Dev 23:2839–2849
Medina PP, Nolde M, Slack FJ (2010) OncomiR addiction in an in vivo model of microRNA-21-induced pre-B-cell lymphoma. Nature 467:86–90
Calin GA, Dumitru CD, Shimizu M et al (2002) Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci USA 99:15524–15529
Klein U, Lia M, Crespo M et al (2010) The DLEU2/miR-15a/16-1 cluster controls B cell proliferation and its deletion leads to chronic lymphocytic leukemia. Cancer Cell 17:28–40
Dorsett Y, McBride KM, Jankovic M et al (2008) MicroRNA-155 suppresses activation-induced cytidine deaminase-mediated Myc-Igh translocation. Immunity 28:630–638
Kluiver J, Haralambieva E, de Jong D et al (2006) Lack of BIC and microRNA miR-155 expression in primary cases of Burkitt lymphoma. Genes Chromosomes Cancer 45:147–153
Gibcus JH, Tan LP, Harms G et al (2009) Hodgkin lymphoma cell lines are characterized by a specific miRNA expression profile. Neoplasia 11:167–176
Zhao JJ, Lin J, Lwin T et al (2010) microRNA expression profile and identification of miR-29 as a prognostic marker and pathogenetic factor by targeting CDK6 in mantle cell lymphoma. Blood 115:2630–2639
Zhou B, Wang S, Mayr C, Bartel DP, Lodish HF (2007) miR-150, a microRNA expressed in mature B and T cells, blocks early B cell development when expressed prematurely. Proc Natl Acad Sci USA 104:7080–7085
Xiao C, Calado DP, Galler G et al (2007) MiR-150 controls B cell differentiation by targeting the transcription factor c-Myb. Cell 131:146–159
Chen C, Ridzon DA, Broomer AJ et al (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33:e179
Wang H, Ach RA, Curry B (2007) Direct and sensitive miRNA profiling from low-input total RNA. RNA 13:151–159
Landgraf P, Rusu M, Sheridan R et al (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129:1401–1414
Basso K, Sumazin P, Morozov P et al (2009) Identification of the human mature B cell miRNome. Immunity 30:744–752
Ebert MS, Neilson JR, Sharp PA (2007) MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells. Nat Methods 4:721–726
Vinther J, Hedegaard MM, Gardner PP, Andersen JS, Arctander P (2006) Identification of miRNA targets with stable isotope labeling by amino acids in cell culture. Nucleic Acids Res 34:e107
Tan LP, Seinen E, Duns G et al (2009) A high throughput experimental approach to identify miRNA targets in human cells. Nucleic Acids Res 37:e137
Hafner M, Landthaler M, Burger L et al (2010) Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141:129–141
Chi SW, Zang JB, Mele A, Darnell RB (2009) Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460:479–486
Dull T, Zufferey R, Kelly M et al (1998) A third-generation lentivirus vector with a conditional packaging system. J Virol 72:8463–8471
Acknowledgment
This work was supported by the Dutch Cancer Society (RUG 2009-4279 to A.v.d.B.).
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Kluiver, J., Slezak-Prochazka, I., van den Berg, A. (2013). Studying MicroRNAs in Lymphoma. In: Küppers, R. (eds) Lymphoma. Methods in Molecular Biology, vol 971. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-269-8_15
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DOI: https://doi.org/10.1007/978-1-62703-269-8_15
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