Alternative splicing enriched cDNA libraries identify breast cancer-associated transcripts

BMC Genomics

Volumn 11, Issue SUPPL. 5, 2010, Pages

  Ferreira, Elisa N ^a,b   Rangel, Maria C R ^a   Galante, Pedro F ^c   de Souza, Jorge E ^c   Molina, Gustavo C ^a   de Souza, Sandro J ^c   Carraro, Dirce M ^a  

^a A C CAMARGO CANCER CENTER   (Brazil)

^b UNIVERSITY OF SÃO PAULO   (Brazil)

^c LUDWIG INSTITUTE FOR CANCER RESEARCH   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; EPIDERMAL GROWTH FACTOR RECEPTOR 2; ESTROGEN RECEPTOR; PROGESTERONE RECEPTOR; PROTEIN P53; OLIGONUCLEOTIDE;

ADULT; AGED; ALTERNATIVE RNA SPLICING; ARTICLE; BREAST CANCER; CANCER CELL; CANCER CELL CULTURE; CANCER GRADING; CANCER STAGING; CAPILLARY ELECTROPHORESIS; CONTROLLED STUDY; DNA LIBRARY; DNA SEQUENCE; EXON; EXPRESSED SEQUENCE TAG; FEMALE; GENE AMPLIFICATION; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENE PROBE; HETERODUPLEX ANALYSIS; HUMAN; HUMAN CELL; NUCLEOTIDE SEQUENCE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA TRANSCRIPTION; BIOLOGY; BREAST TUMOR; GENE EXPRESSION PROFILING; GENE LIBRARY; GENETIC VARIABILITY; GENETICS; METABOLISM; MOLECULAR CLONING; TUMOR CELL LINE;

ALTERNATIVE SPLICING; BREAST NEOPLASMS; CELL LINE, TUMOR; CLONING, MOLECULAR; COMPUTATIONAL BIOLOGY; FEMALE; GENE EXPRESSION PROFILING; GENE LIBRARY; GENETIC VARIATION; HUMANS; OLIGONUCLEOTIDES; RECEPTOR, ERBB-2; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA;

EID: 78650827356     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-S5-S4     Document Type: Article

References (55)

1. Gilbert W. Why genes in pieces?. Nature 1978, 271:501.
2. Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet. 2008, 40:1413-1415.
3. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. Alternative isoform regulation in human tissue transcriptomes. Nature 2008, 456:470-476. 2593745, 18978772.
4. Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis SE, Guigo R. GENCODE: producing a reference annotation for ENCODE. Genome Biol. 2006, 7:1-9.
5. Zavolan M, Van Nimwegen E. The types and prevalence of alternative splice forms. Curr. Opin. Struct. Biol. 2006, 16:362-367.
6. Black DL. Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem 2003, 72:291-336.
7. Yura K, Shionyu M, Hagino K, Hijikata A, Hirashima Y, Nakahara T, Eguchi T, Shinoda K, Yamaguchi A, Takahashi K, Itoh T, Imanishi T, Gojobori T, Mitiko. Alternative splicing in human transcriptome: functional and structural influence on proteins. Gene 2006, 380:63-71.
8. Xing Y, Lee C. Relating alternative splicing to proteome complexity and genome evolution. Adv Exp Med Biol 2007, 623:36-49.
9. Tazi J, Bakkour N, Stamm S. Alternative splicing and disease. Biochim Biophys Acta. 2009, 1792:14-26.
10. Bartel F, Taubert H, Harris LC. Alternative and aberrant splicing of MDM2 mRNA in human cancer. Cancer Cell 2002, 2:9-15.
11. 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, 23:3013-3023.
12. Venables JP, Klinck R, Koh C, Gervais-Bird J, Bramard A, Inkel L, Durand M, Couture S, Froehlich U, Lapointe E, Lucier JF, Thibault P, Rancourt C, Tremblay K, Prinos P, Chabot B, Elela SA. Cancer-associated regulation of alternative splicing. Nat Struct Mol Biol 2009, 16:670-676.
13. Venables JP, Klinck R, Bramard A, Inkel L, Dufresne-Martin G, Koh C, Gervais-Bird J, Lapointe E, Froehlich U, Durand M, Gendron D, Brosseau JP, Thibault P, Lucier JF, Tremblay K, Prinos P, Wellinger RJ, Chabot B, Rancourt C, Elela SA. Identification of alternative splicing markers for breast cancer. Cancer Res 2008, 68:9525-9531.
14. Brinkman BMN. Splice variants as cancer biomarkers. Clinical Biochemistry 2004, 37:584-594.
15. Hsu FR, Chang HY, Lin YL, Tsai YT, Peng HL, Chen YT, Cheng CY, Shih MY, Liu CH, Chen CF. AVATAR: a database for genome-wide alternative splicing event detection using large scale ESTs and mRNAs. Bioinformation 2005, 1:16-8. 1891626, 17597845.
16. Modrek B, Resch A, Grasso C, Lee C. Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res. 2001, 29:2850-2859. 55780, 11433032.
17. 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, 21:423-432.
18. Kan Z, Rouchka EC, Gish WR. Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res. 2001, 5:889-900.
19. Chen FC, Chen CJ, Ho JY, Huang TJ. Identificatyion and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat. BMC Bioinformatics 2006, 7:136. 1479377, 16536879.
20. Johnson JM, Castle J, Garrett-Engele P, Kan Z, Loerch PM, Armour CD, Santos R, Schadt EE, Stoughton R, Shoemaker DD. Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 2003, 302:2141-2144.
21. Gardina PJ, Clark TA, Shimada B, Staples MK, Yang Q, Veitch J, Schweitzer A, Awad T, Sugnet C, Dee S, Davies C, Williams A, Turpaz Y. Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array. BMC Genomics 2006, 7:325. 1769375, 17192196.
22. Cuperlovic-Culf M, Belacel N, Culf AS, Ouellette RJ. Microarray analysis of alternative splicing. OMICS 2006, 10:344-357.
23. Castle JC, Zhang C, Shah JK, Kulkarni AV, Kalsotra A, Cooper TA, Johnson JM. Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines. Nat Genet 2008, 40:1416-1425.
24. Ferreira EN, Rangel MC, Pineda PB, Vidal DO, Camargo AA, Souza SJ, Carraro DM. Heteroduplex formation and S1 digestion for mapping alternative splicing sites. Genet Mol Res 2008, 7:958-969.
25. Watahiki A, Waki K, Hayatsu N, Shiraki T, Kondo S, Nakamura M, Sasaki D, Arakawa T, Kawai J, Harbers M, Hayashizaki Y, Carninci P. Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas. Nat Methods 2004, 3:233-239.
26. Thill G, Casteli V, Pallud S, Salanoubat M, Wincker P, de la Grange P, Auboet D, Schachter V, Weissenbach J. ASEtrap: a biological method for speeding up the exploration of spliceomes. Genome Res. 2006, 16:776-786. 1479860, 16682744.
27. Matz M, Shagin D, Bogdanova E, Britanova O, Lukyanov S, Diatchenko L, Chenchik A. Amplification of cDNA ends based on template-switching effect and step-out PCR. Nucleic Acids Res. 1999, 27:1558-1560. 148354, 10037822.
28. Huang X, Madan A. CAP3: A DNA sequence assembly program. Genome Res. 1999, 9:868-877. 310812, 10508846.
29. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res. 2002, 12:996-1006. 186604, 12045153.
30. Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 1998, 9:967-974.
31. Maere S, Heymans K, Kuiper M. BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in biological networks. Bioinformatics 2005, 21:3448-3449.
32. Lewis BP, Green RE, Brenner SE. Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc Natl Acad Sci U S A 2003, 7:189-192.
33. Green RE, Lewis BP, Hillman RT, Blanchette M, Lareau LF, Garnett AT, Rio DC, Brenner SE. Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes. Bioinformatics 2003, 19:i118-21.
34. Venables JP, Koh CS, Froehlich U, Lapointe E, Couture S, Inkel L, Bramard A, Paquet ER, Watier V, Durand M, Lucier JF, Gervais-Bird J, Tremblay K, Prinos P, Klinck R, Elela SA, Chabot B. Multiple and specific mRNA processing targets for the major human hnRNP proteins. Mol Cell Biol 2008, 28:6033-6043. 2547008, 18644864.
35. Nardi A, Pomari E, Zambon D, Belvedere P, Colombo L, Dalla Valle L. Transcriptional control of human steroid sulfatase. J Steroid Biochem Mol Biol 2009,
36. Jiang Z, Cote J, Kwon JM, Goate AM, Wu JY. Aberrant splicing of tau pre-mRNA caused by intronic mutations associated with the inherited dementia frontotemporal dementia with Parkinson linked cromossome 17. Molecular and Cellular Biology 2000, 20:4036-4048.
37. Diatchenko L, Lau YF, Campbell AP, Chenchik A, Moqadam F, Huang B, Lukyanov S, Lukyanov K, Gurskaya N, Sverdlov ED, Siebert PD. Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci U S A 1996, 93:6025-6030. 39182, 8650213.
38. Albanell J, Baselga J. Unraveling resistance to trastuzumab (Herceptin): insulin-like growth factor-I receptor, a new suspect. J Natl Cancer Inst 2001, 93:1830-183.
39. Slamon DJ, Leyland-Jones B, Shak S, Fuchs H, Paton V, Bajamonde A, Fleming T, Eiermann W, Wolter J, Pegram M, Baselga J, Norton L. Use of chemotherapy plus a monoclonal antibody against HER2 for metastatic breast cancer that overexpresses HER2. N Engl J Med 2001, 344:783-92.
40. Kumar CC, Madison V. Drugs targeted against protein kinases. Expert Opin Emerg Drugs 2001, 6:303-315.
41. Slamon D, Pegram M. Rationale for trastuzumab (Herceptin) in adjuvant breast cancer trials. Semin Oncol 2001, 28:13-19.
42. Harris RA, Eichholtz TJ, Hiles ID, Page MJ, O'Hare MJ. New model of ErbB-2 over-expression in human mammary luminal epithelial cells. Int J Cancer 1999, 80:477-484.
43. Press MF, Hung G, Godolphin W, Slamon DJ. Sensitivity of HER-2/neu antibodies in archival tissue samples: potential source of error in immunohistochemical studies of oncogene expression. Cancer Res. 1994, 54:2771-2777.
44. Stamps AC, Davies SC, Burman J, O'Hare MJ. Analysis of proviral integration in human mammary epithelial cell lines immortalized by retroviral infection with a temperature-sensitive SV40 T-antigen construct. Int. J. Cancer 1994, 57:865-874.
45. Jongeneel CV, Iseli C, Stevenson BJ, Riggins GJ, Lal A, Mackay A, Harris RA, O'Hare MJ, Neville AM, Simpson AJG, Strausberg RL. Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencing. PNAS 2003, 100:4701-4705.
46. dos Santos ML, Palanch CG, Salaorni S, Da Silva WA, Nagai MA. Transcriptome characterization of human mammary cell lines expressing different levels of ERBB2 by serial analysis of gene expression. Int J Oncol. 2006, 28:1441-1461.
47. Fiori JL, Zhu TN, O'Connell MP, Hoek KS, Indig FE, Frank BP, Morris C, Kole S, Hasskamp J, Elias G, Weeraratna AT, Bernier M. Filamin A modulates kinase activation and intracellular trafficking of epidermal growth factor receptors in human melanoma cells. Endocrinology 2009, 150:2551-2560. 2689793, 19213840.
48. Mukherji M, Brill LM, Ficarro SB, Hampton GM, Schultz PG. A phosphoproteomic analysis of the ErbB2 receptor tyrosine kinase signaling pathways. Biochemistry 2006, 45:15529-15540.
49. Yi J, Beckerle MC. The human TRIP6 gene encodes a LIM domain protein and maps to chromosome 7q22, a region associated with tumorigenesis. Genomics 1998, 49:314-316.
50. Wang Y, Dooher JE, Koedood Zhao M, Gilmore TD. Characterization of mouse Trip6: a putative intracellular signaling protein. Gene 1999, 234:403-409.
51. Xu J, Lai YJ, Lin WC, Lin FT. TRIP6 enhances lysophosphatidic acid-induced cell migration by interacting with the lysophosphatidic acid 2 receptor. J Biol Chem 2004, 279:10459-10468.
52. Chastre E, Abdessamad M, Kruglov A, Bruyneel E, Bracke M, Di Gioia Y, Beckerle MC, van Roy F, Kotelevets L. TRIP6, a novel molecular partner of the MAGI-1 scaffolding molecule, promotes invasiveness. FASEB J 2009, 23:916-928.
53. Holt RA, Jones SJ. The new paradigm of flow cell sequencing. Genome Res. 2008, 18:839-846.
54. Glisin V, Crkvenjakov R, Byus C. Ribonucleic acid isolated by cesium chloride centrifugation. Biochemistry 1974, 13:2633-2637.
55. Galante PA, Vidal DO, de Souza JE, Camargo AA, de Souza SJ. Sense-antisense pairs in mammals: Functional and evolutionary considerations. Genome Biol. 2007, 8:R40. 1868933, 17371592.