The two most common histological subtypes of malignant germ cell tumour are distinguished by global microRNA profiles, associated with differential transcription factor expression
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- 作者：Matthew J Murray (1)
Harpreet K Saini (2)
Stijn van Dongen (2)
Roger D Palmer (1)
Balaji Muralidhar (1)
Mark R Pett (1)
Matias Piipari (3)
Claire M Thornton (4)
James C Nicholson (5)
Anton J Enright (2)
Nicholas Coleman (1) (6) - 刊名：Molecular Cancer
- 出版年：2010
- 出版时间：December 2010
- 年：2010
- 卷：9
- 期：1
- 全文大小：1841KB
- 参考文献：1. Murray MJ, Nicholson JC: Germ Cell Tumours in Children and Adolescents. / Paediatrics and Child Health 2010, 20:109鈥?16. CrossRef
2. Bamberg M, Kortmann RD, Calaminus G, Becker G, Meisner C, Harms D, Gobel U: Radiation therapy for intracranial germinoma: results of the German cooperative prospective trials MAKEI 83/86/89. / J Clin Oncol 1999, 17:2585鈥?592.
3. Hoffman HJ, Otsubo H, Hendrick EB, Humphreys RP, Drake JM, Becker LE, Greenberg M, Jenkin D: Intracranial germ-cell tumors in children. / J Neurosurg 1991, 74:545鈥?51. CrossRef
4. Calaminus G, Bamberg M, Harms D, Jurgens H, Kortmann RD, Sorensen N, Wiestler OD, Gobel U: AFP/beta-HCG secreting CNS germ cell tumors: long-term outcome with respect to initial symptoms and primary tumor resection. Results of the cooperative trial MAKEI 89. / Neuropediatrics 2005, 36:71鈥?7. CrossRef
5. International Germ Cell Consensus Classification: a prognostic factor-based staging system for metastatic germ cell cancers. International Germ Cell Cancer Collaborative Group / J Clin Oncol 1997, 15:594鈥?03.
6. Baranzelli MC, Kramar A, Bouffet E, Quintana E, Rubie H, Edan C, Patte C: Prognostic factors in children with localized malignant nonseminomatous germ cell tumors. / J Clin Oncol 1999, 17:1212.
7. Palmer RD, Barbosa-Morais NL, Gooding EL, Muralidhar B, Thornton CM, Pett MR, Roberts I, Schneider DT, Thorne N, Tavare S, / et al.: Pediatric malignant germ cell tumors show characteristic transcriptome profiles. / Cancer Res 2008, 68:4239鈥?247. CrossRef
8. Palmer RD, Murray MJ, Saini HK, van Dongen S, Abreu-Goodger C, Muralidhar B, Pett MR, Thornton CM, Nicholson JC, Enright AJ, Coleman N: Malignant Germ Cell Tumors Display Common microRNA Profiles Resulting in Global Changes in Expression of Messenger RNA Targets. / Cancer Research 2010, 70:2911鈥?923. CrossRef
9. Gillis AJ, Stoop HJ, Hersmus R, Oosterhuis JW, Sun Y, Chen C, Guenther S, Sherlock J, Veltman I, Baeten J, / et al.: High-throughput microRNAome analysis in human germ cell tumours. / J Pathol 2007, 213:319鈥?28. CrossRef
10. Korkola JE, Houldsworth J, Chadalavada RS, Olshen AB, Dobrzynski D, Reuter VE, Bosl GJ, Chaganti RS: Down-regulation of stem cell genes, including those in a 200-kb gene cluster at 12p13.31, is associated with in vivo differentiation of human male germ cell tumors. / Cancer Res 2006, 66:820鈥?27. CrossRef
11. Down TA, Bergman CM, Su J, Hubbard TJ: Large-scale discovery of promoter motifs in Drosophila melanogaster. / PLoS Comput Biol 2007, 3:e7. CrossRef
12. Piipari M, Down TA, Saini H, Enright A, Hubbard TJ: iMotifs: an integrated sequence motif visualization and analysis environment. / Bioinformatics 2010, 26:843鈥?44. CrossRef
13. Benjamini YHY: Controlling the false discovery rate - a practical and powerful approach to multiple testing. / J R Stat Soc Ser B-Methodol 1995, 57:289鈥?00.
14. Muralidhar B, Goldstein LD, Ng G, Winder DM, Palmer RD, Gooding EL, Barbosa-Morais NL, Mukherjee G, Thorne NP, Roberts I, / et al.: Global microRNA profiles in cervical squamous cell carcinoma depend on Drosha expression levels. / J Pathol 2007, 212:368鈥?77. CrossRef
15. Ruxton GD: The unequal variance t-test is an underused alternative to Student's t-test and the Mann-Whitney U test. / Behavioral Ecology 2006, 17:688鈥?90. CrossRef
16. Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T: Identification of novel genes coding for small expressed RNAs. / Science 2001, 294:853鈥?58. CrossRef
17. Lau NC, Lim LP, Weinstein EG, Bartel DP: An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. / Science 2001, 294:858鈥?62. CrossRef
18. Flicek P, Aken BL, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Coates G, Fairley S, / et al.: Ensembl's 10th year. / Nucleic Acids Res 2010, 38:D557鈥?62. CrossRef
19. Morgulis A, Gertz EM, Schaffer AA, Agarwala R: WindowMasker: window-based masker for sequenced genomes. / Bioinformatics 2006, 22:134鈥?41. CrossRef
20. Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, / et al.: TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. / Nucleic Acids Res 2006, 34:D108鈥?10. CrossRef
21. Marson A, Levine SS, Cole MF, Frampton GM, Brambrink T, Johnstone S, Guenther MG, Johnston WK, Wernig M, Newman J, / et al.: Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. / Cell 2008, 134:521鈥?33. CrossRef
22. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM: Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. / Nature 2005, 433:769鈥?73. CrossRef
23. Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA, / et al.: MicroRNA expression profiles classify human cancers. / Nature 2005, 435:834鈥?38. CrossRef
24. Peter ME: Let-7 and miR-200 microRNAs: guardians against pluripotency and cancer progression. / Cell Cycle 2009, 8:843鈥?52. CrossRef
25. Gregory PA, Bert AG, Paterson EL, Barry SC, Tsykin A, Farshid G, Vadas MA, Khew-Goodall Y, Goodall GJ: The miR-200 family and miR-205 regulate epithelial to mesenchymal transition by targeting ZEB1 and SIP1. / Nat Cell Biol 2008, 10:593鈥?01. CrossRef
26. Gee GV, Koestler DC, Christensen BC, Sugarbaker DJ, Ugolini D, Ivaldi GP, Resnick MB, Houseman EA, Kelsey KT, Marsit CJ: Downregulated MicroRNAs in the differential diagnosis of malignant pleural mesothelioma. / Int J Cancer 2010, in press.
27. Gregory PA, Bracken CP, Bert AG, Goodall GJ: MicroRNAs as regulators of epithelial-mesenchymal transition. / Cell Cycle 2008, 7:3112鈥?118. CrossRef
28. Korpal M, Kang Y: The emerging role of miR-200 family of microRNAs in epithelial-mesenchymal transition and cancer metastasis. / RNA Biol 2008, 5:115鈥?19.
29. Olson P, Lu J, Zhang H, Shai A, Chun MG, Wang Y, Libutti SK, Nakakura EK, Golub TR, Hanahan D: MicroRNA dynamics in the stages of tumorigenesis correlate with hallmark capabilities of cancer. / Genes Dev 2009, 23:2152鈥?165. CrossRef
30. Looijenga LH: Human testicular (non)seminomatous germ cell tumours: the clinical implications of recent pathobiological insights. / J Pathol 2009, 218:146鈥?62. CrossRef
31. Wang HW, Wu YH, Hsieh JY, Liang ML, Chao ME, Liu DJ, Hsu MT, Wong TT: Pediatric primary central nervous system germ cell tumors of different prognosis groups show characteristic miRNome traits and chromosome copy number variations. / BMC Genomics 2010, 11:132. CrossRef
32. Zovoilis A, Nolte J, Drusenheimer N, Zechner U, Hada H, Guan K, Hasenfuss G, Nayernia K, Engel W: Multipotent adult germline stem cells and embryonic stem cells have similar microRNA profiles. / Mol Hum Reprod 2008, 14:521鈥?29. CrossRef
33. Suh MR, Lee Y, Kim JY, Kim SK, Moon SH, Lee JY, Cha KY, Chung HM, Yoon HS, Moon SY, / et al.: Human embryonic stem cells express a unique set of microRNAs. / Dev Biol 2004, 270:488鈥?98. CrossRef
34. Barroso-delJesus A, Romero-Lopez C, Lucena-Aguilar G, Melen GJ, Sanchez L, Ligero G, Berzal-Herranz A, Menendez P: Embryonic stem cell-specific miR302鈥?67 cluster: human gene structure and functional characterization of its core promoter. / Mol Cell Biol 2008, 28:6609鈥?619. CrossRef
35. Stadler BM, Ivanovska I, Mehta K, Song S, Nelson A, Tan Y, Mathieu J, Darby GC, Blau CA, Ware C, / et al.: Characterization of microRNAs Involved in Embryonic Stem Cell States. / Stem Cells Dev 2010, 19:935鈥?50. CrossRef
36. Blenkiron C, Goldstein LD, Thorne NP, Spiteri I, Chin SF, Dunning MJ, Barbosa-Morais NL, Teschendorff AE, Green AR, Ellis IO, / et al.: MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype. / Genome Biol 2007, 8:R214. CrossRef
37. Card DA, Hebbar PB, Li L, Trotter KW, Komatsu Y, Mishina Y, Archer TK: Oct4/Sox2-regulated miR-302 targets cyclin D1 in human embryonic stem cells. / Mol Cell Biol 2008, 28:6426鈥?438. CrossRef
38. Looijenga LH, Stoop H, de Leeuw HP, de Gouveia Brazao CA, Gillis AJ, van Roozendaal KE, van Zoelen EJ, Weber RF, Wolffenbuttel KP, van Dekken H, / et al.: POU5F1 (OCT3/4) identifies cells with pluripotent potential in human germ cell tumors. / Cancer Res 2003, 63:2244鈥?250.
39. Yuan Y, Guo L, Shen L, Liu JS: Predicting gene expression from sequence: a reexamination. / PLoS Comput Biol 2007, 3:e243. 30243">CrossRef
40. Kleinjan DA, van Heyningen V: Long-range control of gene expression: emerging mechanisms and disruption in disease. / Am J Hum Genet 2005, 76:8鈥?2. CrossRef
41. Cao D, Guo S, Allan RW, Molberg KH, Peng Y: SALL4 is a novel sensitive and specific marker of ovarian primitive germ cell tumors and is particularly useful in distinguishing yolk sac tumor from clear cell carcinoma. / Am J Surg Pathol 2009, 33:894鈥?04. CrossRef
42. Cao D, Humphrey PA, Allan RW: SALL4 is a novel sensitive and specific marker for metastatic germ cell tumors, with particular utility in detection of metastatic yolk sac tumors. / Cancer 2009, 115:2640鈥?651. CrossRef
43. Cao D, Li J, Guo CC, Allan RW, Humphrey PA: SALL4 is a novel diagnostic marker for testicular germ cell tumors. / Am J Surg Pathol 2009, 33:1065鈥?077. CrossRef
44. Arvey A, Larsson E, Sander C, Leslie CS, Marks DS: Target mRNA abundance dilutes microRNA and siRNA activity. / Mol Syst Biol 2010, 6:363. CrossRef - 作者单位：Matthew J Murray (1)
Harpreet K Saini (2)
Stijn van Dongen (2)
Roger D Palmer (1)
Balaji Muralidhar (1)
Mark R Pett (1)
Matias Piipari (3)
Claire M Thornton (4)
James C Nicholson (5)
Anton J Enright (2)
Nicholas Coleman (1) (6)
1. Medical Research Council Cancer Cell Unit, Cambridge, CB2 0XZ, UK
2. EMBL-European Bioinformatics Institute, CB10 1SD, Hinxton, Cambridge, UK
3. Wellcome Trust Sanger Institute, CB10 1SA, Hinxton, Cambridge, UK
4. Department of Pathology, Royal Group of Hospitals Trust, Belfast, UK
5. Department of Paediatric Haematology and Oncology, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
6. Department of Pathology, University of Cambridge, CB2 1QP, UK - ISSN：1476-4598
文摘
Background We hypothesised that differences in microRNA expression profiles contribute to the contrasting natural history and clinical outcome of the two most common types of malignant germ cell tumour (GCT), yolk sac tumours (YSTs) and germinomas. Results By direct comparison, using microarray data for paediatric GCT samples and published qRT-PCR data for adult samples, we identified microRNAs significantly up-regulated in YSTs (n = 29 paediatric, 26 adult, 11 overlapping) or germinomas (n = 37 paediatric). By Taqman qRT-PCR we confirmed differential expression of 15 of 16 selected microRNAs and further validated six of these (miR-302b, miR-375, miR-200b, miR-200c, miR-122, miR-205) in an independent sample set. Interestingly, the miR-302 cluster, which is over-expressed in all malignant GCTs, showed further over-expression in YSTs versus germinomas, representing six of the top eight microRNAs over-expressed in paediatric YSTs and seven of the top 11 in adult YSTs. To explain this observation, we used mRNA expression profiles of paediatric and adult malignant GCTs to identify 10 transcription factors (TFs) consistently over-expressed in YSTs versus germinomas, followed by linear regression to confirm associations between TF and miR-302 cluster expression levels. Using the sequence motif analysis environment iMotifs, we identified predicted binding sites for four of the 10 TFs (GATA6, GATA3, TCF7L2 and MAF) in the miR-302 cluster promoter region. Finally, we showed that miR-302 family over-expression in YST is likely to be functionally significant, as mRNAs down-regulated in YSTs were enriched for 3' untranslated region sequences complementary to the common seed of miR-302a~miR-302d. Such mRNAs included mediators of key cancer-associated processes, including tumour suppressor genes, apoptosis regulators and TFs. Conclusions Differential microRNA expression is likely to contribute to the relatively aggressive behaviour of YSTs and may enable future improvements in clinical diagnosis and/or treatment.