Bioinformatics, non-coding RNAs and its possible application in personalized medicine

Advances in Experimental Medicine and Biology

Volumn 774, Issue , 2013, Pages 21-37

  Rossi, Simona ^a   Calin, George A ^b  

^a SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^b UNIVERSITY OF TEXAS   (United States)

Author keywords

Biomarker; Cancer; Deep sequencing and network; MicroRNAs; Non coding RNA; Personalized medicine; Prediction; Prognosis; Target prediction

Indexed keywords

LONG UNTRANSLATED RNA; MICRORNA; UNTRANSLATED RNA;

ARTICLE; BIOINFORMATICS; CANCER DIAGNOSIS; CANCER GROWTH; CANCER PROGNOSIS; CANCER SUSCEPTIBILITY; CARCINOGENESIS; CLINICAL PRACTICE; COMPUTER PROGRAM; GENE CONTROL; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE IDENTIFICATION; GENE INTERACTION; GENE PREDICTION; GENE TARGETING; GENE TECHNOLOGY; GENETIC ASSOCIATION; GENETIC CONSERVATION; GENETIC PROCEDURES; GENOME; HIGH THROUGHPUT SEQUENCING; HUMAN; METASTASIS; MOLECULAR CLONING; NEXT GENERATION SEQUENCING; PERSONALIZED MEDICINE; PHENOTYPE; PREDICTION; PRIORITY JOURNAL; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE ANALYSIS; TRANSCRIPTION REGULATION; BIOLOGY; GENETIC PREDISPOSITION; GENETICS; METABOLISM; METHODOLOGY; NEOPLASM; PATHOLOGY; REVIEW;

COMPUTATIONAL BIOLOGY; GENETIC PREDISPOSITION TO DISEASE; HUMANS; INDIVIDUALIZED MEDICINE; NEOPLASMS; RNA, UNTRANSLATED;

MLCS; MLOWN;

EID: 84934434213     PISSN: 00652598     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-94-7-5590-1_2     Document Type: Article

References (62)

1. Mattick JS, Makunin IV (2006) Non-coding RNA. Hum Mol Genet 15(Spec No 1):R17-R29, PMID: 16651366
2. Garzon R, Marcucci G, Croce CM (2010) Targeting microRNAs in cancer: rationale, strategies and challenges. Nat Rev Drug Discov 9(10):775-789
3. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, Wang Y, Brzoska P, Kong B, Li R, West RB, van de Vijver MJ, Sukumar S, Chang HY (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464(7291):1071-1076
4. Wojcik SE, Rossi S, Shimizu M, Nicoloso MS, Cimmino A, Alder H, Herlea V, Rassenti LZ, Rai KR, Kipps TJ, Keating MJ, Croce CM, Calin GA (2010) Non-codingRNA sequence variations in human chronic lymphocytic leukemia and colorectal cancer. Carcinogenesis 31(2):208-215
5. Rossi S, Kopetz S, Davuluri R, Hamilton SR, Calin GA (2010) MicroRNAs, ultraconserved genes and colorectal cancers. Int J Biochem Cell Biol 42(8): 1291-1297
6. Volinia S, Galasso M, Costinean S, Tagliavini L, Gamberoni G, Drusco A, Marchesini J, Mascellani N, Sana ME, Abu Jarour R, Desponts C, Teitell M, Baffa R, Aqeilan R, Iorio MV, Taccioli C, Garzon R, Di Leva G, Fabbri M, Catozzi M, Previati M, Ambs S, Palumbo T, Garofalo M, Veronese A, Bottoni A, Gasparini P, Harris CC, Visone R, Pekarsky Y, de la Chapelle A, Bloomston M, Dillhoff M, Rassenti LZ, Kipps TJ, Huebner K, Pichiorri F, Lenze D, Cairo S, Buendia MA, Pineau P, Dejean A, Zanesi N, Rossi S, Calin GA, Liu CG, Palatini J, Negrini M, Vecchione A, Rosenberg A, Croce CM (2010) Reprogramming of miRNA networks in cancer and leukemia. Genome Res 20(5):589-599
7. Ferracin M, Pedriali M, Veronese A, Zagatti B, Gafà R, Magri E, Lunardi M, Munerato G, Querzoli G, Maestri I, Ulazzi L, Nenci I, Croce CM, Lanza G, Querzoli P, Negrini M (2011) MicroRNA profiling for the identification of cancers with unknown primary tissueof-origin. J Pathol 225(1):43-53. doi: 10.1002/path.2915
8. Mihaela Z, Jaskiewicz L (2009) Computational biology of small regulatory RNAs (chapter 5). In: Appel RD, Ernest F, Appel RD (eds) Bioinformatics: a Swiss perspective, 1st edn. World Scientific Publishing Company, Singapore. ISBN 9812838775
9. Morozova O, Hirst M, Marra MA (2009) Applications of new sequencing technologies for transcriptome analysis. Annu Rev Genomics Hum Genet 10:135-151, PMID: 19715439
10. Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25(15): 1966-1967
11. Mathelier A, Carbone A (2010) MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data. Bioinformatics 26(18):2226-2234
12. Jiang P, Wu H, Wang W, Ma W, Sun X, Lu Z (2007) MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res 35(Web Server issue):W339-W344, PMID: 17553836
13. Sewer A, Paul N, Landgraf P, Aravin A, Pfeffer S, Brownstein MJ, Tuschl T, van Nimwegen E, Zavolan M (2005) Identification of clustered microRNAs using an ab initio prediction method. BMC Bioinformatics 6:267, PMID:16274478
14. Batuwita R, Palade V (2009) microPred: effective classification of pre-miRNAs for human miRNA gene prediction. Bioinformatics 25(8):989-995
15. Friedlander MR et al (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol 26:407-415
16. Moxon S, Moulton V, Kim JT (2008) A scoring matrix approach to detecting miRNA target sites. Algorithms Mol Biol 3:3, PMID: 18377655
17. Hackenberg M, Sturm M, Langenberger D, Falcón-Pérez JM, Aransay AM (2009) miRanalyzer: a micro RNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res 37(Web Server issue):W68-W76, PMID: 19433510
18. Pantano L, Estivill X, Martí E (2010) SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells. Nucleic Acids Res 38(5):e34
19. Huang PJ, Liu YC, Lee CC, Lin WC, Gan RR, Lyu PC, Tang P (2010) DSAP: deep-sequencing small RNA analysis pipeline. Nucleic Acids Res 38(Web Server issue):W385-W391, PMID: 20478825
20. Zhu E, Zhao F, Xu G, Hou H, Zhou L, Li X, Sun Z, Wu J (2010) mirTools: microRNA profiling and discovery based on high-throughput sequencing. Nucleic Acids Res 38(Web Server issue):W392-W397
21. Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Müller P, Spring J, Srinivasan A, Fishman M, Finnerty J, Corbo J, Levine M, Leahy P, Davidson E, Ruvkun G (2000) Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408(6808):86-89
22. Lee RC, Ambros V (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294 (5543):862-864
23. Lai EC, Tomancak P, Williams RW, Rubin GM (2003) Computational identification of Drosophila microRNA genes. Genome Biology 4:R42. doi:10.1186/gb-2003-4-7-r42
24. Berezikov E, van Tetering G, Verheul M, van de Belt J, van Laake L, Vos J, Verloop R, van de Wetering M, Guryev V, Takada S, van Zonneveld A, Mano H, Plasterk R, Cuppen E (2006) Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis. Genome Res 16:1289-1298
25. Pfeffer S, Zavolan M, Grasser F, Chien M, Russo J, Ju J, John B, Enright A, Marks D, Sander C, Tuschl T (2004) Identification of virus encoded microRNAs. Science 304:734-736
26. Berezikov E, Guryev V, van de Belt J, Wienholds E, Plasterk RH, Cuppen E (2005) Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120(1):21-24
27. Mathews DH, Turner DH, Zuker M (2007) RNA secondary structure prediction. Curr Protoc Nucleic Acid Chem; Chapter 11:Unit 11.2. PMID: 18428968
28. Hofacker I, Fekete M, Flamm C, Huynen M, Rauscher S, Stolorz P, Stadler P (1998) Automated detection of conserved RNA structure elements in complete RNA virus genomes. Nucleic Acids Res 26:3825-3826
29. Nam J, Shin K, Han J, Lee Y, Kim V, Zhang B (2005) Human microRNA prediction through a probabilistic colearning model of sequence and structure. Nucleic Acids Res 33:3570-3581
30. Mattick JS, Makunin IV (2005) Small regulatory RNAs in mammals. Hum Mol Genet 14:R121-R132
31. Berezikov E, Guryev V, van de Belt J, Wienholds E, Plasterk RH, Cuppen E (2005) Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120(1):21-24
32. Lai EC, Tomancak P, WilliamsRW, Rubin GM (2003) Computational identification of Drosophila microRNA gene. Genome Biology 4:R42. doi:10.1186/gb-2003-4-7-r42
33. Doran J, Strauss WM (2007) Bio-informatic trends for the determination of miRNA-target interactions in mammals. DNA Cell Biol 26(5):353-360
34. Chang DT, Wang CC, Chen JW (2008) Using a kernel density estimation based classifier to predict speciesspecific microRNA precursors. BMC Bioinformatics 9 Suppl 12:S2
35. Brameier M, Wiuf C (2007) Ab initio identification of human microRNAs based on structure motifs. BMC Bioinformatics 8:478
36. John B, Enright A, Aravin A, Tuschl T, Sander C, Marks D (2004) Human microRNA targets. PLoS Biol 2:e363
37. Vatolin S, Navaratne K, Weil RJ (2006) A novel method to detect functional microRNA targets. J Mol Biol 358(4):983-996
38. Rajewsky N (2006) MicroRNA target predictions in animals. Nat Genet 38:S8-S13
39. Sood P, Krek A, Zavolan M, Macino G, Rajewsky N (2006) Cell-type-specific signatures of microRNAs on target mRNA expression. Proc Natl Acad Sci U S A 103(8):2746-2751
40. Ragan C, Cloonan N, Grimmond SM, Zuker M, Ragan MA (2009) Transcriptome-wide prediction of miRNA targets in human and mouse using FASTH. PLoS One 4(5):e5745
41. Lewis B, Burge C, Bartel D (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120:15-20
42. Brennecke J, Stark A, Russell R, Cohen S (2005) Principles of microRNA-target recognition. PLoS Biol 3:e85
43. Krützfeldt J, Poy MN, Stoffel M (2006) Strategies to determine the biological function of microRNAs. Nat Genet 38(Suppl):S14-S19
44. Calin GA, Dumitru CD, Shimizu M, Bichi R, Zupo S, Noch E, Aldler H, Rattan S, Keating M, Rai K, Rassenti L, Kipps T, Negrini M, Bullrich F, Croce CM (2002) Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci U S A 99(24):15524-15529
45. Calin GA, Liu CG, Sevignani C, Ferracin M, Felli N, Dumitru CD, Shimizu M, Cimmino A, Zupo S, Dono M, Dell'Aquila ML, Alder H, Rassenti L, Kipps TJ, Bullrich F, Negrini M, Croce CM (2004) MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias. Proc Natl Acad Sci U S A 101(32):11755-11760
46. Calin GA, Croce CM (2009) Chronic lymphocytic leukemia: interplay between noncoding RNAs and protein-coding genes. Blood 114(23):4761-4770
47. Fabbri M, Garzon R, Andreeff M, Kantarjian HM, Garcia-Manero G, Calin GA (2008) MicroRNAs and noncoding RNAs in hematological malignancies: molecular, clinical and therapeutic implications. Leukemia 22(6):1095-1105
48. Taby R, Issa JP (2010) Cancer epigenetics. CA Cancer J Clin 60(6):376-392
49. Edwards JK, Pasqualini R, Arap W, Calin GA (2010) MicroRNAs and ultraconserved genes as diagnostic markers and therapeutic targets in cancer and cardiovascular diseases. J Cardiovasc Transl Res 3(3):271-279
50. Venkatachalam R, Ligtenberg MJ, Hoogerbrugge N, Schackert HK, Görgens H, Hahn MM, Kamping EJ, Vreede L, Hoenselaar E, van der Looij E, Goossens M, Churchman M, Carvajal-Carmona L, Tomlinson IP, de Bruijn DR, Van Kessel AG, Kuiper RP (2010) Germline epigenetic silencing of the tumor suppressor gene PTPRJ in early-onset familial colorectal cancer. Gastroenterology 139(6):2221-2224
51. Navarro A, Diaz T, Martinez A, Gaya A, Pons A, Gel B, Codony C, Ferrer G, Martinez C, Montserrat E, Monzo M Regulation of JAK2 by miR-135a: prognostic impact in classic Hodgkin lymphoma. Blood 114(14):2945-2951
52. 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, Andreeff M, Croce CM (2008) MicroRNA signatures associated with cytogenetics and prognosis in acute myeloid leukemia. Blood 111(6):3183-3189
53. Gabriely G, Yi M, Narayan RS, Niers JM, Wurdinger T, Imitola J, Ligon KL, Kesari S, Esau C, Stephens RM, Tannous BA, Krichevsky AM (2011). Human glioma growth is controlled by microRNA-10b. Cancer Res 71(10):3563-3572
54. Schetter AJ, Okayama H, Harris CC (2012) The role of microRNAs in colorectal cancer. Cancer J 18(3):244-252
55. Rossi S, Shimizu M, Barbarotto E, Nicoloso MS, Dimitri F, Sampath D, Fabbri M, Lerner S, Barron LL, Rassenti LZ, Jiang L, Xiao L, Hu J, Secchiero P, Zauli G, Volinia S, Negrini M, Wierda W, Kipps TJ, Plunkett W, Coombes KR, Abruzzo LV, Keating MJ, Calin GA (2010) microRNA fingerprinting of CLL patients with chromosome 17p deletion identify a miR-21 score that stratifies early survival. Blood 116(6):945-952
56. Leite KR, Tomiyama A, Reis ST, Sousa-Canavez JM, Sañudo A, Camara-Lopes LH, Srougi M (2011) MicroRNA expression profiles in the progression of prostate cancer-from high-grade prostate intraepithelial neoplasia to metastasis. Urol Oncol 2011 Aug 29. [Epub ahead of print]
57. Segura MF, Hanniford D, Menendez S, Reavie L, Zou X, Alvarez-Diaz S, Zakrzewski J, Blochin E, Rose A, Bogunovic D, Polsky D, Wei J, Lee P, Belitskaya-Levy I, Bhardwaj N, Osman I, Hernando E (2009) Aberrant miR-182 expression promotes melanoma metastasis by repressing FOXO3 and microphthalmia-associated transcription factor. Proc Natl Acad Sci U S A 106(6):1814-1819
58. Ma L, Teruya-Feldstein J, Weinberg RA (2007) Tumour invasion and metastasis initiated by microRNA-10b in breast cancer. Nature 449(7163):682-688
59. Slaby O, Svoboda M, Fabian P, Smerdova T, Kno flickova D, Bednarikova M, Nenutil R, Vyzula R (2007) Altered expression of miR-21, miR-31, miR-143 and miR-145 is related to clinicopathologic features of colorectal cancer. Oncology 72(5-6):397-402
60. Li J, Huang H, Sun L, Yang M, Pan C, Chen W, Wu D, Lin Z, Zeng C, Yao Y, Zhang P, Song E (2009) MiR-21 indicates poor prognosis in tongue squamous cell carcinomas as an apoptosis inhibitor. Clin Cancer Res 15(12):3998-4008
61. Hurst DR, Edmonds MD, Welch DR (2009) Metastamir: the field of metastasis-regulatory microRNA is spreading. Cancer Res 69(19):7495-7498
62. Tsai WC, Hsu PW, Lai TC, Chau GY, Lin CW, Chen CM, Lin CD, Liao YL, Wang JL, Chau YP, Hsu MT, Hsiao M, Huang HD, Tsou AP (2009) MicroRNA-122, a tumor suppressor microRNA that regulates intrahepatic metastasis of hepatocellular carcinoma. Hepatology 49(5):1571-1582