Poly (A)+ transcriptome assessment of ERBB2-induced alterations in breast cell lines

PLoS ONE

Volumn 6, Issue 6, 2011, Pages

  Carraro, Dirce Maria ^a   Ferreira, Elisa Napolitano ^a,b   de Campos Molina, Gustavo ^a   Puga, Renato David ^a   Abrantes, Eduardo Fernandes ^a   Trapé, Adriana Priscila ^b   Ekhardt, Bedrich L ^c   Nunes, Diana Noronha ^a,c   Brentani, Maria Mitzi ^b   Arap, Wadih ^c   Pasqualini, Renata ^c   Brentani, Helena ^a,b   Dias Neto, Emmanuel ^a,b,c   Brentani, Ricardo Renzo ^a  

^a A C CAMARGO CANCER CENTER   (Brazil)

^b UNIVERSITY OF SÃO PAULO   (Brazil)

^c UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; EPIDERMAL GROWTH FACTOR RECEPTOR 2; POLYADENYLIC ACID; POLYADENYLIC ACID TRANSCRIPTOME; TITANIUM; TRANSCRIPTOME; UNCLASSIFIED DRUG; ERBB2 PROTEIN, HUMAN;

ALTERNATIVE RNA SPLICING; ARTICLE; ATP5L ONCOGENE; BIOINFORMATICS; BREAST CELL; BREAST TUMOR; CANCER CELL CULTURE; CELL POPULATION; CONTROLLED STUDY; DNA LIBRARY; ERBB2 ONCOGENE; EXON; GALNT3 ONCOGENE; GENE CONSTRUCT; GENE EXPRESSION REGULATION; GENE FUSION; GENE OVEREXPRESSION; GENE SEQUENCE; GENETIC VARIABILITY; HUMAN; HUMAN CELL; HUMAN TISSUE; LOX ONCOGENE; MME ONCOGENE; ONCOGENE; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; RNA SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM; BIOLOGY; BREAST; CELL LINE; CYTOLOGY; FEMALE; GENE EXPRESSION PROFILING; GENE LIBRARY; GENETICS; HUMAN GENOME; METABOLISM; NUCLEOTIDE SEQUENCE; REPRODUCIBILITY;

ALTERNATIVE SPLICING; BASE SEQUENCE; BREAST; CELL LINE; COMPUTATIONAL BIOLOGY; FEMALE; GENE EXPRESSION PROFILING; GENE FUSION; GENE LIBRARY; GENOME, HUMAN; HUMANS; POLY A; POLYMORPHISM, SINGLE NUCLEOTIDE; RECEPTOR, ERBB-2; REPRODUCIBILITY OF RESULTS;

EID: 79959423230     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0021022     Document Type: Article

References (52)

1. Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, et al. (2002) Gene expression proffiling predicts clinical outcome of breast cancer. Nature 415: 530-535.
2. Brentani RR, Carraro DM, Verjovski-Almeida S, Reis EM, Neves EJ, et al. (2005) Gene expression arrays in cancer research: methods and applications. Crit Rev Oncol Hematol 54: 95-105.
3. Folgueira MA, Carraro DM, Brentani H, Patrão DF, Barbosa EM, et al. (2005) Gene expression profile associated with response to doxorubicin-based therapy in breast cancer. Clin Cancer Res 11: 7434-7443.
4. Castro NP, Osório CA, Torres C, Bastos EP, Mourão-Neto M, et al. (2008) Evidence that molecular changes in cells occur before morphological alterations during the progression of breast ductal carcinoma. Breast Cancer Res 10: R87 doi:10.1186/bcr2157.
5. Rozenchan PB, Carraro DM, Brentani H, de Carvalho Mota LD, Bastos EP, et al. (2009) Reciprocal changes in gene expression profiles of cocultured breast epithelial cells and primary fibroblasts. I J Cancer 125: 2767-2777.
6. Koike FMA, Brentani H, Carraro DM, De Camargo BFM, Hirata KML, et al. (2009) Gene expression profile of residual breast cancer after doxorubicin and cyclophosphamide neoadjuvant chemotherapy. Oncol Rep 4: 805-813.
7. Perou CM, Sørlie T, Eisen MB, van de Rijn M, Jeffrey SS, et al. (2000) Molecular portraits of human breast tumours. Nature 406: 747-752.
8. Sørlie T, Perou CM, Tibshirani R, Aas T, Geisler S, et al. (2001) Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci U S A 98: 10869-10874.
9. Ross JS, Fletcher JA, (1998) The HER-2/neu Oncogene in Breast Cancer: Prognostic Factor, Predictive Factor, and Target for Therapy. Oncologist 3: 237-252.
10. Campbell CI, Petrik JJ, Moorehead RA, (2010) ErbB2 enhances mammary tumorigenesis, oncogene-independent recurrence and metastasis in a model of IGF-IR-mediated mammary tumorigenesis. Molecular Cancer 9: 235-271.
11. Slamon DJ, Godolphin W, Jones LA, Holt JA, Wong SG, et al. (1989) Studies of the HER-2/neu proto-oncogene in human breast and ovarian cancer. Science 244: 707-712.
12. Slamon DJ, Clark GM, Wong SG, Levin WJ, Ullrich A, et al. (1987) Human breast cancer: correlation of relapse and survival with amplification of the HER-2/neu oncogene. Science 235: 177-182.
13. Purdie CA, Baker L, Ashfield A, Chatterjee S, Jordan LB, et al. (2010) Increased mortality in HER2 positive, oestrogen receptor positiveinvasive breast cancer: a population-based study. B J Cancer 103: 475-481.
14. Ménard S, Pupa SM, Campiglio M, Tagliabue E, (2003) Biologic and therapeutic role of HER2 in cancer. Oncogene 42: 6570-6578.
15. Vogel CL, Cobleigh MA, Tripathy D, Gutheil JC, Harris LN, et al. (2002) Efficacy and Safety of Trastuzumab as a Single Agent in First-Line Treatment of HER2-Overexpressing Metastatic Breast Cancer. Journal of Clinical Oncology 20: 719-726.
16. Stamps AC, Davies SC, Burman J, O'Hare MJ, (1994) Analysis of proviral integration in human mammary epithelial cell lines immortalized by retroviral infection with a temperature-sensitive SV40 T-antigen construct. I J Cancer 57: 865-874.
17. Harris RA, Eichholtz TJ, Hiles ID, Page MJ, O'Hare MJ, (1999) New model of ErbB-2 over-expression in human mammary luminal epithelial cells. Int J Cancer 80: 477-484.
18. Dos Santos ML, Palanch CG, Salaorni S, Da Silva WA Jr, Nagai MA, (2006) Transcriptome characterization of human mammary cell lines expressing different levels of ERBB2 by serial analysis of gene expression. Int J Oncol 28: 1441-1461.
19. Dos Santos ML, Gimenes KP, Silva WA Jr, Nagai MA, (2009) Transcriptome changes induced by docetaxel in human mammary cell lines expressing different levels of ERBB2. Int J Mol Med 23: 733-743.
20. Graveley BR, (2001) Alternative splicing: increasing diversity in the proteomic world. Trends Genet 17: 100-107.
21. Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, et al. (2006) GENCODE: producing a reference annotation for ENCODE. Genome Biol 7 (Suppl 1): S4.1-9.
22. Torres TT, Metta M, Ottenwälder B, Schlötterer C, (2008) Gene expression profiling by massively parallel sequencing. Genome Res 18: 172-177.
23. Maher CA, Palanisamy N, Brenner JC, Cao X, Kalyana-Sundaram S, et al. (2009) Chimeric transcript discovery by paired-end transcriptome sequencing. Proc Nat Acad Sci U S A 106: 12353-12358.
24. Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, et al. (2009) mRNA-Seq whole-transcriptome analysis of a single cell. Nature Methods 6: 377-382.
25. Yassour M, Kaplan T, Fraser HB, Levin JZ, Pfiffner J, et al. (2009) Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci U S A 106: 3264-3269.
26. Pleasance ED, Stephens PJ, O'Meara S, McBride DJ, Meynert A, et al. (2010) A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature 463: 184-190.
27. Dias-Neto E, Correa RG, Verjovski-Almeida S, Briones MR, Nagai MA, et al. (2000) Shotgun sequencing of the human transcriptome with ORF expressed sequence tags. Proc Natl Acad Sci U S A 97: 3491-3496.
28. Ramensky V, Bork P, Sunyaev S, (2002) Human non-synonymous SNPs: server and survey. Nucleic Acids Res 30: 3894-3900.
29. Prifti E, Zucker J, Clement K, Henegar C, (2008) FunNet: an integrative tool for exploring transcriptional interactions. Bioinformatics 24: 2636-2638.
30. Janus A, Robak T, Smolewski P, (2005) The mammalian target of the rapamycin (mTOR) kinase pathway: its role in tumourigenesis and targeted antitumour therapy. Cell Mol Biol Lett 10: 479-498.
31. Creighton CJ, (2007) A gene transcription signature of the Akt/mTOR pathway in clinical breast tumors. Oncogene 26: 4648-4655.
32. Heinonen H, Nieminen A, Saarela M, Kallioniemi A, Klefström J, et al. (2008) Deciphering downstream gene targets of PI3K/mTOR/p70S6K pathway in breast cancer. BMC Genomics 9: 348 doi:10.1186/1471-2164-9-348.
33. Akcakanat A, Zhang L, Tsavachidis S, Meric-Bernstam F, (2009) The rapamycin-regulated gene expression signature determines prognosis for breast cancer. Mol Cancer 8: 75 doi:10.1186/1476-4598-8-75.
34. Meric-Bernstam F, Gonzalez-Angulo AM, (2009) Targeting the mTOR signaling network for cancer therapy. J Clin Oncol 27: 2278-2287.
35. Maher CA, Kumar-Sinha C, Cao X, Kalyana-Sundaram S, Han B, et al. (2009) Transcriptome sequencing to detect gene fusions in cancer. Nature 458: 97-101.
36. Edgren H, Murumagi A, Kangaspeska S, Nicorici D, Hongisto V, et al. (2011) Identification of fusion genes in breast cancer by paired-end RNA-sequencing. Genome Biol 19: 12.
37. McManus CJ, Duff MO, Eipper-Mains J, Graveley BR, (2010) Global analysis of trans-splicing in Drosophila. Proc Natl Acad Sci U S A 107: 12975-12979.
38. Wang XS, Prensner JR, Chen G, Cao Q, Han B, et al. (2009) An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer. Nat Biotechnol 27: 1005-1011.
39. Gu W, Zhang F, Lupski JR, (2008) Mechanisms for human genomic rearrangements. Pathogenetics 1: 4 doi:10.1186/1755-8417-1-4.
40. Stephens PJ, McBride DJ, Lin ML, Varela I, Pleasance ED, et al. (2009) Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature 462: 1005-10.
41. Di Fiore PP, Pierce JH, Kraus MH, Segatro O, King CR, et al. (1987) Erbb-2 is a potent oncogene when overexpressed in NIHI/3T3 Cells. Science 237: 178-181.
42. Ferreira EN, Rangel MC, Galante PF, de Souza JE, Molina GC, et al. (2010) Alternative splicing enriched cDNA libraries identify breast cancer-associated transcripts. BMC Genomics 11: (Suppl 5): S4.
43. Srebrow A, Kornblihtt AR, (2006) The connection between splicing and cancer. J Cell Sci 119: 2635-2641.
44. Stingl J, Caldas C, (2007) Molecular heterogeneity of breast carcinomas and the cancer stem cell hypothesis. Nat Rev Cancer 7: 791-799.
45. Allinen M, Beroukhim R, Cai L, Brennan C, Lahti-Domenici J, et al. (2004) Molecular characterization of the tumor microenvironment in breast cancer. Cancer Cell 6: 17-32.
46. Noblesse E, Cenizo V, Bouez C, Borel A, Gleyzal C, et al. (2004) Lysyl oxidase-like and lysyl oxidase are present in the dermis and epidermis of a skin equivalent and in human skin and are associated to elastic fibers. J Invest Dermatol 122: 621-630.
47. Min C, Kirsch KH, Zhao Y, Jeay S, Palamakumbura AH, et al. (2007) The tumor suppressor activity of the lysyl oxidase propeptide reverses the invasive phenotype of Her-2/neu-driven breast cancer. Cancer Res 67: 1105-1112.
48. Watahiki A, Waki K, Hayatsu N, Shiraki T, Kondo S, et al. (2004) Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas. Nat Methods 3: 233-239.
49. Kent WJ, (2002) BLAT-the BLAST-like alignment tool. Genome Res 4: 656-664.
50. Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, et al. (2006) The UCSC Known Genes. Bioinformatics 22: 1036-1046.
51. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, et al. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29: 308-311.
52. Vêncio RZ, Brentani H, Patrão DF, Pereira CA, (2004) Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE). BMC Bioinformatics 5: 119 doi:10.1186/1471-2105-5-119.