3'UTR shortening and EGF signaling: Implications for breast cancer

Human Molecular Genetics

Volumn 24, Issue 24, 2015, Pages 6910-6920

  Akman, Hesna Begum ^a   Oyken, Merve ^a   Tuncer, Taner ^a   Can, Tolga ^a   Erson Bensan, Ayse Elif ^a  

^a MIDDLE EAST TECHNICAL UNIVERSITY   (Turkey)

Author keywords

[No Author keywords available]

Indexed keywords

CLEAVAGE STIMULATION FACTOR; CLEAVAGE STIMULATION FACTOR 2; DNA TOPOISOMERASE (ATP HYDROLYSING); DNA TOPOISOMERASE TYPE 2ALPHA; EPIDERMAL GROWTH FACTOR; IQ DOMAIN CONTAINING PROTEIN K; MESSENGER RNA; MICRORNA; PROTEIN; RIBOSOMAL PROTEIN L13; SORTING NEXIN 3; UBIQUITIN SPECIFIC PEPTIDASE 9 X LINKED; UNCLASSIFIED DRUG; YME1L1 PROTEIN; 3' UNTRANSLATED REGION; CSTF2T PROTEIN, HUMAN; RNA BINDING PROTEIN;

3' UNTRANSLATED REGION; ALTERNATIVE POLYADENYLATION; ARTICLE; CANCER PATIENT; CANCER PROGNOSIS; CANCER SURVIVAL; COMPARATIVE STUDY; COMPUTER MODEL; CONTROLLED STUDY; GENE CONTROL; GENE EXPRESSION; GENE EXPRESSION REGULATION; HUMAN; HUMAN CELL; HUMAN TISSUE; META ANALYSIS (TOPIC); PHENOTYPE; POLYADENYLATION; PRIORITY JOURNAL; RECURRENCE FREE SURVIVAL; SIGNAL TRANSDUCTION; TRIPLE NEGATIVE BREAST CANCER; UPREGULATION; WESTERN BLOTTING; DISEASE FREE SURVIVAL; FEMALE; GENETICS; METABOLISM; TUMOR CELL LINE;

3' UNTRANSLATED REGIONS; CELL LINE, TUMOR; DISEASE-FREE SURVIVAL; EPIDERMAL GROWTH FACTOR; FEMALE; HUMANS; MICRORNAS; POLYADENYLATION; RNA-BINDING PROTEINS; SIGNAL TRANSDUCTION; TRIPLE NEGATIVE BREAST NEOPLASMS;

EID: 84959200438     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddv391     Document Type: Article

References (51)

1. Moore, M.J. (2005) From birth to death: the complex lives of eukaryotic mRNAs. Science, 309, 1514-1518.
2. Derti, A., Garrett-Engele, P., Macisaac, K.D., Stevens, R.C., Sriram, S., Chen, R., Rohl, C.A., Johnson, J.M. and Babak, T. (2012) Aquantitative atlas of polyadenylation in five mammals. Genome Res., 22, 1173-1183.
3. Sandberg, R., Neilson, J.R., Sarma, A., Sharp, P.A. and Burge, C. B. (2008) Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites. Science, 320, 1643-1647.
4. Elkon, R., Ugalde, A.P. and Agami, R. (2013) Alternative cleavage and polyadenylation: extent, regulation and function. Nat. Rev. Genet., 14, 496-506.
5. Alt, F.W., Bothwell, A.L., Knapp, M., Siden, E., Mather, E., Koshland, M. and Baltimore, D. (1980) Synthesis of secreted and membrane-bound immunoglobulin mu heavy chains is directed by mRNAs that differ at their 3' ends. Cell, 20, 293-301.
6. Early, P., Rogers, J., Davis, M., Calame, K., Bond, M., Wall, R. and Hood, L. (1980) Two mRNAs can be produced from a single immunoglobulin mu gene by alternative RNA processing pathways. Cell, 20, 313-319.
7. Rogers, J., Early, P., Carter, C., Calame, K., Bond, M., Hood, L. andWall, R. (1980) Two mRNAs with different 3' ends encode membrane-bound and secreted forms of immunoglobulin mu chain. Cell, 20, 303-312.
8. Setzer, D.R., McGrogan, M., Nunberg, J.H. and Schimke, R.T. (1980) Size heterogeneity in the 3' end of dihydrofolate reductase messenger RNAs in mouse cells. Cell, 22, 361-370.
9. Ji, Z., Lee, J.Y., Pan, Z., Jiang, B. and Tian, B. (2009) Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. Proc. Natl Acad. Sci. U S A, 106, 7028-7033.
10. Hilgers, V., Perry, M.W., Hendrix, D., Stark, A., Levine, M. and Haley, B. (2011) Neural-specific elongation of 3'UTRs during Drosophila development. Proc. Natl Acad. Sci. USA, 108, 15864- 15869.
11. Li, Y., Sun, Y., Fu, Y., Li, M., Huang, G., Zhang, C., Liang, J., Huang, S., Shen, G., Yuan, S. et al. (2012) Dynamic landscape of tandem 3'UTRs during zebrafish development. Genome Res., 22, 1899-1906.
12. Takagaki, Y. and Manley, J.L. (1998) Levels of polyadenylation factor CstF-64 control IgM heavy chain mRNA accumulation and other events associated with B cell differentiation. Mol. Cell., 2, 761-771.
13. Chuvpilo, S., Zimmer, M., Kerstan, A., Glöckner, J., Avots, A., Escher, C., Fischer, C., Inashkina, I., Jankevics, E., Berberich- Siebelt, F. et al. (1999) Alternative polyadenylation events contribute to the induction of NF-ATc in effector T cells. Immunity, 10, 261-269.
14. Griffiths, C.L. and Olin, J.L. (2012) Triple negative breast cancer: a brief review of its characteristics and treatment options. J. Pharm. Pract., 25, 319-323.
15. Tusher, V.G., Tibshirani, R. and Chu, G. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. U S A, 98, 5116-5121.
16. Akman, B.H., Can, T. and Erson-Bensan, A.E. (2012) Estrogeninduced upregulation and 3'-UTR shortening of CDC6. Nucleic Acids Res., 40, 10679-10688.
17. Chavez, K.J., Garimella, S.V. and Lipkowitz, S. (2010) Triple negative breast cancer cell lines: one tool in the search for better treatment of triple negative breast cancer. Breast Dis., 32, 35-48.
18. Soule, H.D., Maloney, T.M., Wolman, S.R., Peterson, W.D., Brenz, R., McGrath, C.M., Russo, J., Pauley, R.J., Jones, R.F. and Brooks, S.C. (1990) Isolation and characterization of a spontaneously immortalized human breast epithelial cell line, MCF-10. Cancer Res., 50, 6075-6086.
19. Harvey, J.M., Clark, G.M., Osborne, C.K. and Allred, D.C. (1999) Estrogen receptor status by immunohistochemistry is superior to the ligand-binding assay for predicting response to adjuvant endocrine therapy in breast cancer. J. Clin. Oncol., 17, 1474-1481.
20. Wang, Y., Klijn, J.G., Zhang, Y., Sieuwerts, A.M., Look, M.P., Yang, F., Talantov, D., Timmermans, M., Meijer-van Gelder, M.E., Yu, J. et al. (2005) Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet, 365, 671-679.
21. Shell, S.A., Hesse, C., Morris, S.M. and Milcarek, C. (2005) Elevated levels of the 64-kDa cleavage stimulatory factor (CstF-64) in lipopolysaccharide-stimulated macrophages influence gene expression and induce alternative poly(A) site selection. J. Biol. Chem., 280, 39950-39961.
22. Deng, S., Zhou, H., Xiong, R., Lu, Y., Yan, D., Xing, T., Dong, L., Tang, E. and Yang, H. (2007) Over-expression of genes and proteins of ubiquitin specific peptidases (USPs) and proteasome subunits (PSs) in breast cancer tissue observed by the methods of RFDD-PCR and proteomics. Breast Cancer Res. Treat., 104, 21-30.
23. Taya, S., Yamamoto, T., Kanai-Azuma, M., Wood, S.A. and Kaibuchi, K. (1999) The deubiquitinating enzyme Fam interacts with and stabilizes beta-catenin. Genes Cells, 4, 757-767.
24. Murray, R.Z., Jolly, L.A. andWood, S.A. (2004) The FAM deubiquitylating enzyme localizes to multiple points of protein trafficking in epithelia, where it associates with E-cadherin and beta-catenin. Mol. Biol. Cell, 15, 1591-1599.
25. Dupont, S., Mamidi, A., Cordenonsi, M., Montagner, M., Zacchigna, L., Adorno, M., Martello, G., Stinchfield, M.J., Soligo, S., Morsut, L. et al. (2009) FAM/USP9x, a deubiquitinating enzyme essential for TGFbeta signaling, controls Smad4 monoubiquitination. Cell, 136, 123-135.
26. Al-Hakim, A.K., Zagorska, A., Chapman, L., Deak, M., Peggie, M. and Alessi, D.R. (2008) Control of AMPK-related kinases by USP9X and atypical Lys(29)/Lys(33)-linked polyubiquitin chains. Biochem J., 411, 249-260.
27. Sacco, J.J., Coulson, J.M., Clague, M.J. and Urbé, S. (2010) Emerging roles of deubiquitinases in cancer-associated pathways. IUBMB Life, 62, 140-157.
28. Akhavantabasi, S., Akman, H.B., Sapmaz, A., Keller, J., Petty, E. M. and Erson, A.E. (2010) USP32 is an active, membranebound ubiquitin protease overexpressed in breast cancers. Mamm. Genome, 21, 388-397.
29. Zhang, P., Wu, Y., Belenkaya, T.Y. and Lin, X. (2011) SNX3 controls Wingless/Wnt secretion through regulating retromerdependent recycling of Wntless. Cell Res, 21, 1677-1690.
30. Dey, N., Barwick, B.G., Moreno, C.S., Ordanic-Kodani, M., Chen, Z., Oprea-Ilies, G., Tang, W., Catzavelos, C., Kerstann, K.F., Sledge, G.W. et al. (2013) Wnt signaling in triple negative breast cancer is associated with metastasis. BMC Cancer, 13, 537.
31. Stiburek, L., Cesnekova, J., Kostkova, O., Fornuskova, D., Vinsova, K., Wenchich, L., Houstek, J. and Zeman, J. (2012) YME1L controls the accumulation of respiratory chain subunits and is required for apoptotic resistance, cristae morphogenesis, and cell proliferation. Mol. Biol. Cell, 23, 1010-1023.
32. Wan, D., Gong, Y., Qin, W., Zhang, P., Li, J., Wei, L., Zhou, X., Li, H., Qiu, X., Zhong, F. et al. (2004) Large-scale cDNA transfection screening for genes related to cancer development and progression. Proc. Natl Acad. Sci. USA, 101, 15724-15729.
33. Guo, Q.M., Malek, R.L., Kim, S., Chiao, C., He, M., Ruffy, M., Sanka, K., Lee, N.H., Dang, C.V. and Liu, E.T. (2000) Identification of c-myc responsive genes using rat cDNA microarray. Cancer Res., 60, 5922-5928.
34. Mayr, C. and Bartel, D.P. (2009) Widespread shortening of 3' UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell, 138, 673-684.
35. Barrett, T., Troup, D.B., Wilhite, S.E., Ledoux, P., Evangelista, C., Kim, I.F., Tomashevsky, M., Marshall, K.A., Phillippy, K.H., Sherman, P.M. et al. (2011) NCBI GEO: archive for functional genomics data sets-10 years on. Nucleic Acids Res., 39, D1005-D1010.
36. Rody, A., Karn, T., Liedtke, C., Pusztai, L., Ruckhaeberle, E., Hanker, L., Gaetje, R., Solbach, C., Ahr, A., Metzler, D. et al. (2011) A clinically relevant gene signature in triple negative and basal-like breast cancer. Breast Cancer Res., 13, R97.
37. Graham, K., de las Morenas, A., Tripathi, A., King, C., Kavanah, M., Mendez, J., Stone, M., Slama, J., Miller, M., Antoine, G. et al. (2010) Gene expression in histologically normal epithelium from breast cancer patients and from cancer-free prophylactic mastectomy patients shares a similar profile. Br. J. Cancer, 102, 1284-1293.
38. Tripathi, A., King, C., de la Morenas, A., Perry, V.K., Burke, B., Antoine, G.A., Hirsch, E.F., Kavanah, M., Mendez, J., Stone, M. et al. (2008) Gene expression abnormalities in histologically normal breast epithelium of breast cancer patients. Int. J. Cancer, 122, 1557-1566.
39. Liu, R., Wang, X., Chen, G.Y., Dalerba, P., Gurney, A., Hoey, T., Sherlock, G., Lewicki, J., Shedden, K. and Clarke, M.F. (2007) The prognostic role of a gene signature from tumorigenic breast-cancer cells. N. Engl. J. Med., 356, 217-226.
40. Planche, A., Bacac, M., Provero, P., Fusco, C., Delorenzi, M., Stehle, J.C. and Stamenkovic, I. (2011) Identification of prognostic molecular features in the reactive stroma of human breast and prostate cancer. PLoS One, 6, e18640.
41. Kretschmer, C., Sterner-Kock, A., Siedentopf, F., Schoenegg, W., Schlag, P.M. and Kemmner, W. (2011) Identification of early molecular markers for breast cancer. Mol. Cancer, 10, 15.
42. Richardson, A.L., Wang, Z.C., De Nicolo, A., Lu, X., Brown, M., Miron, A., Liao, X., Iglehart, J.D., Livingston, D.M. and Ganesan, S. (2006) X chromosomal abnormalities in basal-like human breast cancer. Cancer Cell, 9, 121-132.
43. Ge, X., Yamamoto, S., Tsutsumi, S., Midorikawa, Y., Ihara, S., Wang, S.M. and Aburatani, H. (2005) Interpreting expression profiles of cancers by genome-wide survey of breadth of expression in normal tissues. Genomics, 86, 127-141.
44. Zhang, H., Hu, J., Recce, M. and Tian, B. (2005) PolyA_DB: a database for mammalian mRNA polyadenylation. Nucleic Acids Res., 33, D116-D120.
45. Huang, d.W., Sherman, B.T. and Lempicki, R.A. (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc., 4, 44-57.
46. Metz, C.E. (1978) Basic principles of ROC analysis. Semin. Nucl. Med., 8, 283-298.
47. Wray, N.R., Yang, J., Goddard, M.E. and Visscher, P.M. (2010) The genetic interpretation of area under the ROC curve in genomic profiling. PLoS Genet., 6, e1000864.
48. Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., Jones, S.J. and Marra, M.A. (2009) Circos: an information aesthetic for comparative genomics. Genome Res., 19, 1639-1645.
49. Bustin, S.A., Benes, V., Garson, J.A., Hellemans, J., Huggett, J., Kubista, M., Mueller, R., Nolan, T., Pfaffl, M.W., Shipley, G.L. et al. (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin. Chem., 55, 611-622.
50. Gur-Dedeoglu, B., Konu, O., Bozkurt, B., Ergul, G., Seckin, S. and Yulug, I.G. (2009) Identification of endogenous reference genes for qRT-PCR analysis in normal matched breast tumor tissues. Oncol. Res., 17, 353-365.
51. Fleige, S., Walf, V., Huch, S., Prgomet, C., Sehm, J. and Pfaffl, M. W. (2006) Comparison of relative mRNA quantification models and the impact of RNA integrity in quantitative real-time RT-PCR. Biotechnol Lett., 28, 1601-1613.