Identifying common and specific microRNAs expressed in peripheral blood mononuclear cell of type 1, type 2, and gestational diabetes mellitus patients

BMC Research Notes

Volumn 6, Issue 1, 2013, Pages

  Collares, Cristhianna Va ^a   Evangelista, Adriane F ^a   Xavier, Danilo J ^a   Rassi, Diane M ^a   Arns, Thais ^a   Foss Freitas, Maria C ^a   Foss, Milton C ^a   Puthier, Denis ^b   Sakamoto Hojo, Elza T ^a   Passos, Geraldo A ^a   Donadi, Eduardo A ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

^b AIX MARSEILLE UNIVERSITY   (France)

Author keywords

Gestational diabetes mellitus; Microarray; microRNA; mRNA; Type 1 diabetes mellitus; Type 2 diabetes mellitus

Indexed keywords

MICRORNA;

FEMALE; GENETICS; HUMAN; INSULIN DEPENDENT DIABETES MELLITUS; METABOLISM; MONOCYTE; NON INSULIN DEPENDENT DIABETES MELLITUS; PREGNANCY; PREGNANCY DIABETES MELLITUS;

DIABETES MELLITUS, TYPE 1; DIABETES MELLITUS, TYPE 2; DIABETES, GESTATIONAL; FEMALE; HUMANS; MICRORNAS; MONOCYTES; PREGNANCY;

EID: 84888156471     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-6-491     Document Type: Article

References (82)

1. Detection of simultaneous group effects in microRNA expression and related target gene sets. Artmann S, Jung K, Bleckmann A, Beissbarth T, PLoS One 2012 7 38365
2. Characterization of microRNA expression profiles in normal human tissues. Liang Y, Ridzon D, Wong L, Chen C, BMC Genomics 2007 8 166
3. MicroRNA-342, microRNA-191 and microRNA-510 are differentially expressed in T regulatory cells of type 1 diabetic patients. Hezova R, Slaby O, Faltejskova P, Mikulkova Z, Buresova I, Raja KR, Hodek J, Ovesna J, Michalek J, Cell Immunol 2010 260 70 74
4. Identification of a common lupus disease-associated microRNA expression pattern in three different murine models of lupus. Dai R, Zhang Y, Khan D, Heid B, Caudell D, Crasta O, Ahmed SA, PLoS One 2010 5 14302
5. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP, Mol Cell 2007 27 91 105 (Pubitemid 46991392)
6. Combinatorial microRNA target predictions. Krek A, Grün D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, Rajewsky N, Nat Genet 2005 37 495 500 (Pubitemid 40617277)
7. miRBase: microRNA sequences, targets and gene nomenclature. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ, Nucleic Acids Res 2006 34 140 D144
8. microRNAs: a new emerging class of players for disease diagnostics and gene therapy. Zhang B, Farwell MA, J Cell Mol Med 2008 12 3 21
9. MicroRNA in autoimmunity and autoimmune diseases. Pauley KM, Cha S, Chan EK, J Autoimmun 2009 32 189 194
10. MicroRNAs as biomarkers of disease onset. Ciesla M, Skrzypek K, Kozakowska M, Loboda A, Jozkowicz A, Dulak J, Anal Bioanal Chem 2011 401 2051 2061
11. World Health Organization http://www.idf.org/diabetesatlas
12. Malonyl-CoA and long chain acyl-CoA esters as metabolic coupling factors in nutrient-induced insulin secretion. Prentki M, Vischer S, Glennon MC, Regazzi R, Deeney JT, Corkey BE, J Biol Chem 1992 267 5802 5810
13. A pancreatic islet-specific microRNA regulates insulin secretion. Poy MN, Eliasson L, Krutzfeldt J, Kuwajima S, Ma X, Macdonald PE, Pfeffer S, Tuschl T, Rajewsky N, Rorsman P, Stoffel M, Nature 2004 432 226 230 (Pubitemid 39545853)
14. MicroRNA-9 controls the expression of granuphilin/Slp4 and the secretory response of insulin-producing cells. Plaisance V, Abderrahmani A, Perret-Menoud V, Jacquemin P, Lemaigre F, Regazzi R, J Biol Chem 2006 281 26932 26942 (Pubitemid 44401722)
15. MiR-375 targets 3′-phosphoinositide-dependent protein kinase-1 and regulates glucose-induced biological responses in pancreatic beta-cells. El Ouaamari A, Baroukh N, Martens GA, Lebrun P, Pipeleers D, van Obberghen E, Diabetes 2008 57 2708 2717
16. Role of microRNAs in diabetes. Tang X, Tang G, Ozcan S, Biochim Biophys Acta 2008 1779 697 701
17. Identification of glucose-regulated miRNAs from pancreatic beta cells reveals a role for miR-30d in insulin transcription. Tang X, Muniappan L, Tang G, Ozcan S, RNA 2009 15 287 293
18. Identification of microRNAs with a role in glucose stimulated insulin secretion by expression profiling of MIN6 cells. Hennessy E, Clynes M, Jeppesen PB, O'Driscoll L, Biochem Biophys Res Commun 2010 396 457 462
19. Meta-regulation: microRNA regulation of glucose and lipid metabolism. Lynn FC, Trends Endocrinol Metab 2009 20 452 459
20. Independent component and pathway-based analysis of miRNA-regulated gene expression in a model of type 1 diabetes. Bang-Berthelsen CH, Pedersen L, Fløyel T, Hagedorn PH, Gylvin T, Pociot F, BMC Genomics 2011 12 97
21. Plasma microRNA profiling reveals loss of endothelial miR-126 and other microRNAs in type 2 diabetes. Zampetaki A, Kiechl S, Drozdov I, Willeit P, Mayr U, Prokopi M, Mayr A, Weger S, Oberhollenzer F, Bonora E, Shah A, Willeit J, Mayr M, Circ Res 2010 107 810 817
22. MicroRNA 144 impairs insulin signaling by inhibiting the expression of insulin receptor substrate 1 in type 2 diabetes mellitus. Karolina DS, Armugam A, Tavintharan S, Wong MT, Lim SC, Sum CF, Jeyaseelan K, PLoS One 2011 6 22839
23. MirWalk http://www.umm.uni-heidelberg.de/apps/zmf/mirwalk
24. MiRanda http://www.microrna.org/microrna/home.do
25. RNAhybrid http://bibiserv.techfak.uni-bielefeld.de/rnahybrid
26. TargetScan http://targetscan.org
27. Basic principles of ROC analysis. Metz CE, Semin Nucl Med 1978 8 283 298 (Pubitemid 9075026)
28. Selection and interpretation of diagnostic tests and procedures. Principles and applications. Griner PF, Mayewski RJ, Mushlin AI, Greenland P, Ann Intern Med 1981 94 557 592
29. Transcriptome meta-analysis of peripheral lymphomononuclear cells indicates that gestational diabetes is closer to type 1 diabetes than to type 2 diabetes mellitus. Collares CV, Evangelista AF, Xavier DJ, Takahashi P, Almeida R, Macedo C, Manoel-Caetano F, Foss MC, Foss-Freitas MC, Rassi DM, Sakamoto-Hojo ET, Passos GA, Donadi EA, Mol Biol Rep 2013 in press
30. MicroRNAs: a new class of regulatory genes affecting metabolism. Krützfeldt J, Stoffel M, Cell Metab 2006 4 9 12 (Pubitemid 43942256)
31. Overexpression of micro ribonucleic acid 29, highly up-regulated in diabetic rats, leads to insulin resistance in 3T3-L1 adipocytes. He A, Zhu L, Gupta N, Chang Y, Fang F, Mol Endocrinol 2007 21 2785 2794 (Pubitemid 350035159)
32. Adipose Tissue MicroRNAs as regulators of CCL2 production in human obesity. Arner E, Mejhert N, Kulyté A, Balwierz PJ, Pachkov M, Cormont M, Lorente-Cebrián S, Ehrlund A, Laurencikiene J, Hedén P, Dahlman-Wright K, Tanti JF, Hayashizaki Y, Rydén M, Dahlman I, van Nimwegen E, Daub CO, Arner P, Diabetes 2012 61 1986 1993
33. The endothelial- specific microRNA miR-126 governs vascular integrity and angiogenesis. Wang S, Aurora AB, Johnson BA, Qi X, McAnally J, Hill JA, Richardson JA, Bassel-Duby R, Olson EN, Dev Cell 2008 15 261 271
34. Downregulation of microRNA-126 in endothelial progenitor cells from diabetes patients, impairs their functional properties, via target gene Spred-1. Meng S, Cao JT, Zhang B, Zhou Q, Shen CX, Wang CQ, J Mol Cell Cardiol 2012 53 64 72
35. Prospective study on circulating MicroRNAs and risk of myocardial infarction. Zampetaki A, Willeit P, Tilling L, Drozdov I, Prokopi M, Renard JM, Mayr A, Weger S, Schett G, Shah A, Boulanger CM, Willeit J, Chowienczyk PJ, Kiechl S, Mayr M, J Am Coll Cardiol 2012 60 290 299
36. MicroRNA-192 in diabetic kidney glomeruli and its function in TGF-beta-induced collagen expression via inhibition of E-box repressors. Kato M, Zhang J, Wang M, Lanting L, Yuan H, Rossi JJ, Natarajan R, Proc Natl Acad Sci U S A 2007 104 3432 3437 (Pubitemid 46364176)
37. Changes in microRNA profile and effects of miR-320 in insulin-resistant 3T3-L1 adipocytes. Ling HY, Ou HS, Feng SD, Zhang XY, Tuo QH, Chen LX, Zhu BY, Gao ZP, Tang CK, Yin WD, Zhang L, Liao DF, Clin Exp Pharmacol Physiol 2009 36 32 e39
38. Up-regulated pancreatic tissue microRNA-375 associates with human type 2 diabetes through beta-cell deficit and islet amyloid deposition. Zhao H, Guan J, Lee HM, Sui Y, He L, Siu JJ, Tse PP, Tong PC, Lai FM, Chan JC, Pancreas 2010 39 843 846
39. Global microRNA expression profiles in insulin target tissues in a spontaneous rat model of type 2 diabetes. Herrera BM, Lockstone HE, Taylor JM, Ria M, Barrett A, Collins S, Kaisaki P, Argoud K, Fernandez C, Travers ME, Grew JP, Randall JC, Gloyn AL, Gauguier D, McCarthy MI, Lindgren CM, Diabetologia 2010 53 1099 1109
40. Circulating miRNA profiles in patients with metabolic syndrome. Karolina DS, Tavintharan S, Armugam A, Sepramaniam S, Pek SL, Wong MT, Lim SC, Sum CF, Jeyaseelan K, J Clin Endocrinol Metab 2012 97 2271 E2276
41. Changes in microRNA expression contribute to pancreatic β-cell dysfunction in prediabetic NOD mice. Roggli E, Gattesco S, Caille D, Briet C, Boitard C, Meda P, Regazzi R, Diabetes 2012 61 1742 1751
42. Expression and cellular localization of microRNA-29b and RAX, an activator of the RNA-dependent protein kinase (PKR), in the retina of streptozotocin-induced diabetic rats. Silva VA, Polesskaya A, Sousa TA, Corrêa VM, André ND, Reis RI, Kettelhut IC, Harel-Bellan A, De Lucca FL, Mol Vis 2011 17 2228 2240
43. Urinary miR-21, miR-29, and miR-93: novel biomarkers of fibrosis. Wang G, Kwan BC, Lai FM, Chow KM, Li PK, Szeto CC, Am J Nephrol 2012 36 412 418
44. Decreased microRNA-142-3p/5p expression causes CD4+ T cell activation and B cell hyperstimulation in systemic lupus erythematosus. Ding S, Liang Y, Zhao M, Liang G, Long H, Zhao S, Wang Y, Yin H, Zhang P, Zhang Q, Lu Q, Arthritis Rheum 2012 64 2953 2963
45. MicroRNA-29a and microRNA-142-3p are regulators of myeloid differentiation and acute myeloid leukemia. Wang XS, Gong JN, Yu J, Wang F, Zhang XH, Yin XL, Tan ZQ, Luo ZM, Yang GH, Shen C, Zhang JW, Blood 2012 119 4992 5004
46. An oncogenic role of miR-142-3p in human T-cell acute lymphoblastic leukemia (T-ALL) by targeting glucocorticoid receptor- and cAMP/PKA pathways. Lv M, Zhang X, Jia H, Li D, Zhang B, Zhang H, Hong M, Jiang T, Jiang Q, Lu J, Huang X, Huang B, Leukemia 2012 26 769 777
47. MiR-142-3p as a potential prognostic biomarker for esophageal squamous cell carcinoma. Lin RJ, Xiao DW, Liao LD, Chen T, Xie ZF, Huang WZ, Wang WS, Jiang TF, Wu BL, Li EM, Xu LY, J Surg Oncol 2012 105 175 182
48. MicroRNA-142-3p, a new regulator of RAC1, suppresses the migration and invasion of hepatocellular carcinoma cells. Wu L, Cai C, Wang X, Liu M, Li X, Tang H, FEBS Lett 2011 585 1322 1330
49. MicroRNA expression profiling identifies activated B cell status in chronic lymphocytic leukemia cells. Li S, Moffett HF, Lu J, Werner L, Zhang H, Ritz J, Neuberg D, Wucherpfennig KW, Brown JR, Novina CD, PLoS One 2011 6 16956
50. Survey of MicroRNA expression in pediatric brain tumors. Birks DK, Barton VN, Donson AM, Handler MH, Vibhakar R, Foreman NK, Pediatr Blood Cancer 2011 56 211 216
51. Comprehensive analysis of microRNA expression patterns in hepatocellular carcinoma and non-tumorous tissues. Murakami Y, Yasuda T, Saigo K, Urashima T, Toyoda H, Okanoue T, Shimotohno K, Oncogene 2006 25 2537 2545
52. Association of MicroRNA expression in hepatocellular carcinomas with hepatitis infection, cirrhosis, and patient survival. Jiang J, Gusev Y, Aderca I, Mettler TA, Nagorney DM, Brackett DJ, Roberts LR, Schmittgen TD, Clin Cancer Res 2008 14 419 427 (Pubitemid 351226109)
53. MicroRNA signatures in human ovarian cancer. Iorio MV, Visone R, Di Leva G, Donati V, Petrocca F, Casalini P, Taccioli C, Volinia S, Liu CG, Alder H, Calin GA, Ménard S, Croce CM, Cancer Res 2007 67 8699 8707 (Pubitemid 47437445)
54. The expression profile of microRNAs in a model of 7,12-dimethyl-benz[a] anthrance-induced oral carcinogenesis in Syrian hamster. Yu T, Wang XY, Gong RG, Li A, Yang S, Cao YT, Wen YM, Wang CM, Yi XZ, J Exp Clin Cancer Res 2009 28 64
55. Integrated miRNA and mRNA expression profiling of the inflammatory breast cancer subtype. Van der Auwera I, Limame R, van Dam P, Vermeulen PB, Dirix LY, Van Laere SJ, Br J Cancer 2010 103 532 541
56. An integrative genomic approach reveals coordinated expression of intronic miR-335, miR-342, and miR-561 with deregulated host genes in multiple myeloma. Ronchetti D, Lionetti M, Mosca L, Agnelli L, Andronache A, Fabris S, Deliliers GL, Neri A, BMC Med Genomics 2008 1 37
57. A miRNA signature of prion induced neurodegeneration. Saba R, Goodman CD, Huzarewich RL, Robertson C, Booth SA, PLoS One 2008 3 3652
58. Differential expression of microRNAs in adipose tissue after long-term high-fat diet-induced obesity in mice. Chartoumpekis DV, Zaravinos A, Ziros PG, Iskrenova RP, Psyrogiannis AI, Kyriazopoulou VE, Habeos IG, PLoS One 2012 7 34872
59. Organ-specific testosterone-insensitive response of miRNA expression of C57BL/6 mice to plasmodium chabaudi malaria. Al-Quraishy S, Dkhil MA, Delic D, Abdel-Baki AA, Wunderlich F, Parasitol Res 2012 111 1093 1101
60. RAS is regulated by the let-7 microRNA family. Johnson SM, Grosshans H, Shingara J, Byrom M, Jarvis R, Cheng A, Labourier E, Reinert KL, Brown D, Slack FJ, Cell 2005 120 635 647 (Pubitemid 40343076)
61. The tumor suppressor microRNA let-7 represses the HMGA2 oncogene. Lee Y, Dutta A, Genes Dev 2007 21 1025 1030 (Pubitemid 46686471)
62. Control of glucose homeostasis and insulin sensitivity by the Let-7 family of microRNAs. Frost RJ, Olson EN, Proc Natl Acad Sci U S A 2011 108 21075 21080
63. A miRNA-tRNA mix-up: tRNA origin of proposed miRNA. Schopman NC, Heynen S, Haasnoot J, Berkhout B, RNA Biol 2010 7 573 576
64. Early second-trimester serum miRNA profiling predicts gestational diabetes mellitus. Zhao C, Dong J, Jiang T, Shi Z, Yu B, Zhu Y, Chen D, Xu J, Huo R, Dai J, Xia Y, Pan S, Hu Z, Sha J, PLoS One 2011 6 23925
65. MicroRNAs induced during adipogenesis that accelerate fat cell development are downregulated in obesity. Xie H, Lim B, Lodish HF, Diabetes 2009 58 1050 1057
66. MicroRNA expression patterns to differentiate pancreatic adenocarcinoma from normal pancreas and chronic pancreatitis. Bloomston M, Frankel WL, Petrocca F, Volinia S, Alder H, Hagan JP, Liu CG, Bhatt D, Taccioli C, Croce CM, JAMA 2007 297 1901 1908 (Pubitemid 46707844)
67. MicroRNAs in the growth plate are responsive to nutritional cues: association between miR-140 and SIRT1. Pando R, Even-Zohar N, Shtaif B, Edry L, Shomron N, Phillip M, Gat-Yablonski G, J Nutr Biochem 2012 23 1474 1481
68. Calorie restriction promotes mammalian cell survival by inducing the SIRT1 deacetylase. Cohen HY, Miller C, Bitterman KJ, Wall NR, Hekking B, Kessler B, Howitz KT, Gorospe M, de Cabo R, Sinclair DA, Science 2004 305 390 392 (Pubitemid 38938153)
69. Tissue-specific regulation of SIRT1 by calorie restriction. Chen D, Bruno J, Easlon E, Lin SJ, Cheng HL, Alt FW, Guarente L, Genes Dev 2008 22 1753 1757 (Pubitemid 351915500)
70. MicroRNA expression in human omental and subcutaneous adipose tissue. Klöting N, Berthold S, Kovacs P, Schön MR, Fasshauer M, Ruschke K, Stumvoll M, Blüher M, PLoS One 2009 4 4699
71. The miR-30 family microRNAs confer epithelial phenotype to human pancreatic cells. Joglekar MV, Patil D, Joglekar VM, Rao GV, Reddy DN, Mitnala S, Shouche Y, Hardikar AA, Islets 2009 1 137 147
72. Downregulation of miR-181a upregulates sirtuin-1 (SIRT1) and improves hepatic insulin sensitivity. Zhou B, Li C, Qi W, Zhang Y, Zhang F, Wu JX, Hu YN, Wu DM, Liu Y, Yan TT, Jing Q, Liu MF, Zhai QW, Diabetologia 2012 55 2032 2043
73. Circulating levels of microRNA from children with newly diagnosed type 1 diabetes and healthy controls: evidence that miR-25 associates to residual beta-cell function and glycaemic control during disease progression. Nielsen LB, Wang C, Sørensen K, Bang-Berthelsen CH, Hansen L, Andersen ML, Hougaard P, Juul A, Zhang CY, Pociot F, Mortensen HB, Exp Diabetes Res 2012 2012 896362
74. Mir2disease http://www.mir2disease.org
75. ArrayExpress http://www.ebi.ac.uk/arrayexpress
76. R environment http://www.r-project.org
77. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bolstad B, Irizarry R, Astrand M, Speed T, Bioinformatics 2003 19 185 193 (Pubitemid 36181903)
78. affy-analysis of Affymetrix GeneChip data at the probe level. Gautier L, Cope L, Bolstad BM, Irizarry RA, Bioinformatics 2004 20 307 315 (Pubitemid 38262761)
79. RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis. Hong F, Breitling R, McEntee CW, Wittner BS, Nemhauser JL, Chory J, Bioinformatics 2006 22 2825 2827 (Pubitemid 44742407)
80. Bayesian inference of MicroRNA targets from sequence and expression data. Huang JC, Morris QD, Frey BJ, J Comput Biol 2007 14 550 563 (Pubitemid 47047813)
81. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T, Genome Res 2003 13 2498 2504 (Pubitemid 37428274)
82. ROCR package http://cran.r-project.org/web/packages/ROCR/index.html