Quantitative proteomic strategies for the identification of microRNA targets

Expert Review of Proteomics

Volumn 9, Issue 5, 2012, Pages 549-559

  Li, Chongyang ^a,b   Xiong, Qian ^a   Zhang, Jia ^a,c   Ge, Feng ^a   Bi, Li Jun ^c  

^a INSTITUTE OF HYDROBIOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c INSTITUTE OF BIOPHYSICS   (China)

Author keywords

2D difference gel electrophoresis; isobaric tags for relative and absolute quantification; isotope coded affinity tags; microRNAs; pulsed stable isotope labeling by amino acids in cell culture; quantitative proteomics; stable isotope labeling by amino acids in cell culture

Indexed keywords

MICRORNA; MICRORNA 1; MICRORNA 122A; MICRORNA 124; MICRORNA 143; MICRORNA 155; MICRORNA 16; MICRORNA 17 92; MICRORNA 181; MICRORNA 193B; MICRORNA 200S; MICRORNA 21; MICRORNA 223; MICRORNA 29A; MICRORNA 30A; MICRORNA 34A; MICRORNA 372; MICRORNA 373; MICRORNA 7; MICRORNA LET 7B; UNCLASSIFIED DRUG;

ANALYTIC METHOD; BASE PAIRING; BODY FLUID; CELL CULTURE; HUMAN; INTERMETHOD COMPARISON; ISOBARIC TAG FOR RELATIVE AND ABSOLUTE QUANTIFICATION; ISOTOPE CODED AFFINITY TAG; ISOTOPE LABELING; NEOPLASM; NONHUMAN; PROTEIN MICROARRAY; PROTEOMICS; PUBLICATION; PULSED STABLE ISOTOPE LABELING BY AMINO ACID IN CELL CULTURE; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; RNA ANALYSIS; STABLE ISOTOPE LABELING BY AMINO ACID IN CELL CULTURE; TIME OF FLIGHT MASS SPECTROMETRY; TRANSLATION REGULATION; TWO DIMENSIONAL DIFFERENCE GEL ELECTROPHORESIS;

GENE EXPRESSION REGULATION; HUMANS; ISOTOPE LABELING; MICRORNAS; PROTEIN BIOSYNTHESIS; PROTEOMICS; RNA, MESSENGER; TWO-DIMENSIONAL DIFFERENCE GEL ELECTROPHORESIS;

EID: 84870577216     PISSN: 14789450     EISSN: 17448387     Source Type: Journal    
DOI: 10.1586/epr.12.49     Document Type: Review

References (76)

1. Lee RC, Ambros V. An extensive class of small RNAs in Caenorhabditis elegans. Science 294(5543), 862-864 (2001).
2. Ambros V, Lee RC, Lavanway A, Williams PT, Jewell D. MicroRNAs and other tiny endogenous RNAs in C elegans. Curr. Biol. 13(10), 807-818 (2003).
3. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116(2), 281-297 (2004).
4. Lee Y, Ahn C, Han J et al. The nuclear RNase III Drosha initiates microRNA processing. Nature 425(6956), 415-419 (2003).
5. Yi R, Qin Y, Macara IG, Cullen BR. Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev. 17(24), 3011-3016 (2003).
6. Gregory RI, Chendrimada TP, Cooch N, Shiekhattar R. Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell 123(4), 631-640 (2005).
7. Rana TM. Illuminating the silence: understanding the structure and function of small RNAs. Nat. Rev. Mol. Cell Biol. 8(1), 23-36 (2007).
8. Kim VN. MicroRNA biogenesis: coordinated cropping and dicing. Nat. Rev. Mol. Cell Biol. 6(5), 376-385 (2005).
9. Wiemer EA. The role of microRNAs in cancer: no small matter. Eur. J. Cancer 43(10), 1529-1544 (2007).
10. Tang G, Reinhart BJ, Bartel DP, Zamore PD. A biochemical framework for RNA silencing in plants. Genes Dev. 17(1), 49-63 (2003).
11. Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP. Prediction of plant microRNA targets. Cell 110(4), 513-520 (2002).
12. Berezikov E. Evolution of microRNA diversity and regulation in animals. Nat. Rev. Genet. 12(12), 846-860 (2011).
13. Thomson DW, Bracken CP, Goodall GJ. Experimental strategies for microRNA target identifcation. Nucleic Acids Res. 39(16), 6845-6853 (2011).
14. Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often fanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120(1), 15-20 (2005).
15. Ryan BM, Robles AI, Harris CC. Genetic variation in microRNA networks: the implications for cancer research. Nat. Rev. Cancer 10(6), 389-402 (2010).
16. Broderick JA, Zamore PD. MicroRNA therapeutics. Gene Ther. 18(12), 1104-1110 (2011).
17. Wu S, Huang S, Ding J et al. Multiple microRNAs modulate p21Cip1/Waf1 expression by directly targeting its 3́ untranslated region. Oncogene 29(15), 2302-2308 (2010).
18. Thomas M, Lieberman J, Lal A. Desperately seeking microRNA targets. Nat. Struct. Mol. Biol. 17(10), 1169-1174 (2010).
19. Griffths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res. 36 (Database issue), D154-D158 (2008).
20. Krek A, Grün D, Poy MN et al. Combinatorial microRNA target predictions. Nat. Genet. 37(5), 495-500 (2005).
21. Ritchie W, Flamant S, Rasko JE. Predicting microRNA targets and functions: traps for the unwary. Nat. Methods 6(6), 397-398 (2009).
22. Alexiou P, Maragkakis M, Papadopoulos GL, Reczko M, Hatzigeorgiou AG. Lost in translation: an assessment and perspective for computational microRNA target identifcation. Bioinformatics 25(23), 3049-3055 (2009).
23. Bentwich I. Prediction and validation of microRNAs and their targets. FEBS Lett. 579(26), 5904-5910 (2005).
24. Sethupathy P, Megraw M, Hatzigeorgiou AG. A guide through present computational approaches for the identifcation of mammalian microRNA targets. Nat. Methods 3(11), 881-886 (2006).
25. Baek D, Villén J, Shin C, Camargo FD, Gygi SP, Bartel DP. The impact of microRNAs on protein output. Nature 455(7209), 64-71 (2008).
26. Grosshans H, Filipowicz W. Proteomics joins the search for microRNA targets. Cell 134(4), 560-562 (2008).
27. Hendrickson DG, Hogan DJ, Herschlag D, Ferrell JE, Brown PO. Systematic identifcation of mRNAs recruited to argonaute 2 by specifc microRNAs and corresponding changes in transcript abundance. PLoS ONE 3(5), e2126 (2008).
28. Karginov FV, Conaco C, Xuan Z et al. A biochemical approach to identifying microRNA targets. Proc. Natl Acad. Sci. USA 104(49), 19291-19296 (2007).
29. Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell 136(2), 215-233 (2009).
30. Brodersen P, Voinnet O. Revisiting the principles of microRNA target recognition and mode of action. Nat. Rev. Mol. Cell Biol. 10(2), 141-148 (2009).
31. Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP. MicroRNA targeting specifcity in mammals: determinants beyond seed pairing. Mol. Cell 27(1), 91-105 (2007).
32. Elmén J, Lindow M, Schütz S et al. LNA-mediated microRNA silencing in non-human primates. Nature 452(7189), 896-899 (2008).
33. Leivonen SK, Rokka A, Ostling P et al. Identifcation of miR-193b targets in breast cancer cells and systems biological analysis of their functional impact. Mol. Cell Proteomics 10(7), M110.005322 (2011).
34. Schiess R, Wollscheid B, Aebersold R. Targeted proteomic strategy for clinical biomarker discovery. Mol. Oncol. 3(1), 33-44 (2009).
35. Rajcevic U, Niclou SP, Jimenez CR. Proteomics strategies for target identifcation and biomarker discovery in cancer. Front. Biosci. 14, 3292-3303 (2009).
36. Schramedei K, Mörbt N, Pfeifer G et al. MicroRNA-21 targets tumor suppressor genes ANP32A and SMARCA4. Oncogene 30(26), 2975-2985 (2011).
37. Yang Y, Chaerkady R, Beer MA, Mendell JT, Pandey A. Identifcation of miR-21 targets in breast cancer cells using a quantitative proteomic approach. Proteomics 9(5), 1374-1384 (2009).
38. Xiong Q, Zhong Q, Zhang J et al. Identifcation of novel miR-21 target proteins in multiple myeloma cells by quantitative proteomics. J. Proteome Res. 11(4), 2078-2090 (2012).
39. Coombs KM. Quantitative proteomics of complex mixtures. Expert Rev. Proteomics 8(5), 659-677 (2011).
40. Issaq H, Veenstra T. Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE): advances and perspectives. BioTechniques 44(5), 697-698, 700 (2008).
41. Marko-Varga G, Lindberg H, Löfdahl CG et al. Discovery of biomarker candidates within disease by protein profling: principles and concepts. J. Proteome Res. 4 (4), 1200-1212 (2005).
42. Diao S, Zhang JF, Wang H et al. Proteomic identifcation of microRNA-122a target proteins in hepatocellular carcinoma. Proteomics 10(20), 3723-3731 (2010).
43. Kanzaki H, Ito S, Hanafusa H et al. Identifcation of direct targets for the miR-17-92 cluster by proteomic analysis. Proteomics 11(17), 3531-3539 (2011).
44. Unlü M, Morgan ME, Minden JS. Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18(11), 2071-2077 (1997).
45. Muniyappa MK, Dowling P, Henry M et al. MiRNA-29a regulates the expression of numerous proteins and reduces the invasiveness and proliferation of human carcinoma cell lines. Eur. J. Cancer 45(17), 3104-3118 (2009).
46. Lai JH, She TF, Juang YM et al. Comparative proteomic profling of human lung adenocarcinoma cells (CL 1-0) expressing miR-372. Electrophoresis 33(4), 675-688 (2012).
47. Yang CH, Yue J, Fan M, Pfeffer LM. IFN induces miR-21 through a signal transducer and activator of transcription 3-dependent pathway as a suppressive negative feedback on IFN-induced apoptosis. Cancer Res. 70(20), 8108-8116 (2010).
48. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affnity tags. Nat. Biotechnol 17(10), 994-999 (1999).
49. Sethuraman M, McComb ME, Heibeck T, Costello CE, Cohen RA. Isotope-coded affnity tag approach to identify and quantify oxidant-sensitive protein thiols. Mol. Cell Proteomics 3 (3), 273-278 (2004).
50. Chen QR, Yu LR, Tsang P et al. Systematic proteome analysis identifes transcription factor YY1 as a direct target of miR-34a. J. Proteome Res. 10(2), 479-487 (2011).
51. Schmidt A, Kellermann J, Lottspeich F. A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 5(1), 4-15 (2005).
52. Ross PL, Huang YN, Marchese JN et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell Proteomics 3(12), 1154-1169 (2004).
53. Elliott MH, Smith DS, Parker CE, Borchers C. Current trends in quantitative proteomics. J. Mass Spectrom. 44(12), 1637-1660 (2009).
54. Mann M. Functional and quantitative proteomics using SILAC. Nat. Rev. Mol Cell Biol. 7(12), 952-958 (2006).
55. Gruhler S, Kratchmarova I. Stable isotope labeling by amino acids in cell culture (SILAC). Methods Mol. Biol. 424, 101-111 (2008).
56. Vinther J, Hedegaard MM, Gardner PP, Andersen JS, Arctander P. Identifcation of miRNA targets with stable isotope labeling by amino acids in cell culture. Nucleic Acids Res. 34(16), e107 (2006).
57. Yang Y, Chaerkady R, Kandasamy K et al. Identifying targets of miR-143 using a SILAC-based proteomic approach. Mol. Biosyst. 6(10), 1873-1882 (2010).
58. Korpal M, Ell BJ, Buffa FM et al. Direct targeting of Sec23a by miR-200s infuences cancer cell secretome and promotes metastatic colonization. Nat. Med. 17(9), 1101-1108 (2011).
59. Yan GR, Xu SH, Tan ZL, Liu L, He QY Global identifcation of miR-373-regulated genes in breast cancer by quantitative proteomics. Proteomics 11(5), 912-920 (2011).
60. Lössner C, Meier J, Warnken U et al Quantitative proteomics identify novel miR-155 target proteins. PLoS ONE 6(7), e22146 (2011).
61. Chou YT, Lin HH, Lien YC et al. EGFR promotes lung tumorigenesis by activating miR-7 through a Ras/ERK/Myc pathway that targets the Ets2 transcriptional repressor ERF. Cancer Res. 70(21), 8822-8831 (2010).
62. Selbach M, Schwanhäusser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N. Widespread changes in protein synthesis induced by microRNAs. Nature 455 (7209), 58-63 (2008).
63. Schwanhäusser B, Gossen M, Dittmar G, Selbach M. Global analysis of cellular protein translation by pulsed SILAC. Proteomics 9(1), 205-209 (2009).
64. Kaller M, Liffers ST, Oeljeklaus S et al. Genome-wide characterization of miR-34a induced changes in protein and mRNA expression by a combined pulsed SILAC and microarray analysis. Mol. Cell Proteomics 10(8), M111.010462 (2011).
65. Looso M, Borchardt T, Krüger M, Braun T. Advanced identifcation of proteins in uncharacterized proteomes by pulsed in vivo stable isotope labeling-based mass spectrometry. Mol. Cell Proteomics 9(6), 1157-1166 (2010).
66. Zhu W, Smith JW, Huang CM. Mass spectrometry-based label-free quantitative proteomics. J. Biomed. Biotechnol. 2010, 840518 (2010).
67. Fiedler J, Gupta SK, Thum T. Identifcation of cardiovascular microRNA targetomes. J. Mol. Cell. Cardiol. 51(5), 674-681 (2011).
68. Jin H, Tuo W, Lian H, Liu Q, Zhu XQ Gao H. Strategies to identify microRNA targets: new advances. N. Biotechnol. 27(6), 734-738 (2010).
69. Lehrbach NJ, Miska EA. Functional genomic, computational and proteomic analysis of C elegans microRNAs. Brief Funct. Genomic Proteomic 7(3), 228-235 (2008).
70. ∅rom UA, Lund AH. Experimental identifcation of microRNA targets. Gene 451(1-2), 1-5 (2010).
71. Krüger M, Moser M, Ussar S et al. SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell 134(2), 353-364 (2008).
72. Gouw JW, Pinkse MW, Vos HR et al. In vivo stable isotope labeling of fruit fies reveals post-transcriptional regulation in the maternal-to-zygotic transition. Mol. Cell Proteomics 8 (7), 1566-1578 (2009).
73. Liao L, McClatchy DB, Park SK, Xu T, Lu B, Yates JR 3rd. Quantitative analysis of brain nuclear phosphoproteins identifes developmentally regulated phosphorylation events. J. Proteome Res. 7(11), 4743-4755 (2008).
74. Westman-Brinkmalm A, Abramsson A, Pannee J et al. SILAC zebrafsh for quantitative analysis of protein turnover and tissue regeneration. J. Proteomics 75(2), 425-434 (2011).
75. Wang KC, Chang HY. Molecular mechanisms of long noncoding RNAs. Mol. Cell 43(6), 904-914 (2011).
76. Wapinski O, Chang HY. Long noncoding RNAs and human disease. Trends Cell Biol. 21(6), 354-361 (2011).