Integrative analysis of differential miRNA and functional study of miR-21 by seed-targeting inhibition in multiple myeloma cells in response to berberine

BMC Systems Biology

Volumn 8, Issue 1, 2014, Pages

  Luo, Xiaochuang ^a   Gu, Jingyi ^a   Zhu, Rongxuan ^a   Feng, Maoxiao ^a   Zhu, Xuejiao ^a   Li, Yumin ^a   Fei, Jia ^a  

^a MEDICAL COLLEGE OF JINAN UNIVERSITY   (China)

Author keywords

Apoptosis; Berberine; Bioinformatic; Cell cycle; miRNA 21; Multiple myeloma; Programmed cell death 4; Tumor protein p53

Indexed keywords

ANTINEOPLASTIC AGENT; APOPTOSIS REGULATORY PROTEIN; BERBERINE; INTERLEUKIN 6; MESSENGER RNA; MICRORNA; MIRN21 MICRORNA, MOUSE; PDCD4 PROTEIN, HUMAN; RNA BINDING PROTEIN; SMALL INTERFERING RNA; STAT3 PROTEIN;

APOPTOSIS; BIOLOGY; CELL PROLIFERATION; DEFICIENCY; DOWN REGULATION; DRUG EFFECTS; G2 PHASE CELL CYCLE CHECKPOINT; GENE EXPRESSION REGULATION; GENE SILENCING; GENETICS; HUMAN; METABOLISM; MULTIPLE MYELOMA; PATHOLOGY; TUMOR CELL LINE; UPREGULATION;

ANTINEOPLASTIC AGENTS; APOPTOSIS; APOPTOSIS REGULATORY PROTEINS; BERBERINE; CELL LINE, TUMOR; CELL PROLIFERATION; COMPUTATIONAL BIOLOGY; DOWN-REGULATION; G2 PHASE CELL CYCLE CHECKPOINTS; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE SILENCING; HUMANS; INTERLEUKIN-6; MICRORNAS; MULTIPLE MYELOMA; RNA, MESSENGER; RNA, SMALL INTERFERING; RNA-BINDING PROTEINS; STAT3 TRANSCRIPTION FACTOR; UP-REGULATION;

EID: 84903688096     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-8-82     Document Type: Article

References (47)

1. Raab MS, Podar K, Breitkreutz I, Richardson PG, Anderson KC. Multiple myeloma. Lancet 2009, 374(9686):324-339. 10.1016/S0140-6736(09)60221-X, 19541364.
2. Ge F, Bi LJ, Tao SC, Xu XD, Zhang ZP, Kitazato K, Zhang XE. Proteomic analysis of multiple myeloma: current status and future perspectives. Proteomics Clin Appl 2011, 5(1-2):30-37.
3. 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(4):1546-1558. 10.1158/0008-5472.CAN-03-2876, 14989251.
4. Calin GA, Croce CM. MicroRNAs and chromosomal abnormalities in cancer cells. Oncogene 2006, 25(46):6202-6210. 10.1038/sj.onc.1209910, 17028600.
5. Calin GA, Croce CM. MicroRNA-cancer connection: the beginning of a new tale. Cancer Res 2006, 66(15):7390-7394. 10.1158/0008-5472.CAN-06-0800, 16885332.
6. Lionetti M, Biasiolo M, Agnelli L, Todoerti K, Mosca L, Fabris S, Sales G, Deliliers GL, Bicciato S, Lombardi L, Bortoluzzi S, Neri A. Identification of microRNA expression patterns and definition of a microRNA/ mRNA regulatory network in distinct molecular groups of multiple myeloma. Blood 2009, 114(25):e20-26. 10.1182/blood-2009-08-237495, 19846888.
7. Bartel DP. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297. 10.1016/S0092-8674(04)00045-5, 14744438.
8. He L, Hannon GJ. MicroRNAs: Small RNAs with a big role in gene regulation. Nature Rev Genet 2004, 5:522-531. 10.1038/nrg1379, 15211354.
9. Yu Z, Jian Z, Shen SH, Purisima E, Wang E. Global analysis of microRNA target gene expression reveals that miRNA targets are lower expressed in mature mouse and Drosophila tissues than in the embryos. Nucleic Acids Res 2007, 35:152-164. 1802562, 17158157.
10. Cho WC. OncomiRs: the discovery and progress of microRNAs in cancers. Mol Cancer 2007, 6:60. 10.1186/1476-4598-6-60, 2098778, 17894887.
11. Esquela-Kerscher A, Slack FJ. Oncomirs-microRNAs with a role in cancer. Nat Rev Cancer 2006, 6:259-269. 10.1038/nrc1840, 16557279.
12. Pichiorri F, De Luca L, Aqeilan RI. MicroRNAs: new players in multiple myeloma. Front Genet 2011, 2:22. 3268577, 22303318.
13. Munker R, Liu CG, Taccioli C, Alder H, Heerema N. MicroRNA profiles of drug-resistant myeloma cell lines. Acta Haematol 2010, 123(4):201-204. 10.1159/000302889, 2881892, 20357429.
14. Pichiorri F, Suh SS, Ladetto M, Kuehl M, Palumbo T, Drandi D, Taccioli C, Zanesi N, Alder H, Hagan JP, Munker R, Volinia S, Boccadoro M, Garzon R, Palumbo A, Aqeilan RI, Croce CM. MicroRNAs regulate critical genes associated with multiple myeloma pathogenesis. Proc Natl Acad Sci U S A 2008, 105(35):12885-12890. 10.1073/pnas.0806202105, 2529070, 18728182.
15. Xiong Q, Zhong Q, Zhang J, Yang M, Li C, Zheng P, Bi LJ, Ge F. Identification of novel mir-21 target proteins in multiple myeloma cells by quantitative proteomics. J Proteome Res 2012, 11(4):2078-2090. 10.1021/pr201079y, 22316494.
16. Löffler D, Brocke-Heidrich K, Pfeifer G, Stocsits C, Hackermüller 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(4):1330-1333. 10.1182/blood-2007-03-081133, 17496199.
17. Zhang X, Gu L, Li J, Shah N, He J, Yang L, Hu Q, Zhou M. Degradation of MDM2 by the interaction between berberine and DAXX leads to potent apoptosis in MDM2-overexpressing cancer cells. Cancer Res 2010, 70(23):9895-9904. 10.1158/0008-5472.CAN-10-1546, 2999659, 20935220.
18. Pandey MK, Sung B, Kunnumakkara AB, Sethi G, Chaturvedi MM, Aggarwal BB. Berberine modifies cysteine 179 of IKBA kinase, suppresses nuclear factor-KB-regulated antiapoptotic gene products, and potentiates apoptosis. Cancer Res 2008, 68(13):5370-5379. 10.1158/0008-5472.CAN-08-0511, 18593939.
19. Yu FS, Yang JS, Lin HJ, Yu CS, Tan TW, Lin YT, Lin CC, Lu HF, Chung JG. Berberine inhibits WEHI-3 leukemia cells in vivo. In Vivo 2007, 21:407-412.
20. Mantena SK, Sharma SD, Katiyar SK. Berberine inhibits growth, induces G1 arrest and apoptosis in human epidermoid carcinoma A431 cells by regulating Cdki-Cdk-cyclin cascade, disruption of mitochondrial membrane potential and cleavage of caspase 3 and PARP. Carcinogenesis 2006, 27:2018-2027. 10.1093/carcin/bgl043, 16621886.
21. Anis KV, Rajeshkumar NV, Kuttan R. Inhibition of chemical carcinogenesis by berberine in rats and mice. J Pharm Pharmacol 2001, 53:763-768. 10.1211/0022357011775901, 11370717.
22. Nishino H, Kitagawa K, Fujiki H, Iwashima A. Berberine sulfate inhibits tumor-promoting activity of teleocidin in two-stage carcinogenesis on mouse skin. Oncology 1986, 43:131-134. 10.1159/000226349, 3081844.
23. Sun Y, Xun K, Wang Y, Chen X. A systematic review of the anticancer properties of berberine, a natural product from Chinese herbs. Anticancer Drugs 2009, 20:757-769. 10.1097/CAD.0b013e328330d95b, 19704371.
24. Wang X. Composition of seed sequence is a major determinant of microRNA targeting patterns. Bioinformatics 2014, 2014 Feb 12. [Epub ahead of print].
25. Rottiers V, Obad S, Petri A, McGarrah R, Lindholm MW, Black JC, Sinha S, Goody RJ, Lawrence MS, deLemos AS, Hansen HF, Whittaker S, Henry S, Brookes R, Najafi-Shoushtari SH, Chung RT, Whetstine JR, Gerszten RE, Kauppinen S, Näär AM. Pharmacological inhibition of a microRNA family in nonhuman primates by a seed-targeting 8-mer antimiR. Sci Transl Med 2013, 5(212):212ra162. 10.1126/scitranslmed.3006840, 24259050.
26. Obad S, dos Santos CO, Petri A, Heidenblad M, Broom O, Ruse C, Fu C, Lindow M, Stenvang J, Straarup EM, Hansen HF, Koch T, Pappin D, Hannon GJ, Kauppinen S. Silencing of microRNA families by seed-targeting tiny LNAs. Nat Genet 2011, 43(4):371-378. 10.1038/ng.786, 3541685, 21423181.
27. Lu Z, Liu M, Stribinskis V. MicroRNA-21 promotes cell transformation by targeting the programmed cell death 4 gene. Oncogene 2008, 27:4373-4379. 10.1038/onc.2008.72, 18372920.
28. Asangani IA, Rasheed SA, Nikolova DA, Leupold JH, Colburn NH, Post S, Allgayer H. MicroRNA-21 (miR-21) post-transcriptionally downregulates tumor suppressor Pdcd4 and stimulates invasion, intravasation and metastasis in colorectal cancer. Oncogene 2008, 27:2128-2136. 10.1038/sj.onc.1210856, 17968323.
29. Si ML, Zhu S, Wu H, Lu Z, Wu F, Mo YY. miR-21-mediated tumor growth. Oncogene 2007, 26(19):2799-2803. 10.1038/sj.onc.1210083, 17072344.
30. Medina PP, Nolde M, Slack FJ. OncomiR addiction in an vivo model of microRNA-21-induced pre-B-cell lymphoma. Nature 2010, 467(7311):86-90. 10.1038/nature09284, 20693987.
31. Esau CC. Inhibition of microRNA with antisense oligonucleotides. Methods 2008, 44:55-60. 10.1016/j.ymeth.2007.11.001, 18158133.
32. Cheng AM, Byrom MW, Shelton J, Ford LP. Antisense inhibition of human miRNAs and indications for an involvement of miRNA in cell growth and apoptosis. Nucleic Acids Res 2005, 33:1290-1297. 10.1093/nar/gki200, 552951, 15741182.
33. Weiler J, Hunziker J, Hall J. Anti-miRNA oligonucleotides (AMOs): ammunition to target miRNAs implicated in human disease?. Gene Ther 2005, 13:496-502.
34. Krichevsky AM, Gabriely G. miR-21: a small multi-faceted RNA. J Cell Mol Med 2009, 13(1):39-53.
35. Selcuklu SD, Donoghue MT, Spillane C. miR-21 as a key regulator of oncogenic processes. Biochem Soc Trans 2009, 37(Pt 4):918-925.
36. Lankat-Buttgereit B, Göke R. The tumour suppressor Pdcd4: recent advances in the elucidation of function and regulation. Biol Cell 2009, 101(6):309-317. 10.1042/BC20080191, 19356152.
37. Sonenberg N, Pause A. Protein synthesis and oncogenesis meet again. Science 2006, 314(5798):428-429. 10.1126/science.1134031, 17053135.
38. Leupold JH, Asangani IA, Mudduluru G, Allgayer H. Promoter cloning and characterization of the human programmed cell death protein 4 (pdcd4) gene: evidence for ZBP-89 and Sp-binding motifs as essential Pdcd4-regulators. Biosci Rep 2012, 32(3):281-297. 10.1042/BSR20110045, 22111549.
39. Li X, Xin S, Yang D, Li X, He Z, Che X, Wang J, Chen F, Wang X, Song X. Down-regulation of PDCD4 expression is an independent predictor of poor prognosis in human renal cell carcinoma patients. J Cancer Res Clin Oncol 2012, 138(3):529-535. 10.1007/s00432-011-1121-y, 22203471.
40. Yang HS, Knies JL, Stark C, Colburn NH. Pdcd4 suppresses tumor phenotype in JB6 cells by inhibiting AP-1 transactivation. Oncogene 2003, 22:3712-3720. 10.1038/sj.onc.1206433, 12802278.
41. Bitomsky N, Böhm M, Klempnauer KH. Transformation suppressor protein Pdcd4 interferes with JNK-mediated phosphorylation of c-Jun and recruitment of the coactivator p300 by c-Jun. Oncogene 2004, 23(45):7484-7493. 10.1038/sj.onc.1208064, 15334056.
42. Leupold JH, Yang HS, Colburn NH, Asangani I, Post S, Allgayer H. Tumor suppressor Pdcd4 inhibits invasion/intravasation and regulates urokinase receptor (u-PAR) gene expression via Sp-transcription factors. Oncogene 2007, 26(31):4550-4562. 10.1038/sj.onc.1210234, 17297470.
43. Bitomsky N, Wethkamp N, Marikkannu R, Klempnauer KH. siRNA-mediated knockdown of Pdcd4 expression causes upregulation of p21(Waf1/Cip1) expression. Oncogene 2008, 27(35):4820-9. Epub 2008 Apr 21, 10.1038/onc.2008.115, 18427550.
44. Wedeken L, Singh P, Klempnauer KH. Tumor suppressor protein Pdcd4 inhibits translation of p53 mRNA. J Biol Chem 2011, 286(50):42855-62. Epub 2011 Oct 27, 10.1074/jbc.M111.269456, 3234825, 22033922.
45. Fraser M, Leung BM, Yan X, Dan HC, Cheng JQ, Tsang BK. p53 is a determinant of X-linked inhibitor of apoptosis protein/Akt-mediated chemoresistance in human ovarian cancer cells. Cancer Res 2003, 63:7081-7088.
46. Fraser M, Leung B, Jahani-Asl A, Yan X, Thompson WE, Tsang BK. Chemoresistance in human ovarian cancer: the role of apoptotic regulators. Reprod Biol Endocrinol 2003, 1:66. 10.1186/1477-7827-1-66, 270001, 14609433.
47. Hu HY, Li KP, Wang XJ, Liu Y, Lu ZG, Dong RH, Guo HB, Zhang MX. Set9, NF-κB, and microRNA-21 mediate berberine-induced apoptosis of human multiple myeloma cells. 2013, 34(1):157-166.