MicroRNAs act complementarily to regulate disease-related mRNA modules in human diseases

RNA

Volumn 19, Issue 11, 2013, Pages 1552-1562

  Chavali, Sreenivas ^a   Bruhn, Sören ^b   Tiemann, Katrin ^b   Sætrom, Pal ^c   Barrenäs, Fredrik ^b   Saito, Takaya ^c   Kanduri, Kartiek ^d   Wang, Hui ^b,d   Benson, Mikael ^b,e  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

^b LINKÖPING UNIVERSITY HOSPITAL   (Sweden)

^c NORWEGIAN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Norway)

^d UNIVERSITY OF GOTHENBURG   (Sweden)

^e QUEEN SILVIA CHILDREN'S HOSPITAL   (Sweden)

Author keywords

Diseases; MicroRNA; Modules; Regulation

Indexed keywords

MESSENGER RNA; MICRORNA; MICRORNA 139; MICRORNA 223; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

ARTICLE; CD4+ T LYMPHOCYTE; GENE CONTROL; GENE EXPRESSION; GENE TARGETING; GENOTYPE ENVIRONMENT INTERACTION; HAY FEVER; HUMAN; PATHOGENESIS; PHENOTYPE; PREDICTION; PRIORITY JOURNAL; RNA ANALYSIS;

DISEASES; MICRORNA; MODULES; REGULATION;

CARCINOMA, RENAL CELL; DIABETES MELLITUS, TYPE 2; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; HUMANS; INTERLEUKIN-13; INTERLEUKIN-5; KIDNEY NEOPLASMS; MICRORNAS; PANCREATIC NEOPLASMS; PRECURSOR CELL LYMPHOBLASTIC LEUKEMIA-LYMPHOMA; PULMONARY DISEASE, CHRONIC OBSTRUCTIVE; RHINITIS, ALLERGIC, SEASONAL; RNA, MESSENGER; TH2 CELLS;

EID: 84886002994     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.038414.113     Document Type: Article

References (43)

1. Akdis M, Verhagen J, Taylor A, Karamloo F, Karagiannidis C, Crameri R, Thunberg S, Deniz G, Valenta R, Fiebig H, et al. 2004. Immune responses in healthy and allergic individuals are characterized by a fine balance between allergen-specific T regulatory 1 and T helper 2 cells. J Exp Med 199: 1567-1575. (Pubitemid 38780411)
2. Barabasi AL, Albert R. 1999. Emergence of scaling in random networks. Science 286: 509-512.
3. Barabasi AL, Gulbahce N, Loscalzo J. 2011. Network medicine: A network-based approach to human disease. Nat Rev Genet 12: 56-68.
4. Barrenas F, Chavali S, Couto Alves A, Coin L, Jarvelin MR, Jornsten R, Langston MA, Ramasamy A, Rogers G, Wang H, et al. 2012. Highly interconnected genes in disease-specific networks are enriched for disease-associated polymorphisms. Genome Biol 13: R46.
5. Benson M, Carlsson L, Guillot G, Jernas M, Langston MA, Rudemo M, Andersson B. 2006a. A network-based analysis of allergen-challenged CD4+ T cells from patients with allergic rhinitis. Genes Immun 7: 514-521. (Pubitemid 44323685)
6. Benson M, Langston MA, Adner M, Andersson B, Torinssson-Naluai A, Cardell LO. 2006b. A network-based analysis of the late-phase reaction of the skin. J Allergy Clin Immunol 118: 220-225. (Pubitemid 43946468)
7. Bonnet E, Michoel T, Van de Peer Y. 2010a. Prediction of a gene regulatory network linked to prostate cancer from gene expression, microRNA and clinical data. Bioinformatics 26: i638-i644.
8. Bonnet E, Tatari M, Joshi A, Michoel T, Marchal K, Berx G, Van de Peer Y. 2010b. Module network inference from a cancer gene expression data set identifies microRNA regulated modules. PLoS One 5: e10162.
9. Bosco A, McKenna KL, Firth MJ, Sly PD, Holt PG. 2009. A network modeling approach to analysis of the Th2 memory responses underlying human atopic disease. J Immunol 182: 6011-6021.
10. Boyce JA, Bochner B, Finkelman FD, Rothenberg ME. 2012. Advances in mechanisms of asthma, allergy, and immunology in 2011. J Allergy Clin Immunol 129: 335-341.
11. Chiba Y, Tanabe M, Goto K, Sakai H, Misawa M. 2009. Down-regulation of miR-133a contributes to up-regulation of RhoA in bronchial smooth muscle cells. Am J Respir Crit Care Med 180: 713-719.
12. Esquela-Kerscher A, Slack FJ. 2006. Oncomirs-microRNAs with a role in cancer. Nat Rev Cancer 6: 259-269.
13. Gennarino VA, D'Angelo G, Dharmalingam G, Fernandez S, Russolillo G, Sanges R, Mutarelli M, Belcastro V, Ballabio A, Verde P, et al. 2012. Identification of microRNA-regulated gene networks by expression analysis of target genes. Genome Res 22: 1163-1172.
14. Goncharova EA, Lim PN, Chisolm A, Fogle HW III, Taylor JH, Goncharov DA, Eszterhas A, Panettieri RA Jr, Krymskaya VP. 2010. Interferons modulate mitogen-induced protein synthesis in airway smooth muscle. Am J Physiol Lung Cell Mol Physiol 299: L25-L35.
15. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. 2008. miRBase: Tools for microRNA genomics. Nucleic Acids Res 36(Database issue): D154-D158. (Pubitemid 351149713)
16. Guo H, Ingolia NT, Weissman JS, Bartel DP. 2010. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466: 835-840.
17. Hagg S, Skogsberg J, Lundstrom J, Noori P, Nilsson R, Zhong H, Maleki S, Shang MM, Brinne B, Bradshaw M, et al. 2009. Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: The Stockholm Atherosclerosis Gene Expression (STAGE) study. PLoS Genet 5: e1000754.
18. Huang da W, Sherman BT, Tan Q, Kir J, Liu D, Bryant D, Guo Y, Stephens R, Baseler MW, Lane HC, et al. 2007. DAVID bioinformatics resources: Expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res 35(Web Server issue): W169-W175.
19. Lage K, Karlberg EO, Storling ZM, Olason PI, Pedersen AG, Rigina O, Hinsby AM, Tumer Z, Pociot F, Tommerup N, et al. 2007. A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol 25: 309-316. (Pubitemid 46402863)
20. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB. 2003. Prediction of mammalian microRNA targets. Cell 115: 787-798. (Pubitemid 38058492)
21. Lim J, Hao T, Shaw C, Patel AJ, Szabo G, Rual JF, Fisk CJ, Li N, Smolyar A, Hill DE, et al. 2006. A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell 125: 801-814. (Pubitemid 43732348)
22. Love TM, Moffett HF, Novina CD. 2008. Not miR-ly small RNAs: Big potential for microRNAs in therapy. J Allergy Clin Immunol 121: 309-319. (Pubitemid 351215186)
23. Lu TX, Munitz A, Rothenberg ME. 2009. MicroRNA-21 is up-regulated in allergic airway inflammation and regulates IL-12p35 expression. J Immunol 182: 4994-5002.
24. Lu TX, Sherrill JD, Wen T, Plassard AJ, Besse JA, Abonia JP, Franciosi JP, Putnam PE, Eby M, Martin LJ, et al. 2012. MicroRNA signature in patients with eosinophilic esophagitis, reversibility with glucocorticoids, and assessment as disease biomarkers. J Allergy Clin Immunol 129: 1064-1075. e9.
25. Mattes J, Collison A, Plank M, Phipps S, Foster PS. 2009. Antagonism of microRNA-126 suppresses the effector function of TH2 cells and the development of allergic airways disease. Proc Natl Acad Sci 106: 18704-18709.
26. Mobini R, Andersson BA, Erjefalt J, Hahn-Zoric M, Langston MA, Perkins AD, Cardell LO, Benson M. 2009. A module-based analytical strategy to identify novel disease-associated genes shows an inhibitory role for interleukin 7 receptor in allergic inflammation. BMC Syst Biol 3: 19.
27. O'Connell RM, Rao DS, Chaudhuri AA, Baltimore D. 2010. Physiological and pathological roles for microRNAs in the immune system. Nat Rev Immunol 10: 111-122.
28. Petretto E, Liu ET, Aitman TJ. 2007. A gene harvest revealing the archeology and complexity of human disease. Nat Genet 39: 1299-1301. (Pubitemid 350035009)
29. Saito T, Saetrom P. 2010. A two-step site and mRNA-level model for predicting microRNA targets. BMC Bioinformatics 11: 612.
30. Sass S, Dietmann S, Burk UC, Brabletz S, Lutter D, Kowarsch A, Mayer KF, Brabletz T, Ruepp A, Theis FJ, et al. 2011. Micro-RNAs coordinately regulate protein complexes. BMC Syst Biol 5: 136.
31. Segal E, Friedman N, Koller D, Regev A. 2004. A module map showing conditional activity of expression modules in cancer. Nat Genet 36: 1090-1098. (Pubitemid 41184471)
32. Sioud M, Cekaite L. 2010. Profiling of miRNA expression and prediction of target genes. Methods Mol Biol 629: 257-271.
33. Su WL, Kleinhanz RR, Schadt EE. 2011. Characterizing the role of miRNAs within gene regulatory networks using integrative genomics techniques. Mol Syst Biol 7: 490.
34. Tsang JS, Ebert MS, van Oudenaarden A. 2010. Genome-wide dissection of microRNA functions and cotargeting networks using gene set signatures. Mol Cell 38: 140-153.
35. Ulitsky I, Laurent LC, Shamir R. 2010. Towards computational prediction of microRNA function and activity. Nucleic Acids Res 38: e160.
36. van Rooij E, Olson EN. 2007. MicroRNAs: Powerful new regulators of heart disease and provocative therapeutic targets. J Clin Invest 117: 2369-2376. (Pubitemid 47494334)
37. von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, Foglierini M, Jouffre N, Huynen MA, Bork P. 2005. STRING: Known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res 33(Database issue): D433-D437. (Pubitemid 40207910)
38. Wang H, Barrenas F, Bruhn S, Mobini R, Benson M. 2009a. Increased IFN-γ activity in seasonal allergic rhinitis is decreased by corticosteroid treatment. J Allergy Clin Immunol 124: 1360-1362.
39. Wang L, Tang H, Thayanithy V, Subramanian S, Oberg AL, Cunningham JM, Cerhan JR, Steer CJ, Thibodeau SN. 2009b. Gene networks and microRNAs implicated in aggressive prostate cancer. Cancer Res 69: 9490-9497.
40. Weinberg MS, Wood MJ. 2009. Short non-coding RNA biology and neurodegenerative disorders: Novel disease targets and therapeutics. Hum Mol Genet 18(R1): R27-R39.
41. Williams AE, Larner-Svensson H, Perry MM, Campbell GA, Herrick SE, Adcock IM, Erjefalt JS, Chung KF, Lindsay MA. 2009. MicroRNA expression profiling in mild asthmatic human airways and effect of corticosteroid therapy. PLoS One 4: e5889.
42. Woodfolk JA. 2007. T-cell responses to allergens. J Allergy Clin Immunol 119: 280-294. (Pubitemid 46204819)
43. Xiao C, Srinivasan L, Calado DP, Patterson HC, Zhang B, Wang J, Henderson JM, Kutok JL, Rajewsky K. 2008. Lymphoproliferative disease and autoimmunity in mice with increased miR-17-92 expression in lymphocytes. Nat Immunol 9: 405-414. (Pubitemid 351405110)