MicroRNA biomarker identification for pediatric acute myeloid leukemia based on a novel bioinformatics model

Oncotarget

Volumn 6, Issue 28, 2015, Pages 26424-26436

  Yan, Wenying ^a,b,c   Xu, Lihua ^d,e   Sun, Zhandong ^a   Lin, Yuxin ^a   Zhang, Wenyu ^a   Chen, Jiajia ^f   Hu, Shaoyan ^d   Shen, Bairong ^a  

^a SOOCHOW UNIVERSITY   (China)

^b Taicang Center for Translational Bioinformatics   (China)

^c The 100th Hospital of PLA   (China)

^d CHILDREN S HOSPITAL OF SOOCHOW UNIVERSITY   (China)

^e First People's Hospital of Lianyungang   (China)

^f SUZHOU UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

Bioinformatics model; MicroRNA biomarkers; MicroRNA regulatory network; Pediatric acute myeloid leukemia; Transcription factor

Indexed keywords

MESSENGER RNA; MICRORNA; MICRORNA 155; MICRORNA 196B; MICRORNA 25; UNCLASSIFIED DRUG; MIRN155 MICRORNA, HUMAN; MIRN196 MICRORNA, HUMAN; TUMOR MARKER;

ACUTE MYELOBLASTIC LEUKEMIA; ADOLESCENT; ARTICLE; BIOINFORMATICS; CANCER CLASSIFICATION; CHILD; CONTROLLED STUDY; GENE EXPRESSION PROFILING; GENE OVEREXPRESSION; GENE REGULATORY NETWORK; GENETIC ASSOCIATION; HUMAN; HUMAN CELL; IN VITRO STUDY; INFANT; LEUKEMOGENESIS; MAJOR CLINICAL STUDY; NEWBORN; POLYMERASE CHAIN REACTION; PREDICTION; RNA ANALYSIS; RNA STRUCTURE; BIOLOGY; GENE EXPRESSION REGULATION; GENETIC ASSOCIATION STUDY; GENETIC DATABASE; GENETIC PREDISPOSITION; GENETIC TRANSCRIPTION; GENETICS; LEUKEMIA, MYELOID, ACUTE; ONSET AGE; PHENOTYPE; PRESCHOOL CHILD; REPRODUCIBILITY;

ADOLESCENT; AGE OF ONSET; BIOMARKERS, TUMOR; CHILD; CHILD, PRESCHOOL; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; GENETIC ASSOCIATION STUDIES; GENETIC PREDISPOSITION TO DISEASE; HUMANS; INFANT; INFANT, NEWBORN; LEUKEMIA, MYELOID, ACUTE; MICRORNAS; PHENOTYPE; REPRODUCIBILITY OF RESULTS; TRANSCRIPTION, GENETIC;

EID: 84944463427     PISSN: None     EISSN: 19492553     Source Type: Journal    
DOI: 10.18632/oncotarget.4459     Document Type: Article

References (50)

1. Kaspers GJ, Creutzig U. Pediatric acute myeloid leukemia: international progress and future directions. Leukemia. 2005; 19:2025-2029.
2. Pui CH, Carroll WL, Meshinchi S, Arceci RJ. Biology, risk stratification, and therapy of pediatric acute leukemias: an update. J Clin Oncol. 2011; 29:551-565.
3. Creutzig U, van den Heuvel-Eibrink MM, Gibson B, Dworzak MN, Adachi S, de Bont E, Harbott J, Hasle H, Johnston D, Kinoshita A, Lehrnbecher T, Leverger G, Mejstrikova E, Meshinchi S, Pession A, Raimondi SC, et al. Diagnosis and management of acute myeloid leukemia in children and adolescents: recommendations from an international expert panel. Blood. 2012; 120:3187-3205.
4. Moore AS, Kearns PR, Knapper S, Pearson AD, Zwaan CM. Novel therapies for children with acute myeloid leukaemia. Leukemia. 2013; 27:1451-1460.
5. Friedman RC, Farh KK, Burge CB, Bartel DP. Most mammalianmRNAs are conserved targets of microRNAs. Genome Res. 2009; 19:92-105.
6. Carleton M, Cleary MA, Linsley PS. MicroRNAs and cell cycle regulation. Cell Cycle. 2007; 6:2127-2132.
7. Shivdasani RA. MicroRNAs: regulators of gene expression and cell differentiation. Blood. 2006; 108:3646-3653.
8. Lindsay MA. microRNAs and the immune response. Trends Immunol. 2008; 29:343-351.
9. Lee YS, Dutta A. MicroRNAs in cancer. Annu Rev Pathol. 2009; 4:199-227.
10. Gong JN, Yu J, Lin HS, Zhang XH, Yin XL, Xiao Z, Wang F, Wang XS, Su R, Shen C, Zhao HL, Ma YN, Zhang JW. The role, mechanism and potentially therapeutic application of microRNA-29 family in acute myeloid leukemia. Cell Death Differ. 2014; 21:100-112.
11. Pulikkan JA, Dengler V, Peramangalam PS, Peer Zada AA, Muller-Tidow C, Bohlander SK, Tenen DG, Behre G. Cell-cycle regulator E2F1 and microRNA-223 comprise an autoregulatory negative feedback loop in acute myeloid leukemia. Blood. 2010; 115:1768-1778.
12. Gao XN, Lin J, Gao L, Li YH, Wang LL, Yu L. MicroRNA-193b regulates c-Kit proto-oncogene and represses cell proliferation in acute myeloid leukemia. Leuk Res. 2011; 35:1226-1232.
13. Garzon R, Volinia S, Liu CG, Fernandez-Cymering C, Palumbo T, Pichiorri F, Fabbri M, Coombes K, Alder H, Nakamura T, Flomenberg N, Marcucci G, Calin GA, Kornblau SM, Kantarjian H, Bloomfield CD, et al. MicroRNA signatures associated with cytogenetics and prognosis in acute myeloid leukemia. Blood. 2008; 111:3183-3189.
14. O'Connell RM, Rao DS, Chaudhuri AA, Boldin MP, Taganov KD, Nicoll J, Paquette RL, Baltimore D. Sustained expression of microRNA-155 in hematopoietic stem cells causes a myeloproliferative disorder. J Exp Med. 2008; 205:585-594.
15. Dixon-McIver A, East P, Mein CA, Cazier JB, Molloy G, Chaplin T, Andrew Lister T, Young BD, Debernardi S. Distinctive patterns of microRNA expression associated with karyotype in acute myeloid leukaemia. PLoS One. 2008; 3:e2141.
16. Chen J, Zhang D, Zhang W, Tang Y, Yan W, Guo L, Shen B. Clear cell renal cell carcinoma associated microRNA expression signatures identified by an integrated bioinformatics analysis. J Transl Med. 2013; 11:169.
17. Huang J, Sun Z, Yan W, Zhu Y, Lin Y, Chen J, Shen B, Wang J. Identification of microRNA as sepsis biomarker based on miRNAs regulatory network analysis. Biomed Res Int. 2014; 2014:594350.
18. Zhang W, Zang J, Jing X, Sun Z, Yan W, Yang D, Guo F, Shen B. Identification of candidate miRNA biomarkers from miRNA regulatory network with application to prostate cancer. J Transl Med. 2014; 12:66.
19. Tseng CW, Lin CC, Chen CN, Huang HC, Juan HF. Integrative network analysis reveals active microRNAs and their functions in gastric cancer. BMC Syst Biol. 2011; 5:99.
20. Li Y, Xu J, Chen H, Bai J, Li S, Zhao Z, Shao T, Jiang T, Ren H, Kang C, Li X. Comprehensive analysis of the functional microRNA-mRNA regulatory network identifies miRNA signatures associated with glioma malignant progression. Nucleic Acids Res. 2013; 41:e203.
21. Alshalalfa M, Bader GD, Goldenberg A, Morris Q, Alhajj R. Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study. BMC Syst Biol. 2012; 6:112.
22. Delfino KR, Rodriguez-Zas SL. Transcription factor-microRNA-target gene networks associated with ovarian cancer survival and recurrence. PLoS One. 2013; 8:e58608.
23. Zhang HM, Kuang S, Xiong X, Gao T, Liu C, Guo AY. Transcription factor and microRNA co-regulatory loops: important regulatory motifs in biological processes and diseases. Brief Bioinform. 2013.
24. Daschkey S, Rottgers S, Giri A, Bradtke J, Teigler-Schlegel A, Meister G, Borkhardt A, Landgraf P. MicroRNAs distinguish cytogenetic subgroups in pediatric AML and contribute to complex regulatory networks in AML-relevant pathways. PLoS One. 2013; 8:e56334.
25. Xu J, Haigis KM, Firestone AJ, McNerney ME, Li Q, Davis E, Chen SC, Nakitandwe J, Downing J, Jacks T, Le Beau MM, Shannon K. Dominant role of oncogene dosage and absence of tumor suppressor activity in Nras-driven hematopoietic transformation. Cancer Discov. 2013; 3:993-1001.
26. Smyth GK. limma: Linear Models for Microarray Data. Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S. Bioinformatics and Computational Biology Solutions Using R and Bioconductor: Springer New York. 2005 ,pp. 397-420.
27. Zhu YM, Das-Gupta EP, Russell NH. Microsatellite instability and p53 mutations are associated with abnormal expression of the MSH2 gene in adult acute leukemia. Blood. 1999; 94:733-740.
28. Mao G, Yuan F, Absher K, Jennings CD, Howard DS, Jordan CT, Gu L. Preferential loss of mismatch repair function in refractory and relapsed acute myeloid leukemia: potential contribution to AML progression. Cell Res. 2008; 18:281-289.
29. Hirano T. Chromosome cohesion, condensation, and separation. Annu Rev Biochem. 2000; 69:115-144. 30. Kon A, Shih LY, Minamino M, Sanada M, Shiraishi Y, Nagata Y, Yoshida K, Okuno Y, Bando M, Nakato R, Ishikawa S, Sato-Otsubo A, Nagae G, Nishimoto A, Haferlach C, Nowak D, et al. Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms. Nat Genet. 2013; 45:1232-1237.
30. Kon A, Shih LY, Minamino M, Sanada M, Shiraishi Y, Nagata Y, Yoshida K, Okuno Y, Bando M, Nakato R, Ishikawa S, Sato-Otsubo A, Nagae G, Nishimoto A, Haferlach C, Nowak D, et al. Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms. Nat Genet. 2013; 45:1232-1237
31. Hanahan D, Weinberg RA. The hallmarks of cancer. Cell. 2000; 100:57-70.
32. Popovic R, Riesbeck LE, Velu CS, Chaubey A, Zhang J, Achille NJ, Erfurth FE, Eaton K, Lu J, Grimes HL, Chen J, Rowley JD, Zeleznik-Le NJ. Regulation of mir-196b by MLL and its overexpression by MLL fusions contributes to immortalization. Blood. 2009; 113:3314-3322.
33. Wang Y, Li Z, He C, Wang D, Yuan X, Chen J, Jin J. MicroRNAs expression signatures are associated with lineageand survival in acute leukemias. Blood Cells Mol Dis. 2010; 44:191-197.
34. Diaz-Beya M, Brunet S, Nomdedeu J, Tejero R, Diaz T, Pratcorona M, Tormo M, Ribera JM, Escoda L, Duarte R, Gallardo D, Heras I, Queipo de Llano MP, Bargay J, Monzo M, Sierra J, et al. MicroRNA expression at diagnosis adds relevant prognostic information to molecular categorization in patients with intermediate-risk cytogenetic acute myeloid leukemia. Leukemia. 2014; 28:804-812.
35. Costinean S, Zanesi N, Pekarsky Y, Tili E, Volinia S, Heerema N, Croce CM. Pre-B cell proliferation and lymphoblastic leukemia/high-grade lymphoma in E(mu)-miR155 transgenic mice. Proc Natl Acad Sci U S A. 2006; 103:7024-7029.
36. Thai TH, Calado DP, Casola S, Ansel KM, Xiao C, Xue Y, Murphy A, Frendewey D, Valenzuela D, Kutok JL, Schmidt-Supprian M, Rajewsky N, Yancopoulos G, Rao A, Rajewsky K. Regulation of the germinal center response by microRNA-155. Science. 2007; 316:604-608.
37. Georgantas RW 3rd, Hildreth R, Morisot S, Alder J, Liu CG, Heimfeld S, Calin GA, Croce CM, Civin CI. CD34+ hematopoietic stem-progenitor cell microRNA expression and function: a circuit diagram of differentiation control. Proc Natl Acad Sci U S A. 2007; 104:2750-2755.
38. Rodriguez A, Vigorito E, Clare S, Warren MV, Couttet P, Soond DR, van Dongen S, Grocock RJ, Das PP, Miska EA, Vetrie D, Okkenhaug K, Enright AJ, Dougan G, Turner M, Bradley A. Requirement of bic/microRNA-155 for normal immune function. Science. 2007; 316:608-611.
39. Cammarata G, Augugliaro L, Salemi D, Agueli C, La Rosa M, Dagnino L, Civiletto G, Messana F, Marfia A, Bica MG, Cascio L, Floridia PM, Mineo AM, Russo M, Fabbiano F, Santoro A. Differential expression of specific microRNA and their targets in acute myeloid leukemia. Am J Hematol. 2010; 85:331-339.
40. Jongen-Lavrencic M, Sun SM, Dijkstra MK, Valk PJ, Lowenberg B. MicroRNA expression profiling in relation to the genetic heterogeneity of acute myeloid leukemia. Blood. 2008; 111:5078-5085.
41. Garzon R, Garofalo M, Martelli MP, Briesewitz R, Wang L, Fernandez-Cymering C, Volinia S, Liu CG, Schnittger S, Haferlach T, Liso A, Diverio D, Mancini M, Meloni G,Foa R, Martelli MF, et al. Distinctive microRNA signature of acute myeloid leukemia bearing cytoplasmic mutated nucleophosmin. Proc Natl Acad Sci U S A. 2008; 105:3945-3950.
42. Li Z, Lu J, Sun M, Mi S, Zhang H, Luo RT, Chen P, Wang Y, Yan M, Qian Z, Neilly MB, Jin J, Zhang Y, Bohlander SK, Zhang DE, Larson RA, et al. Distinct microRNA expression profiles in acute myeloid leukemia with common translocations. Proc Natl Acad Sci U S A. 2008; 105:15535-15540.
43. Luo X, Burwinkel B, Tao S, Brenner H. MicroRNA signatures:novel biomarker for colorectal cancer? Cancer Epidemiol Biomarkers Prev. 2011; 20:1272-1286.
44. Li T, Leong MH, Harms B, Kennedy G, Chen L. MicroRNA-21 as a potential colon and rectal cancer biomarker. World J Gastroenterol. 2013; 19:5615-5621.
45. Kim YK, Yu J, Han TS, Park SY, Namkoong B, Kim DH, Hur K, Yoo MW, Lee HJ, Yang HK, Kim VN. Functional links between clustered microRNAs: suppression of cell-cycle inhibitors by microRNA clusters in gastric cancer. Nucleic Acids Res. 2009; 37:1672-1681.
46. Zhang H, Zuo Z, Lu X, Wang L, Wang H, Zhu Z. MiR-25 regulates apoptosis by targeting Bim in human ovarian cancer. Oncol Rep. 2012; 27:594-598.
47. Kan T, Sato F, Ito T, Matsumura N, David S, Cheng Y, Agarwal R, Paun BC, Jin Z, Olaru AV, Selaru FM, Hamilton JP, Yang J, Abraham JM, Mori Y, Meltzer SJ. The miR-106b-25 polycistron, activated by genomic amplification, functions as an oncogene by suppressing p21 and Bim. Gastroenterology. 2009; 136:1689-1700.
48. Li M, Guan X, Sun Y, Mi J, Shu X, Liu F, Li C. miR-92a family and their target genes in tumorigenesis and metastasis. Exp Cell Res. 2014; 323:1-6.
49. Dacic S, Kelly L, Shuai Y, Nikiforova MN. miRNA expressionprofiling of lung adenocarcinomas: correlation with mutational status. Mod Pathol. 2010; 23:1577-1582.
50. Greif PA, Dufour A, Konstandin NP, Ksienzyk B, Zellmeier E, Tizazu B, Sturm J, Benthaus T, Herold T, Yaghmaie M, Dorge P, Hopfner KP, Hauser A, Graf A, Krebs S, Blum H, et al. GATA2 zinc finger 1 mutations associated with biallelic CEBPA mutations define a unique genetic entity of acute myeloid leukemia. Blood. 2012; 120:395-403.