Exon array analysis reveals neuroblastoma tumors have distinct alternative splicing patterns according to stage and MYCN amplification status

BMC Medical Genomics

Volumn 4, Issue , 2011, Pages

  Guo, Xiang ^a,b   Chen, Qing Rong ^a   Song, Young K ^a   Wei, Jun S ^a   Khan, Javed ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b SAIC FREDERICK INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MYC PROTEIN; MYCN PROTEIN, HUMAN; NUCLEAR PROTEIN; ONCOPROTEIN;

ALTERNATIVE RNA SPLICING; ARTICLE; CANCER STAGING; CHILD; CONTROLLED STUDY; COPY NUMBER VARIATION; DNA SEQUENCE; EXON; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENETIC ASSOCIATION; HUMAN; HUMAN CELL; INFANT; MICROARRAY ANALYSIS; NEUROBLASTOMA; NUCLEOTIDE SEQUENCE; PRESCHOOL CHILD; PRIORITY JOURNAL; SCHOOL CHILD; SEQUENCE ANALYSIS; TRANSCRIPTION REGULATION; DNA MICROARRAY; GENE EXPRESSION REGULATION; GENETICS; PATHOLOGY; PRINCIPAL COMPONENT ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

ALTERNATIVE SPLICING; EXONS; GENE AMPLIFICATION; GENE EXPRESSION REGULATION, NEOPLASTIC; NEOPLASM STAGING; NEUROBLASTOMA; NUCLEAR PROTEINS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ONCOGENE PROTEINS; PRINCIPAL COMPONENT ANALYSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

EID: 79955095575     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/1755-8794-4-35     Document Type: Article

References (41)

1. Splicing in disease: disruption of the splicing code and the decoding machinery. GS Wang TA Cooper, Nat Rev Genet 2007 8 10 749 761 10.1038/nrg2164 17726481 (Pubitemid 47429207)
2. Alternative splicing in colon, bladder, and prostate cancer identified by exon-array analysis. K Thorsen KD Sorensen AS Brems-Eskildsen C Modin M Gaustadnes AM Hein M Kruhoffer S Laurberg M Borre K Wang S Brunak AR Krainer N Tørring L Dyrskjøt CL Andersen TF Orntoft, Mol Cell Proteomics 2008 18353764
3. Global analysis of aberrant pre-mRNA splicing in glioblastoma using exon expression arrays. HC Cheung KA Baggerly S Tsavachidis LL Bachinski VL Neubauer TJ Nixon KD Aldape GJ Cote R Krahe, BMC Genomics 2008 9 1 216 10.1186/1471-2164-9-216 18474104
4. Profiling alternatively spliced mRNA isoforms for prostate cancer classification. C Zhang HR Li JB Fan J Wang-Rodriguez T Downs XD Fu MQ Zhang, BMC Bioinformatics 2006 7 202 10.1186/1471-2105-7-202 16608523
5. Multiple alternative splicing markers for ovarian cancer. R Klinck A Bramard L Inkel G Dufresne-Martin J Gervais-Bird R Madden ER Paquet C Koh JP Venables P Prinos,, et al. Cancer Res 2008 68 3 657 663 10.1158/0008-5472.CAN- 07-2580 18245464 (Pubitemid 351206740)
6. Identification of differentially regulated splice variants and novel exons in glial brain tumors using exon expression arrays. PJ French J Peeters S Horsman E Duijm I Siccama MJ van den Bent TM Luider JM Kros P van der Spek PA Sillevis Smitt, Cancer Res 2007 67 12 5635 5642 10.1158/0008-5472.CAN-06-2869 17575129 (Pubitemid 46984994)
7. Recent advances in neuroblastoma. JM Maris, N Engl J Med 362 23 2202 2211 10.1056/NEJMra0804577 20558371
8. Revisions of the international criteria for neuroblastoma diagnosis, staging, and response to treatment. GM Brodeur J Pritchard F Berthold NL Carlsen V Castel RP Castelberry B De Bernardi AE Evans M Favrot F Hedborg,, et al. J Clin Oncol 1993 11 8 1466 1477 8336186 (Pubitemid 23228250)
9. Genomic medicine and neuroblastoma. O Oppenheimer M Alaminos WL Gerald, Expert Rev Mol Diagn 2003 3 1 39 54 10.1586/14737159.3.1.39 12528363 (Pubitemid 36061549)
10. Association of multiple copies of the N-myc oncogene with rapid progression of neuroblastomas. RC Seeger GM Brodeur H Sather A Dalton SE Siegel KY Wong D Hammond, N Engl J Med 1985 313 18 1111 1116 10.1056/ NEJM198510313131802 4047115 (Pubitemid 16216827)
11. TrkA alternative splicing: a regulated tumor-promoting switch in human neuroblastoma. A Tacconelli AR Farina L Cappabianca G Desantis A Tessitore A Vetuschi R Sferra N Rucci B Argenti I Screpanti,, et al. Cancer Cell 2004 6 4 347 360 10.1016/j.ccr.2004.09.011 15488758 (Pubitemid 39361436)
12. KIF1Bbeta functions as a haploinsufficient tumor suppressor gene mapped to chromosome 1p36.2 by inducing apoptotic cell death. AK Munirajan K Ando A Mukai M Takahashi Y Suenaga M Ohira T Koda T Hirota T Ozaki A Nakagawara, J Biol Chem 2008 283 36 24426 24434 10.1074/jbc.M802316200 18614535
13. The kinesin KIF1Bbeta acts downstream from EglN3 to induce apoptosis and is a potential 1p36 tumor suppressor. S Schlisio RS Kenchappa LC Vredeveld RE George R Stewart H Greulich K Shahriari NV Nguyen P Pigny PL Dahia,, et al. Genes Dev 2008 22 7 884 893 10.1101/gad.1648608 18334619 (Pubitemid 351482842)
14. Detection and measurement of alternative splicing using splicing-sensitive microarrays. K Srinivasan L Shiue JD Hayes R Centers S Fitzwater R Loewen LR Edmondson J Bryant M Smith C Rommelfanger,, et al. Methods 2005 37 4 345 359 10.1016/j.ymeth.2005.09.007 16314264 (Pubitemid 41682505)
15. Significance analysis of microarrays applied to the ionizing radiation response. VG Tusher R Tibshirani G Chu, Proc Natl Acad Sci USA 2001 98 9 5116 5121 10.1073/pnas.091062498 11309499 (Pubitemid 32397092)
16. AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. D Emig N Salomonis J Baumbach T Lengauer BR Conklin M Albrecht, Nucleic Acids Res 38 Suppl 755 762 20513647
17. Genomic structure and mutational analysis of the human KIF1Balpha gene located at 1p36.2 in neuroblastoma. YY Chen J Takita YZ Chen HW Yang R Hanada K Yamamoto Y Hayashi, Int J Oncol 2003 23 3 737 744 12888911
18. The M2 splice isoform of pyruvate kinase is important for cancer metabolism and tumour growth. HR Christofk MG Vander Heiden MH Harris A Ramanathan RE Gerszten R Wei MD Fleming SL Schreiber LC Cantley, Nature 2008 452 7184 230 233 10.1038/nature06734 18337823 (Pubitemid 351380249)
19. Structural basis for tumor pyruvate kinase M2 allosteric regulation and catalysis. JD Dombrauckas BD Santarsiero AD Mesecar, Biochemistry 2005 44 27 9417 9429 10.1021/bi0474923 15996096 (Pubitemid 40962040)
20. Global genomic and proteomic analysis identifies biological pathways related to high-risk neuroblastoma. QR Chen YK Song LR Yu JS Wei JY Chung SM Hewitt TD Veenstra J Khan, J Proteome Res 2010 9 1 373 382 10.1021/pr900701v 19921788
21. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. W Huang da BT Sherman RA Lempicki, Nat Protoc 2009 4 1 44 57 10.1038/nprot.2008.211 19131956
22. Altered expression of cell cycle genes distinguishes aggressive neuroblastoma. AL Krasnoselsky CC Whiteford JS Wei S Bilke F Westermann QR Chen J Khan, Oncogene 2005 24 9 1533 1541 10.1038/sj.onc.1208341 15592497 (Pubitemid 40396083)
23. Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Q Pan O Shai C Misquitta W Zhang AL Saltzman N Mohammad T Babak H Siu TR Hughes QD Morris,, et al. Mol Cell 2004 16 6 929 941 10.1016/j.molcel.2004.12.004 15610736 (Pubitemid 40018403)
24. Global analysis of alternative splicing during T-cell activation. JY Ip A Tong Q Pan JD Topp BJ Blencowe KW Lynch, RNA 2007 13 4 563 572 10.1261/rna.457207 17307815 (Pubitemid 46506939)
25. Genome-wide analysis of gene expression associated with MYCN in human neuroblastoma. M Alaminos J Mora NK Cheung A Smith J Qin L Chen WL Gerald, Cancer Res 2003 63 15 4538 4546 12907629 (Pubitemid 36951027)
26. Distinct transcriptional MYCN/c-MYC activities are associated with spontaneous regression or malignant progression in neuroblastomas. F Westermann D Muth A Benner T Bauer KO Henrich A Oberthuer B Brors T Beissbarth J Vandesompele F Pattyn,, et al. Genome Biol 2008 9 10 150 10.1186/gb-2008-9-10- r150 18851746
27. Reflecting on 25 years with MYC. N Meyer LZ Penn, Nat Rev Cancer 2008 8 12 976 990 10.1038/nrc2231 19029958
28. An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets. KI Zeller AG Jegga BJ Aronow KA O'Donnell CV Dang, Genome Biol 2003 4 10 69 10.1186/gb-2003-4-10-r69 14519204
29. HnRNP proteins controlled by c-Myc deregulate pyruvate kinase mRNA splicing in cancer. CJ David M Chen M Assanah P Canoll JL Manley, Nature 463 7279 364 368 10.1038/nature08697 20010808
30. Splicing factors PTBP1 and PTBP2 promote proliferation and migration of glioma cell lines. HC Cheung T Hai W Zhu KA Baggerly S Tsavachidis R Krahe GJ Cote, Brain 2009 132 Pt 8 2277 2288 10.1093/brain/awp153 19506066
31. Crossregulation and functional redundancy between the splicing regulator PTB and its paralogs nPTB and ROD1. R Spellman M Llorian CW Smith, Mol Cell 2007 27 3 420 434 10.1016/j.molcel.2007.06.016 17679092 (Pubitemid 47126939)
32. Proteomic analysis of in vivo-assembled pre-mRNA splicing complexes expands the catalog of participating factors. YI Chen RE Moore HY Ge MK Young TD Lee SW Stevens, Nucleic Acids Res 2007 35 12 3928 3944 10.1093/nar/gkm347 17537823 (Pubitemid 47248460)
33. Pyruvate kinase type M2 and its role in tumor growth and spreading. S Mazurek CB Boschek F Hugo E Eigenbrodt, Semin Cancer Biol 2005 15 4 300 308 10.1016/j.semcancer.2005.04.009 15908230 (Pubitemid 41058775)
34. Tumor cell metabolism: cancer's Achilles' heel. G Kroemer J Pouyssegur, Cancer Cell 2008 13 6 472 482 10.1016/j.ccr.2008.05.005 18538731 (Pubitemid 351766797)
35. Elevated expression of protein regulator of cytokinesis 1, involved in the growth of breast cancer cells. A Shimo T Nishidate T Ohta M Fukuda Y Nakamura T Katagiri, Cancer Sci 2007 98 2 174 181 10.1111/j.1349-7006.2006. 00381.x 17233835 (Pubitemid 44941869)
36. Microtubule-associated protein 2, a marker of neuronal differentiation, induces mitotic defects, inhibits growth of melanoma cells, and predicts metastatic potential of cutaneous melanoma. MH Soltani R Pichardo Z Song N Sangha F Camacho K Satyamoorthy OP Sangueza V Setaluri, Am J Pathol 2005 166 6 1841 1850 10.1016/S0002-9440(10)62493-5 15920168 (Pubitemid 40734406)
37. Two-dimensional transcriptome profiling: identification of messenger RNA isoform signatures in prostate cancer from archived paraffin-embedded cancer specimens. HR Li J Wang-Rodriguez TM Nair JM Yeakley YS Kwon M Bibikova C Zheng L Zhou K Zhang T Downs,, et al. Cancer Res 2006 66 8 4079 4088 10.1158/0008-5472.CAN-05-4264 16618727
38. Enhanced genomic instabilities caused by deregulated microtubule dynamics and chromosome segregation: a perspective from genetic studies in mice. CV Rao HY Yamada Y Yao W Dai, Carcinogenesis 2009 30 9 1469 1474 10.1093/carcin/bgp081 19372138
39. Purification of total RNA from mammalian cells and tissues. JSKJ Wei, DNA microarrays: a molecular cloning manual Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press, D Bowtell JS, 2002 110 119
40. Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors. N Salomonis B Nelson K Vranizan AR Pico K Hanspers A Kuchinsky L Ta M Mercola BR Conklin, PLoS Comput Biol 2009 5 11 1000553 10.1371/journal.pcbi.1000553 19893621
41. SpliceCenter: a suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies. MC Ryan BR Zeeberg NJ Caplen JA Cleland AB Kahn H Liu JN Weinstein, BMC Bioinformatics 2008 9 313 10.1186/1471-2105-9-313 18638396