Characterization of the uterine leiomyoma microRNAome by deep sequencing

Genomics

Volumn 99, Issue 5, 2012, Pages 275-281

  Georgieva, Boryana ^a   Milev, Ivan ^a   Minkov, Ivan ^a   Dimitrova, Irina ^b   Bradford, Andrew P ^b   Baev, Vesselin ^a  

^a UNIVERSITY OF PLOVDIV   (Bulgaria)

^b UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

Author keywords

Deep sequencing; MiRNAs; Myometrium; Small RNAs; Uterine leiomyoma

Indexed keywords

MICRORNA; MICRORNA 137; MICRORNA 217; MICRORNA 363; MICRORNA 4792; MICRORNA 490; RNA; TRANSCRIPTOME; UNCLASSIFIED DRUG;

ARTICLE; CARCINOGENESIS; CONTROLLED STUDY; FEMALE; GENE DOSAGE; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE LIBRARY; GENE LOCUS; GENE MAPPING; GENETIC ASSOCIATION; GENETIC CODE; GENETIC VARIABILITY; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN TISSUE; MICROARRAY ANALYSIS; MYOMETRIUM; PRIORITY JOURNAL; RNA ANALYSIS; RNA SEQUENCE; SEQUENCE ANALYSIS; TRANSCRIPTOMICS; UTERUS MYOMA;

BASE SEQUENCE; DNA, COMPLEMENTARY; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LEIOMYOMA; MICRORNAS; MOLECULAR SEQUENCE DATA; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; TRANSCRIPTOME; UTERINE NEOPLASMS;

EID: 84860697954     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2012.03.003     Document Type: Article

References (48)

1. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297.
2. Lagos-Quintana M., Rauhut R., Lendeckel W., Tuschl T. Identification of novel genes coding for small expressed RNAs. Science 2001, 294:853-858.
3. Hammell C.M. The microRNA-argonaute complex: a platform for mRNA modulation. RNA Biol. 2008, 5:123-127.
4. Lee Y., Han J., Yeom K.H., Jin H., Kim V.N. Drosha in primary microRNA processing. Cold Spring Harb. Symp. Quant. Biol. 2006, 71:51-57.
5. Tijsterman M., Plasterk R.H. Dicers at RISC; the mechanism of RNAi. Cell 2004, 117:1-3.
6. Okamura K., Ishizuka A., Siomi H., Siomi M.C. Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways. Genes Dev. 2004, 18:1655-1666.
7. Alvarez-Garcia I., Miska E.A. MicroRNA functions in animal development and human disease. Development 2005, 132:4653-4662.
8. Lu J., Getz G., Miska E.A., Alvarez-Saavedra E., Lamb J., Peck D., Sweet-Cordero A., Ebert B.L., Mak R.H., Ferrando A.A., Downing J.R., Jacks T., Horvitz H.R., Golub T.R. MicroRNA expression profiles classify human cancers. Nature 2005, 435:834-838.
9. Volinia S., Calin G.A., Liu C.G., Ambs S., Cimmino A., Petrocca F., Visone R., Iorio M., Roldo C., Ferracin M., Prueitt R.L., Yanaihara N., Lanza G., Scarpa A., Vecchione A., Negrini M., Harris C.C., Croce C.M. A microRNA expression signature of human solid tumors defines cancer gene targets. Proc. Natl. Acad. Sci. U. S. A. 2006, 103:2257-2261.
10. Stenvang J., Lindow M., Kauppinen S. Targeting of microRNAs for therapeutics. Biochem. Soc. Trans. 2008, 36:1197-1200.
11. Stenvang J., Kauppinen S. MicroRNAs as targets for antisense-based therapeutics. Expert. Opin. Biol. Ther. 2008, 8:59-81.
12. Marsh E.E., Lin Z., Yin P., Milad M., Chakravarti D., Bulun S.E. Differential expression of microRNA species in human uterine leiomyoma versus normal myometrium. Fertil. Steril. 2008, 89:1771-1776.
13. Pan Q., Luo X., Chegini N. Differential expression of microRNAs in myometrium and leiomyomas and regulation by ovarian steroids. J. Cell. Mol. Med. 2008, 12:227-240.
14. Wang T., Zhang X., Obijuru L., Laser J., Aris V., Lee P., Mittal K., Soteropoulos P., Wei J.J. A micro-RNA signature associated with race, tumor size, and target gene activity in human uterine leiomyomas. Genes Chromosom. Cancer 2007, 46:336-347.
15. Cesen-Cummings K., Copland J.A., Barrett J.C., Walker C.L., Davis B.J. Pregnancy, parturition, and prostaglandins: defining uterine leiomyomas. Environ. Health Perspect. 2000, 108(Suppl. 5):817-820.
16. Ligon A.H., Morton C.C. Leiomyomata: heritability and cytogenetic studies. Hum. Reprod. Update 2001, 7:8-14.
17. Whiteman M.K., Kuklina E., Jamieson D.J., Hillis S.D., Marchbanks P.A. Inpatient hospitalization for gynecologic disorders in the United States. Am. J. Obstet. Gynecol. 2010, 202(541):e541-546.
18. Okolo S. Incidence, aetiology and epidemiology of uterine fibroids. Best Pract. Res. Clin. Obstet. Gynaecol. 2008, 22:571-588.
19. Cramer S.F., Patel A. The frequency of uterine leiomyomas. Am. J. Clin. Pathol. 1990, 94:435-438.
20. Buttram V.C. Uterine leiomyomata-aetiology, symptomatology and management. Prog. Clin. Biol. Res. 1986, 225:275-296.
21. Creighton C.J., Reid J.G., Gunaratne P.H. Expression profiling of microRNAs by deep sequencing. Brief. Bioinform. 2009, 10:490-497.
22. Git A., Dvinge H., Salmon-Divon M., Osborne M., Kutter C., Hadfield J., Bertone P., Caldas C. Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression. RNA 2010, 16:991-1006.
23. t Hoen P.A., Ariyurek Y., Thygesen H.H., Vreugdenhil E., Vossen R.H., de Menezes R.X., Boer J.M., van Ommen G.J., den Dunnen J.T. Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res. 2008, 36:e141.
24. Yang N., Zhang L., Kazazian H.H. L1 retrotransposon-mediated stable gene silencing. Nucleic Acids Res. 2005, 33:e57.
25. Landgraf P., Rusu M., Sheridan R., Sewer A., Iovino N., Aravin A., Pfeffer S., Rice A., Kamphorst A.O., Landthaler M., Lin C., Socci N.D., Hermida L., Fulci V., Chiaretti S., Foa R., Schliwka J., Fuchs U., Novosel A., Muller R.U., Schermer B., Bissels U., Inman J., Phan Q., Chien M., Weir D.B., Choksi R., De Vita G., Frezzetti D., Trompeter H.I., Hornung V., Teng G., Hartmann G., Palkovits M., Di Lauro R., Wernet P., Macino G., Rogler C.E., Nagle J.W., Ju J., Papavasiliou F.N., Benzing T., Lichter P., Tam W., Brownstein M.J., Bosio A., Borkhardt A., Russo J.J., Sander C., Zavolan M., Tuschl T. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 2007, 129:1401-1414.
26. Morin R.D., O'Connor M.D., Griffith M., Kuchenbauer F., Delaney A., Prabhu A.L., Zhao Y., McDonald H., Zeng T., Hirst M., Eaves C.J., Marra M.A. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res. 2008, 18:610-621.
27. Ruby J.G., Jan C., Player C., Axtell M.J., Lee W., Nusbaum C., Ge H., Bartel D.P. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 2006, 127:1193-1207.
28. Guo L., Lu Z. Global expression analysis of miRNA gene cluster and family based on isomiRs from deep sequencing data. Comput. Biol. Chem. 2010, 34:165-171.
29. Anders S., Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010, 11:R106.
30. Piriyapongsa J., Jordan I.K. A family of human microRNA genes from miniature inverted-repeat transposable elements. PLoS One 2007, 2:e203.
31. Creighton C.J., Benham A.L., Zhu H., Khan M.F., Reid J.G., Nagaraja A.K., Fountain M.D., Dziadek O., Han D., Ma L., Kim J., Hawkins S.M., Anderson M.L., Matzuk M.M., Gunaratne P.H. Discovery of novel microRNAs in female reproductive tract using next generation sequencing. PLoS One 2010, 5:e9637.
32. Altuvia Y., Landgraf P., Lithwick G., Elefant N., Pfeffer S., Aravin A., Brownstein M.J., Tuschl T., Margalit H. Clustering and conservation patterns of human microRNAs. Nucleic Acids Res. 2005, 33:2697-2706.
33. Pan Q., Luo X., Chegini N. microRNA 21: response to hormonal therapies and regulatory function in leiomyoma, transformed leiomyoma and leiomyosarcoma cells. Mol. Hum. Reprod. 2010, 16:215-227.
34. Schramedei K., Morbt N., Pfeifer G., Lauter J., Rosolowski M., Tomm J.M., von Bergen M., Horn F., Brocke-Heidrich K. MicroRNA-21 targets tumor suppressor genes ANP32A and SMARCA4. Oncogene 2011, 30:2975-2985.
35. Arslan A.A., Gold L.I., Mittal K., Suen T.C., Belitskaya-Levy I., Tang M.S., Toniolo P. Gene expression studies provide clues to the pathogenesis of uterine leiomyoma: new evidence and a systematic review. Hum. Reprod. 2005, 20:852-863.
36. Hao J., Zhang S., Zhou Y., Hu X., Shao C. MicroRNA 483-3p suppresses the expression of DPC4/Smad4 in pancreatic cancer. FEBS Lett. 2011, 585:207-213.
37. Lee E.J., Kong G., Lee S.H., Rho S.B., Park C.S., Kim B.G., Bae D.S., Kavanagh J.J., Lee J.H. Profiling of differentially expressed genes in human uterine leiomyomas. Int. J. Gynecol. Cancer 2005, 15:146-154.
38. Veronese A., Lupini L., Consiglio J., Visone R., Ferracin M., Fornari F., Zanesi N., Alder H., D'Elia G., Gramantieri L., Bolondi L., Lanza G., Querzoli P., Angioni A., Croce C.M., Negrini M. Oncogenic role of miR-483-3p at the IGF2/483 locus. Cancer Res. 2010, 70:3140-3149.
39. Snowdon J., Zhang X., Childs T., Tron V.A., Feilotter H. The microRNA-200 family is upregulated in endometrial carcinoma. PLoS One 2011, 6:e22828.
40. Brase J.C., Johannes M., Schlomm T., Falth M., Haese A., Steuber T., Beissbarth T., Kuner R., Sultmann H. Circulating miRNAs are correlated with tumor progression in prostate cancer. Int. J. Cancer 2011, 128:608-616.
41. Li A., Omura N., Hong S.M., Vincent A., Walter K., Griffith M., Borges M., Goggins M. Pancreatic cancers epigenetically silence SIP1 and hypomethylate and overexpress miR-200a/200b in association with elevated circulating miR-200a and miR-200b levels. Cancer Res. 2010, 70:5226-5237.
42. Wyman S.K., Parkin R.K., Mitchell P.S., Fritz B.R., O'Briant K., Godwin A.K., Urban N., Drescher C.W., Knudsen B.S., Tewari M. Repertoire of microRNAs in epithelial ovarian cancer as determined by next generation sequencing of small RNA cDNA libraries. PLoS One 2009, 4:e5311.
43. Zhang H., Su S.B., Zhou Q.M., Lu Y.Y. Differential expression profiles of microRNAs between breast cancer cells and mammary epithelial cells. Ai Zheng 2009, 28:493-499.
44. Langmead B., Trapnell C., Pop M., Salzberg S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10:R25.
45. Griffiths-Jones S. miRBase: microRNA sequences and annotation. Curr. Protoc. Bioinform. 2010, 12(12):19 11-10. Chapter, Unit.
46. Griffiths-Jones S. miRBase: the microRNA sequence database. Meth. Mol Biol 2006, 342:129-138.
47. Zhu E., Zhao F., Xu G., Hou H., Zhou L., Li X., Sun Z., Wu J. mirTools: microRNA profiling and discovery based on high-throughput sequencing. Nucleic Acids Res. 2010, 38:W392-W397.
48. Friedlander M.R., Chen W., Adamidi C., Maaskola J., Einspanier R., Knespel S., Rajewsky N. Discovering microRNAs from deep sequencing data using miRDeep. Nat. Biotechnol. 2008, 26:407-415.