Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array

BMC Genomics

Volumn 7, Issue , 2006, Pages

  Gardina, Paul J ^a   Clark, Tyson A ^a   Shimada, Brian ^a   Staples, Michelle K ^a   Yang, Qing ^a   Veitch, James ^a   Schweitzer, Anthony ^a   Awad, Tarif ^a   Sugnet, Charles ^a   Dee, Suzanne ^a   Davies, Christopher ^a   Williams, Alan ^a   Turpaz, Yaron ^a  

^a Thermo Fisher Scientific   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSKELETON PROTEIN; INTEGRIN; SCLEROPROTEIN;

ALTERNATIVE RNA SPLICING; ARTICLE; CELL MOTILITY; CELL PROLIFERATION; COLON CANCER; CONTROLLED STUDY; EXON; EXPRESSED SEQUENCE TAG; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENETIC ALGORITHM; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENOME ANALYSIS; HUMAN; HUMAN GENOME; HUMAN TISSUE; MICROARRAY ANALYSIS; ONCOGENE; PREDICTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SIGNAL TRANSDUCTION;

ALGORITHMS; ALTERNATIVE SPLICING; COLONIC NEOPLASMS; EXONS; GENE EXPRESSION; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

EID: 33846467191     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-7-325     Document Type: Article

References (63)

1. Black DL Mechanisms of alternative pre-messenger RNA splicing Annu Rev Biochem 2003 72 291-336 10.1146/annurev.biochem.72.121801.161720 12626338
2. Faustino NA Cooper TA Pre-mRNA splicing and human disease Genes Dev 2003 17 4 419-437 10.1101/gad.1048803 12600935
3. Venables JP Unbalanced alternative splicing and its significance in cancer Bioessays 2006 28 4 378-386 10.1002/bies.20390 16547952
4. Finn L Dougherty G Finley G Meisler A Becich M Cooper DL Alternative splicing of CD44 pre-mRNA in human colorectal tumors Biochem Biophys Res Commun 1994 200 2 1015-1022 10.1006/bbrc.1994.1551 7513991
5. Goodison S Urquidi V Tarin D CD44 cell adhesion molecules Mol Pathol 1999 52 4 189-196 395698 10694938
6. Sternberg LR Byrd JC Hansson GC Liu KF Bresalier RS Alternative splicing of the human MUC2 gene Arch Biochem Biophys 2004 421 1 21-33 10.1016/ j.abb.2003.10.002 14678781
7. Patten LC Belaguli NS Baek MJ Fagan SP Awad SS Berger DH Serum response factor is alternatively spliced in human colon cancer J Surg Res 2004 121 1 92-100 10.1016/j.jss.2004.02.031 15313381
8. Huerta S Srivatsan ES Venkatesan N Peters J Moatamed F Renner S Livingston EH Alternative mRNA splicing in colon cancer causes loss of expression of neural cell adhesion molecule Surgery 2001 130 5 834-843 10.1067/msy.2001.116415 11685193
9. Genuardi M Viel A Bonora D Capozzi E Bellacosa A Leonardi F Valle R Ventura A Pedroni M Boiocchi M Neri G Characterization of MLH1 and MSH2 alternative splicing and its relevance to molecular testing of colorectal cancer susceptibility Hum Genet 1998 102 1 15-20 10.1007/ s004390050648 9490293
10. Pospisil H Herrmann A Butherus K Pirson S Reich JG Kemmner W Verification of predicted alternatively spliced Wnt genes reveals two new splice variants (CTNNB1 and LRP5) and altered Axin-1 expression during tumour progression BMC Genomics 2006 7 1 148 1523213 16772034 10.1186/1471-2164-7-148
11. Affymetrix_Inc. Affymetrix White Papers: Exon Probeset Annotations and Transcript Cluster Groupings v1.0; Exon Array Background Correction v1.0; Guide to Probe Logarithmic Intensity Error (PLIER) Estimation; Gene Signal Estimates from Exon Arrays v1.0; Statistical Algorithms Reference Guide; Alternative Transcript Analysis Methods for Exon Arrays v1.1 http://www.affymetrix.com/support/technical/whitepapers.affx
12. Fisher H Stenling R Rubio C Lindblom A Differential expression of aquaporin 8 in human colonic epithelial cells and colorectal tumors BMC Physiol 2001 1 1 32180 11231887 10.1186/1472-6793-1-1
13. Sereti E Gavriil A Agnantis N Golematis VC Voloudakis-Baltatzis IE Immunoelectron study of somatostatin, gastrin and glucagon in human colorectal adenocarcinomas and liver metastases Anticancer Res 2002 22 4 2117-2123 12174892
14. Tseng WW Liu CD Peptide YY and cancer: Current findings and potential clinical applications Peptides 2002 23 2 389-395 10.1016/ S0196-9781(01)00616-7 11825654
15. Jang MS Park JE Lee JA Park SG Myung PK Lee do H Park BC Cho S Binding and regulation of hypoxia-inducible factor-1 by the inhibitory PAS proteins Biochem Biophys Res Commun 2005 337 1 209-215 10.1016/ j.bbrc.2005.09.038 16182248
16. Bauer TW Fan F Liu W Johnson M Parikh NU Parry GC Callahan J Mazar AP Gallick GE Ellis LM Insulinlike growth factor-I-mediated migration and invasion of human colon carcinoma cells requires activation of c-Met and urokinase plasminogen activator receptor Ann Surg 2005 241 5 748-56; discussion 756-8 1357129 15849510 10.1097/01.sla.0000160699.59061.92
17. Wong MP Cheung N Yuen ST Leung SY Chung LP Vascular endothelial growth factor is up-regulated in the early pre-malignant stage of colorectal tumour progression Int J Cancer 1999 81 6 845-850 10.1002/ (SICI)1097-0215(19990611)81:6<845::AID-IJC1>3.0.CO;2-5 10362127
18. Brembeck FH Rosario M Birchmeier W Balancing cell adhesion and Wnt signaling, the key role of beta-catenin Curr Opin Genet Dev 2006 16 1 51-59 10.1016/j.gde.2005.12.007 16377174
19. Clark TA Sugnet CW Ares M Jr. Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays Science 2002 296 5569 907-910 10.1126/science.1069415 11988574
20. Srinivasan K Shiue L Hayes JD Centers R Fitzwater S Loewen R Edmondson LR Bryant J Smith M Rommelfanger C Welch V Clark TA Sugnet CW Howe KJ Mandel-Gutfreund Y Ares M Jr. Detection and measurement of alternative splicing using splicing-sensitive microarrays Methods 2005 37 4 345-359 10.1016/j.ymeth.2005.09.007 16314264
21. Zacharias DA Garamszegi N Strehler EE Characterization of persistent artifacts resulting from RT-PCR of alternatively spliced mRNAs Biotechniques 1994 17 4 652-655 7833018
22. Venables JP Burn J EASI - enrichment of alternatively spliced isoforms Nucleic Acids Res 2006 34 15 e103 1616956 16951290 10.1093/nar/gkl592
23. Feral CC Nishiya N Fenczik CA Stuhlmann H Slepak M Ginsberg MH CD98hc (SLC3A2) mediates integrin signaling Proc Natl Acad Sci U S A 2005 102 2 355-360 544283 15625115 10.1073/pnas.0404852102
24. Henderson NC Collis EA Mackinnon AC Simpson KJ Haslett C Zent R Ginsberg M Sethi T CD98hc (SLC3A2) interaction with beta 1 integrins is required for transformation J Biol Chem 2004 279 52 54731-54741 10.1074/ jbc.M408700200 15485886
25. Fiegen D Haeusler LC Blumenstein L Herbrand U Dvorsky R Vetter IR Ahmadian MR Alternative splicing of Rac1 generates Rac1b, a self-activating GTPase J Biol Chem 2004 279 6 4743-4749 10.1074/ jbc.M310281200 14625275
26. Cheung N Wong MP Yuen ST Leung SY Chung LP Tissue-specific expression pattern of vascular endothelial growth factor isoforms in the malignant transformation of lung and colon Hum Pathol 1998 29 9 910-914 10.1016/ S0046-8177(98)90195-2 9744306
27. Collesi C Santoro MM Gaudino G Comoglio PM A splicing variant of the RON transcript induces constitutive tyrosine kinase activity and an invasive phenotype Mol Cell Biol 1996 16 10 5518-5526 231551 8816464
28. Matsushita K Tomonaga T Shimada H Shioya A Higashi M Matsubara H Harigaya K Nomura F Libutti D Levens D Ochiai T An essential role of alternative splicing of c-myc suppressor FUSE-binding protein-interacting repressor in carcinogenesis Cancer Res 2006 66 3 1409-1417 10.1158/0008-5472.CAN-04-4459 16452196
29. Clarke AS Lotz MM Mercurio AM A novel structural variant of the human beta 4 integrin cDNA Cell Adhes Commun 1994 2 1 1-6 7982032
30. McCullough RM Cantor CR Ding C High-throughput alternative splicing quantification by primer extension and matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry Nucleic Acids Res 2005 33 11 e99 1153715 15967806 10.1093/nar/gni098
31. Wang Z Lo HS Yang H Gere S Hu Y Buetow KH Lee MP Computational analysis and experimental validation of tumor-associated alternative RNA splicing in human cancer Cancer Res 2003 63 3 655-657 12566310
32. Kirschbaum-Slager N Parmigiani RB Camargo AA de Souza SJ Identification of human exons overexpressed in tumors through the use of genome and expressed sequence data Physiol Genomics 2005 21 3 423-432 10.1152/ physiolgenomics.00237.2004 15784694
33. Hui L Zhang X Wu X Lin Z Wang Q Li Y Hu G Identification of alternatively spliced mRNA variants related to cancers by genome-wide ESTs alignment Oncogene 2004 23 17 3013-3023 10.1038/sj.onc.1207362 15048092
34. Herynk MH Tsan R Radinsky R Gallick GE Activation of c-Met in colorectal carcinoma cells leads to constitutive association of tyrosine-phosphorylated beta-catenin Clin Exp Metastasis 2003 20 4 291-300 10.1023/A:1024024218529 12856716
35. Jaffe AB Hall A Rho GTPases in transformation and metastasis Adv Cancer Res 2002 84 57-80 11883532
36. Raval GN Bharadwaj S Levine EA Willingham MC Geary RL Kute T Prasad GL Loss of expression of tropomyosin-1, a novel class II tumor suppressor that induces anoikis, in primary breast tumors Oncogene 2003 22 40 6194-6203 10.1038/sj.onc.1206719 13679858
37. Leonardi CL Warren RH Rubin RW Lack of tropomyosin correlates with the absence of stress fibers in transformed rat kidney cells Biochim Biophys Acta 1982 720 2 154-162 10.1016/0167-4889(82)90007-6 6282338
38. Hendricks M Weintraub H Multiple tropomyosin polypeptides in chicken embryo fibroblasts: Differential repression of transcription by Rous sarcoma virus transformation Mol Cell Biol 1984 4 9 1823-1833 368992 6208481
39. Varga AE Stourman NV Zheng Q Safina AF Quan L Li X Sossey-Alaoui K Bakin AV Silencing of the Tropomyosin-1 gene by DNA methylation alters tumor suppressor function of TGF-beta Oncogene 2005 24 32 5043-5052 10.1038/ sj.onc.1208688 15897890
40. Lin JL Geng X Bhattacharya SD Yu JR Reiter RS Sastri B Glazier KD Mirza ZK Wang KK Amenta PS Das KM Lin JJ Isolation and sequencing of a novel tropomyosin isoform preferentially associated with colon cancer Gastroenterology 2002 123 1 152-162 10.1053/gast.2002.34154 12105844
41. Otey CA Carpen O Alpha-actinin revisited: A fresh look at an old player Cell Motil Cytoskeleton 2004 58 2 104-111 10.1002/cm.20007 15083532
42. Honda K Yamada T Seike M Hayashida Y Idogawa M Kondo T Ino Y Hirohashi S Alternative splice variant of actinin-4 in small cell lung cancer Oncogene 2004 23 30 5257-5262 10.1038/sj.onc.1207652 15122314
43. Bois PR Borgon RA Vonrhein C Izard T Structural dynamics of alpha-actinin-vinculin interactions Mol Cell Biol 2005 25 14 6112-6122 1168820 15988023 10.1128/MCB.25.14.6112-6122.2005
44. Li Y Lin JL Reiter RS Daniels K Soll DR Lin JJ Caldesmon mutant defective in Ca(2+)-calmodulin binding interferes with assembly of stress fibers and affects cell morphology, growth and motility J Cell Sci 2004 117 Pt 16 3593-3604 10.1242/jcs.01216 15226374
45. Cuomo ME Knebel A Platt G Morrice N Cohen P Mittnacht S Regulation of microfilament organization by Kaposi sarcoma-associated herpes virus-cyclin.CDK6 phosphorylation of caldesmon J Biol Chem 2005 280 43 35844-35858 10.1074/jbc.M503877200 16115893
46. McManus MJ Lingle WL Salisbury JL Maihle NJ A transformation-associated complex involving tyrosine kinase signal adapter proteins and caldesmon links v-erbB signaling to actin stress fiber disassembly Proc Natl Acad Sci U S A 1997 94 21 11351-11356 23463 9326613 10.1073/pnas.94.21.11351
47. Zhang LH Tian B Diao LR Xiong YY Tian SF Zhang BH Li WM Ren H Li Y Ji JF Dominant expression of 85-kDa form of cortactin in colorectal cancer J Cancer Res Clin Oncol 2006 132 2 113-120 10.1007/s00432-005-0046-8 16261345
48. Chuma M Sakamoto M Yasuda J Fujii G Nakanishi K Tsuchiya A Ohta T Asaka M Hirohashi S Overexpression of cortactin is involved in motility and metastasis of hepatocellular carcinoma J Hepatol 2004 41 4 629-636 10.1016/j.jhep.2004.06.018 15464244
49. van Rossum AG de Graaf JH Schuuring-Scholtes E Kluin PM Fan YX Zhan X Moolenaar WH Schuuring E Alternative splicing of the actin binding domain of human cortactin affects cell migration J Biol Chem 2003 278 46 45672-45679 10.1074/jbc.M306688200 12952985
50. Clark EA Golub TR Lander ES Hynes RO Genomic analysis of metastasis reveals an essential role for RhoC Nature 2000 406 6795 532-535 10.1038/ 35020106 10952316
51. Astrof S Crowley D George EL Fukuda T Sekiguchi K Hanahan D Hynes RO Direct test of potential roles of EIIIA and EIIIB alternatively spliced segments of fibronectin in physiological and tumor angiogenesis Mol Cell Biol 2004 24 19 8662-8670 516752 15367684 10.1128/ MCB.24.19.8662-8670.2004
52. Mercurio AM Rabinovitz I Towards a mechanistic understanding of tumor invasion--lessons from the alpha6beta 4 integrin Semin Cancer Biol 2001 11 2 129-141 10.1006/scbi.2000.0364 11322832
53. Mercurio AM Bachelder RE Chung J O'Connor KL Rabinovitz I Shaw LM Tani T Integrin laminin receptors and breast carcinoma progression J Mammary Gland Biol Neoplasia 2001 6 3 299-309 10.1023/A:1011323608064 11547899
54. Hara K Kudoh H Enomoto T Hashimoto Y Masuko T Malignant transformation of NIH3T3 cells by overexpression of early lymphocyte activation antigen CD98 Biochem Biophys Res Commun 1999 262 3 720-725 10.1006/ bbrc.1999.1051 10471392
55. Ule J Ule A Spencer J Williams A Hu JS Cline M Wang H Clark T Fraser C Ruggiu M Zeeberg BR Kane D Weinstein JN Blume J Darnell RB Nova regulates brain-specific splicing to shape the synapse Nat Genet 2005 37 8 844-852 10.1038/ng1610 16041372
56. Woolard J Wang WY Bevan HS Qiu Y Morbidelli L Pritchard-Jones RO Cui TG Sugiono M Waine E Perrin R Foster R Digby-Bell J Shields JD Whittles CE Mushens RE Gillatt DA Ziche M Harper SJ Bates DO VEGF165b, an inhibitory vascular endothelial growth factor splice variant: Mechanism of action, in vivo effect on angiogenesis and endogenous protein expression Cancer Res 2004 64 21 7822-7835 10.1158/0008-5472.CAN-04-0934 15520188
57. Okumura M Kondo S Ogata M Kanemoto S Murakami T Yanagida K Saito A Imaizumi K Candidates for tumor-specific alternative splicing Biochem Biophys Res Commun 2005 334 1 23-29 10.1016/j.bbrc.2005.06.057 16018876
58. Xu Q Lee C Discovery of novel splice forms and functional analysis of cancer-specific alternative splicing in human expressed sequences Nucleic Acids Res 2003 31 19 5635-5643 206480 14500827 10.1093/nar/gkg786
59. Roy M Xu Q Lee C Evidence that public database records for many cancer-associated genes reflect a splice form found in tumors and lack normal splice forms Nucleic Acids Res 2005 33 16 5026-5033 1201329 16147986 10.1093/nar/gki792
60. Affymetrix_Inc. HuEx-1_0-st-v2-colon-cancer-data-set http://www.affymetrix.com/support/technical/sample_data/ exon_array_data.affx
61. Affymetrix_Inc. Whole Transcript Sense Target Labeling Assay http://www.affymetrix.com/support/downloads/manuals
62. UCSC_Genome_Browser UCSC Genome Browser http://www.genome.ucsc.edu
63. Affymetrix_Inc. HuEx-1_0-st-v2 Transcript Cluster ID Mappings to HG-U133 Plus 2.0 http://www.affymetrix.com/support/technical/ byproduct.affx?product=huexon-st