An integrative genomic approach reveals coordinated expression of intronic miR-335, miR-342, and miR-561 with deregulated host genes in multiple myeloma

BMC Medical Genomics - 2008
Domenica Ronchetti1, Marta Lionetti1, Laura Mosca1, Luca Agnelli1, Adrian Andronache1, Sonia Fabris1, Giorgio Lambertenghi Deliliers1, Antonino Neri1
1Department of Medical Sciences, Leukemia Study Center, University of Milan, Italy

Tóm tắt

Abstract Background

The role of microRNAs (miRNAs) in multiple myeloma (MM) has yet to be fully elucidated. To identify miRNAs that are potentially deregulated in MM, we investigated those mapping within transcription units, based on evidence that intronic miRNAs are frequently coexpressed with their host genes. To this end, we monitored host transcript expression values in a panel of 20 human MM cell lines (HMCLs) and focused on transcripts whose expression varied significantly across the dataset.

 Methods

miRNA expression was quantified by Quantitative Real-Time PCR. Gene expression and genome profiling data were generated on Affymetrix oligonucleotide microarrays. Significant Analysis of Microarrays algorithm was used to investigate differentially expressed transcripts. Conventional statistics were used to test correlations for significance. Public libraries were queried to predict putative miRNA targets.

 Results

We identified transcripts specific to six miRNA host genes (CCPG1, GULP1, EVL, TACSTD1, MEST, and TNIK) whose average changes in expression varied at least 2-fold from the mean of the examined dataset. We evaluated the expression levels of the corresponding intronic miRNAs and identified a significant correlation between the expression levels of MEST, EVL, and GULP1 and those of the corresponding miRNAs miR-335, miR-342-3p, and miR-561, respectively. Genome-wide profiling of the 20 HMCLs indicated that the increased expression of the three host genes and their corresponding intronic miRNAs was not correlated with local copy number variations. Notably, miRNAs and their host genes were overexpressed in a fraction of primary tumors with respect to normal plasma cells; however, this finding was not correlated with known molecular myeloma groups. The predicted putative miRNA targets and the transcriptional profiles associated with the primary tumors suggest that MEST/miR-335 and EVL/miR-342-3p may play a role in plasma cell homing and/or interactions with the bone marrow microenvironment.

 Conclusion

Our data support the idea that intronic miRNAs and their host genes are regulated dependently, and may contribute to the understanding of their biological roles in cancer. To our knowledge, this is the first evidence of deregulated miRNA expression in MM, providing insights that may lead to the identification of new biomarkers and altered molecular pathways of the disease.

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Tài liệu tham khảo

Fonseca R, Barlogie B, Bataille R, Bastard C, Bergsagel PL, Chesi M, Davies FE, Drach J, Greipp PR, Kirsch IR, Kuehl WM, Hernandez JM, Minvielle S, Pilarski LM, Shaughnessy JD, Stewart AK, Avet-Loiseau H: Genetics and cytogenetics of multiple myeloma: a workshop report. Cancer Res. 2004, 64: 1546-1558. 10.1158/0008-5472.CAN-03-2876.

Bergsagel PL, Kuehl WM, Zhan F, Sawyer J, Barlogie B, Shaughnessy J: Cyclin D dysregulation: an early and unifying pathogenic event in multiple myeloma. Blood. 2005, 106: 296-303. 10.1182/blood-2005-01-0034.

Chesi M, Bergsagel PL, Shonukan OO, Martelli ML, Brents LA, Chen T, Schrock E, Ried T, Kuehl WM: Frequent dysregulation of the c-maf proto-oncogene at 16q23 by translocation to an Ig locus in multiple myeloma. Blood. 1998, 91: 4457-4463.

Richelda R, Ronchetti D, Baldini L, Cro L, Viggiano L, Marzella R, Rocchi M, Otsuki T, Lombardi L, Maiolo AT, Neri A: A novel chromosomal translocation t(4; 14)(p16.3; q32) in multiple myeloma involves the fibroblast growth-factor receptor 3 gene. Blood. 1997, 90: 4062-4070.

Ronchetti D, Finelli P, Richelda R, Baldini L, Rocchi M, Viggiano L, Cuneo A, Bogni S, Fabris S, Lombardi L, Maiolo AT, Neri A: Molecular analysis of 11q13 breakpoints in multiple myeloma. Blood. 1999, 93: 1330-1337.

Bartel DP: MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004, 116: 281-297. 10.1016/S0092-8674(04)00045-5.

Calin GA, Ferracin M, Cimmino A, Di Leva G, Shimizu M, Wojcik SE, Iorio MV, Visone R, Sever NI, Fabbri M, Iuliano R, Palumbo T, Pichiorri F, Roldo C, Garzon R, Sevignani C, Rassenti L, Alder H, Volinia S, Liu CG, Kipps TJ, Negrini M, Croce CM: A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. N Engl J Med. 2005, 353: 1793-1801. 10.1056/NEJMoa050995.

Calin GA, Croce CM: MicroRNA signatures in human cancers. Nat Rev Cancer. 2006, 6: 857-866. 10.1038/nrc1997.

Calin GA, Croce CM: MicroRNAs and chromosomal abnormalities in cancer cells. Oncogene. 2006, 25: 6202-6210. 10.1038/sj.onc.1209910.

Loffler D, Brocke-Heidrich K, Pfeifer G, Stocsits C, Hackermuller J, Kretzschmar AK, Burger R, Gramatzki M, Blumert C, Bauer K, Cvijic H, Ullmann AK, Stadler PF, Horn F: Interleukin-6 dependent survival of multiple myeloma cells involves the Stat3-mediated induction of microRNA-21 through a highly conserved enhancer. Blood. 2007, 110: 1330-1333. 10.1182/blood-2007-03-081133.

Baskerville S, Bartel DP: Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA. 2005, 11: 241-247. 10.1261/rna.7240905.

Li SC, Tang P, Lin WC: Intronic microRNA: discovery and biological implications. DNA Cell Biol. 2007, 26: 195-207. 10.1089/dna.2006.0558.

Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A: Identification of mammalian microRNA host genes and transcription units. Genome Res. 2004, 14: 1902-1910. 10.1101/gr.2722704.

Kim YK, Kim VN: Processing of intronic microRNAs. EMBO J. 2007, 26: 775-783. 10.1038/sj.emboj.7601512.

Borchert GM, Lanier W, Davidson BL: RNA polymerase III transcribes human microRNAs. Nat Struct Mol Biol. 2006, 13: 1097-1101. 10.1038/nsmb1167.

Lombardi L, Poretti G, Mattioli M, Fabris S, Agnelli L, Bicciato S, Kwee I, Rinaldi A, Ronchetti D, Verdelli D, Lambertenghi-Deliliers G, Bertoni F, Neri A: Molecular characterization of human multiple myeloma cell lines by integrative genomics: insights into the biology of the disease. Genes Chromosomes Cancer. 2007, 46: 226-238. 10.1002/gcc.20404.

Verdelli D, Mattioli M, Fabris S, Nobili L, Intini D, Guerneri S, Todoerti K, Zanella A, Deliliers GL, Lombardi L, Neri A: Molecular and biological characterization of three novel interleukin-6-dependent human myeloma cell lines. Haematologica. 2005, 90: 1541-1548.

miRanda. 2008, [http://www.microrna.org/]

John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS: Human MicroRNA targets. PLoS Biol. 2004, 2: e363-10.1371/journal.pbio.0020363.

TargetScan. 2008, [http://www.targetscan.org/]

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. 10.1016/j.cell.2004.12.035.

PicTar. 2008, [http://pictar.bio.nyu.edu/]

Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da P, Gunsalus KC, Stoffel M, Rajewsky N: Combinatorial microRNA target predictions. Nat Genet. 2005, 37: 495-500. 10.1038/ng1536.

Diana microT. 2008, [http://diana.pcbi.upenn.edu/cgi-bin/micro_t.cgi]

Kiriakidou M, Nelson PT, Kouranov A, Fitziev P, Bouyioukos C, Mourelatos Z, Hatzigeorgiou A: A combined computational-experimental approach predicts human microRNA targets. Genes Dev. 2004, 18: 1165-1178. 10.1101/gad.1184704.

Gene Expression Omnibus. 2008, [http://www.ncbi.nlm.nih.gov/geo/]

Gutierrez NC, Ocio EM, de Las RJ, Maiso P, Delgado M, Ferminan E, Arcos MJ, Sanchez ML, Hernandez JM, San Miguel JF: Gene expression profiling of B lymphocytes and plasma cells from Waldenstrom's macroglobulinemia: comparison with expression patterns of the same cell counterparts from chronic lymphocytic leukemia, multiple myeloma and normal individuals. Leukemia. 2007, 21: 541-549. 10.1038/sj.leu.2404520.

Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003, 4: 249-264. 10.1093/biostatistics/4.2.249.

SAM software version 2.21. 2008, [http://www-stat.stanford.edu/~tibs/SAM/index.html]

Tusher VG, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A. 2001, 98: 5116-5121. 10.1073/pnas.091062498.

Database for Annotation, Visualization and Integrated Discovery Tool 2006. 2008, [http://david.abcc.ncifcrf.gov]

NetAffx. 2008, [https://www.affymetrix.com/analysis/netaffx/]

Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A: Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res. 2005, 33: D121-D124. 10.1093/nar/gki081.

Sanger database. 2008, [http://www.sanger.ac.uk/]

Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, Lao KQ, Livak KJ, Guegler KJ: Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res. 2005, 33: e179-10.1093/nar/gni178.

Genome Browser Database. 2008, [http://genome.ucsc.edu/]

Hideshima T, Bergsagel PL, Kuehl WM, Anderson KC: Advances in biology of multiple myeloma: clinical applications. Blood. 2004, 104: 607-618. 10.1182/blood-2004-01-0037.

Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM: Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature. 2005, 433: 769-773. 10.1038/nature03315.

Zhang L, Huang J, Yang N, Greshock J, Megraw MS, Giannakakis A, Liang S, Naylor TL, Barchetti A, Ward MR, Yao G, Medina A, O'brien-Jenkins A, Katsaros D, Hatzigeorgiou A, Gimotty PA, Weber BL, Coukos G: microRNAs exhibit high frequency genomic alterations in human cancer. Proc Natl Acad Sci U S A. 2006, 103: 9136-9141. 10.1073/pnas.0508889103.

Tavazoie SF, Alarcon C, Oskarsson T, Padua D, Wang Q, Bos PD, Gerald WL, Massague J: Endogenous human microRNAs that suppress breast cancer metastasis. Nature. 2008, 451: 147-152. 10.1038/nature06487.

Sathyan P, Golden HB, Miranda RC: Competing interactions between micro-RNAs determine neural progenitor survival and proliferation after ethanol exposure: evidence from an ex vivo model of the fetal cerebral cortical neuroepithelium. J Neurosci. 2007, 27: 8546-8557. 10.1523/JNEUROSCI.1269-07.2007.

Grady WM, Parkin RK, Mitchell PS, Lee JH, Kim YH, Tsuchiya KD, Washington MK, Paraskeva C, Willson JK, Kaz AM, Kroh EM, Allen A, Fritz BR, Markowitz SD, Tewari M: Epigenetic silencing of the intronic microRNA hsa-miR-342 and its host gene EVL in colorectal cancer. Oncogene. 2008, 27: 3880-3888. 10.1038/onc.2008.10.

Guglielmelli P, Tozzi L, Pancrazzi A, Bogani C, Antonioli E, Ponziani V, Poli G, Zini R, Ferrari S, Manfredini R, Bosi A, Vannucchi AM: MicroRNA expression profile in granulocytes from primary myelofibrosis patients. Exp Hematol. 2007, 35: 1708-1718. 10.1016/j.exphem.2007.08.020.

Garzon R, Pichiorri F, Palumbo T, Visentini M, Aqeilan R, Cimmino A, Wang H, Sun H, Volinia S, Alder H, Calin GA, Liu CG, Andreeff M, Croce CM: MicroRNA gene expression during retinoic acid-induced differentiation of human acute promyelocytic leukemia. Oncogene. 2007, 26: 4148-4157. 10.1038/sj.onc.1210186.

Krause M, Dent EW, Bear JE, Loureiro JJ, Gertler FB: Ena/VASP proteins: regulators of the actin cytoskeleton and cell migration. Annu Rev Cell Dev Biol. 2003, 19: 541-564. 10.1146/annurev.cellbio.19.050103.103356.

Su HP, Nakada-Tsukui K, Tosello-Trampont AC, Li Y, Bu G, Henson PM, Ravichandran KS: Interaction of CED-6/GULP, an adapter protein involved in engulfment of apoptotic cells with CED-1 and CD91/low density lipoprotein receptor-related protein (LRP). J Biol Chem. 2002, 277: 11772-11779. 10.1074/jbc.M109336200.

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