Influence of DNA copy number and mRNA levels on the expression of breast cancer related proteins

Molecular Oncology

Volumn 7, Issue 3, 2013, Pages 704-718

  Myhre, Simen ^a,b   Lingjærde, Ole Christian ^a,d   Hennessy, Bryan T ^e,f   Aure, Miriam R ^a,c   Carey, Mark S ^f   Alsner, Jan ^g   Tramm, Trine ^g   Overgaard, Jens ^g   Mills, Gordon B ^f   Børresen Dale, Anne Lise ^a,c   Sørlie, Therese ^a  

^a OSLO UNIVERSITY HOSPITAL   (Norway)

^b Atlantis Medical University College   (Norway)

^c UNIVERSITY OF OSLO   (Norway)

^d UNIVERSITY OF OSLO   (Norway)

^e ROYAL COLLEGE OF SURGEONS IN IRELAND   (Ireland)

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

^g AARHUS UNIVERSITY HOSPITAL   (Denmark)

Author keywords

Breast cancer; CASP7; Correlation; Cyclin B1; DNA copy number; Gene expression; Molecular subtypes; Protein expression; RPPA

Indexed keywords

BETA CATENIN; BRCA1 PROTEIN; CASPASE 7; CAVEOLIN 1; COLLAGEN TYPE 6; CYCLIN B1; CYCLIN D1; CYCLIN DEPENDENT KINASE 4; CYCLIN E; DNA; EPIDERMAL GROWTH FACTOR RECEPTOR 2; MAMMALIAN TARGET OF RAPAMYCIN; MESSENGER RNA; MICRORNA 29; MITOGEN ACTIVATED PROTEIN KINASE 1; MITOGEN ACTIVATED PROTEIN KINASE KINASE 1; PHOSPHATIDYLINOSITOL 3 KINASE; PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE 1; PROTEIN BCL 2; PROTEIN C JUN; PROTEIN HYDROLYSATE; PROTEIN KINASE B; PROTEIN P21; PROTEIN P53; PROTEIN S6; STAT3 PROTEIN; STATHMIN; TUBERIN; TUMOR PROTEIN; UVOMORULIN;

ARTICLE; BASAL LIKE BREAST CANCER; BREAST CANCER; CANCER SURVIVAL; CONTROLLED STUDY; FEMALE; GENE DOSAGE; GENE EXPRESSION; GENE PROBE; GENETIC REGULATION; HUMAN; HUMAN TISSUE; MICROARRAY ANALYSIS; OVERALL SURVIVAL; PRIORITY JOURNAL; PROTEIN EXPRESSION; REPRESSOR GENE; SIGNAL TRANSDUCTION;

EID: 84878111444     PISSN: 15747891     EISSN: 18780261     Source Type: Journal    
DOI: 10.1016/j.molonc.2013.02.018     Document Type: Article

References (59)

1. Aaltonen K., Amini R.M., Heikkila P., Aittomaki K., Tamminen A., Nevanlinna H., Blomqvist C. High cyclin B1 expression is associated with poor survival in breast cancer. Br. J. Cancer 2009, 100:1055-1060.
2. Agarwal R., Gonzalez-Angulo A.M., Myhre S., Carey M., Lee J.S., Overgaard J., et al. Integrative analysis of cyclin protein levels identifies cyclin b1 as a classifier and predictor of outcomes in breast cancer. Clin. Cancer Res. 2009, 15:3654-3662.
3. Androic I., Kramer A., Yan R., Rodel F., Gatje R., Kaufmann M., et al. Targeting cyclin B1 inhibits proliferation and sensitizes breast cancer cells to taxol. BMC Cancer 2008, 8:391.
4. Baek D., Villen J., Shin C., Camargo F.D., Gygi S.P., Bartel D.P. The impact of microRNAs on protein output. Nature 2008, 455:64-71.
5. Barbareschi M., Pelosio P., Caffo O., Buttitta F., Pellegrini S., Barbazza R., et al. Cyclin-D1-gene amplification and expression in breast carcinoma: relation with clinicopathologic characteristics and with retinoblastoma gene product, p53 and p21WAF1 immunohistochemical expression. Int. J. Cancer 1997, 74:171-174.
6. Bartel D.P. MicroRNAs: target recognition and regulatory functions. Cell 2009, 136:215-233.
7. Baumbusch L.O., Aaroe J., Johansen F.E., Hicks J., Sun H., Bruhn L., et al. Comparison of the Agilent, ROMA/NimbleGen and Illumina platforms for classification of copy number alterations in human breast tumors. BMC Genomics 2008, 9:379.
8. Castaneda C.A., Cortes-Funes H., Gomez H.L., Ciruelos E.M. The phosphatidyl inositol 3-kinase/AKT signaling pathway in breast cancer. Cancer Metastasis Rev. 2010, 29:751-759.
9. Charboneau L., Tory H., Chen T., Winters M., Petricoin E.F., Liotta L.A., Paweletz C.P. Utility of reverse phase protein arrays: applications to signalling pathways and human body arrays. Brief. Funct. Genom. Proteom. 2002, 1:305-315.
10. Cheng K.W., Lahad J.P., Kuo W.L., Lapuk A., Yamada K., Auersperg N., et al. The RAB25 small GTPase determines aggressiveness of ovarian and breast cancers. Nat. Med. 2004, 10:1251-1256.
11. D'Amours D., Sallmann F.R., Dixit V.M., Poirier G.G. Gain-of-function of poly(ADP-ribose) polymerase-1 upon cleavage by apoptotic proteases: implications for apoptosis. J.Cell. Sci. 2001, 114:3771-3778.
12. deConinck E.C., McPherson L.A., Weigel R.J. Transcriptional regulation of estrogen receptor in breast carcinomas. Mol. Cell. Biol. 1995, 15:2191-2196.
13. Tamoxifen for early breast cancer: an overview of the randomised trials. Lancet 1998, 351:1451-1467. Early Breast Cancer Trialists' Collaborative Group.
14. Enerly E., Steinfeld I., Kleivi K., Leivonen S.K., Aure M.R., Russnes H.G., et al. miRNA-mRNA integrated analysis reveals roles for miRNAs in primary breast tumors. PLoS One 2011, 6:e16915.
15. Espina V., Mehta A.I., Winters M.E., Calvert V., Wulfkuhle J., Petricoin E.F., Liotta L.A. Protein microarrays: molecular profiling technologies for clinical specimens. Proteomics 2003, 3:2091-2100.
16. Fisher E.R., Redmond C.K., Liu H., Rockette H., Fisher B. Correlation of estrogen receptor and pathologic characteristics of invasive breast cancer. Cancer 1980, 45:349-353.
17. Fisher B., Costantino J., Redmond C., Poisson R., Bowman D., Couture J., et al. A randomized clinical trial evaluating tamoxifen in the treatment of patients with node-negative breast cancer who have estrogen-receptor-positive tumors. N.Engl. J. Med. 1989, 320:479-484.
18. Gafni J., Cong X., Chen S.F., Gibson B.W., Ellerby L.M. Calpain-1 cleaves and activates caspase-7. J.Biol. Chem. 2009, 284:25441-25449.
19. Geyer C.E., Forster J., Lindquist D., Chan S., Romieu C.G., Pienkowski T., et al. Lapatinib plus capecitabine for HER2-positive advanced breast cancer. N.Engl. J. Med. 2006, 355:2733-2743.
20. Gry M., Rimini R., Stromberg S., Asplund A., Ponten F., Uhlen M., Nilsson P. Correlations between RNA and protein expression profiles in 23 human cell lines. BMC Genomics 2009, 10:365.
21. Guo H., Ingolia N.T., Weissman J.S., Bartel D.P. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 2010, 466:835-840.
22. Haakensen V.D., Biong M., Lingjaerde O.C., Holmen M.M., Frantzen J.O., Chen Y., et al. Expression levels of uridine 5'-diphospho-glucuronosyltransferase genes in breast tissue from healthy women are associated with mammographic density. Breast Cancer Res. 2010, 12:R65.
23. Hennessy B.T., Lu Y., Gonzalez-Angulo A.M., Carey M.S., Myhre S., Ju Z., et al. A technical assessment of the utility of reverse phase protein arrays for the study of the functional proteome in non-microdissected human breast cancers. Clin. Proteomics 2010, 6:129-151.
24. Horlings H.M., Bergamaschi A., Nordgard S.H., Kim Y.H., Han W., Noh D.Y., et al. ESR1 gene amplification in breast cancer: a common phenomenon?. Nat. Genet. 2008, 40:807-808.
25. Hui R., Cornish A.L., McClelland R.A., Robertson J.F., Blamey R.W., Musgrove E.A., et al. Cyclin D1 and estrogen receptor messenger RNA levels are positively correlated in primary breast cancer. Clin. Cancer Res. 1996, 2:923-928.
26. Hyman E., Kauraniemi P., Hautaniemi S., Wolf M., Mousses S., Rozenblum E., et al. Impact of DNA amplification on gene expression patterns in breast cancer. Cancer Res. 2002, 62:6240-6245.
27. Jaenisch R., Bird A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat. Genet. 2003, 33(Suppl.):245-254.
28. Kirchhoff M., Bisgaard A.M., Stoeva R., Dimitrov B., Gillessen-Kaesbach G., Fryns J.P., et al. Phenotype and 244k array-CGH characterization of chromosome 13q deletions: an update of the phenotypic map of 13q21.1-qter. Am. J. Med. Genet. A 2009, 149A:894-905.
29. Kyndi M., Overgaard M., Nielsen H.M., Sorensen F.B., Knudsen H., Overgaard J. High local recurrence risk is not associated with large survival reduction after postmastectomy radiotherapy in high-risk breast cancer: a subgroup analysis of DBCG 82 b&c. Radiother. Oncol. 2009, 90:74-79.
30. Langerod A., Zhao H., Borgan O., Nesland J.M., Bukholm I.R., Ikdahl T., et al. TP53 mutation status and gene expression profiles are powerful prognostic markers of breast cancer. Breast Cancer Res. 2007, 9:R30.
31. Lu P., Vogel C., Wang R., Yao X., Marcotte E.M. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat. Biotechnol. 2007, 25:117-124.
32. Maurer M., Su T., Saal L.H., Koujak S., Hopkins B.D., Barkley C.R., et al. 3-Phosphoinositide-dependent kinase 1 potentiates upstream lesions on the phosphatidylinositol 3-kinase pathway in breast carcinoma. Cancer Res. 2009, 69:6299-6306.
33. Megha T., Lazzi S., Ferrari F., Vatti R., Howard C.M., Cevenini G., et al. Expression of the G2-M checkpoint regulators cyclin B1 and P34CDC2 in breast cancer: a correlation with cellular kinetics. Anticancer Res. 1999, 19:163-169.
34. Muggerud A.A., Hallett M., Johnsen H., Kleivi K., Zhou W., Tahmasebpoor S., et al. Molecular diversity in ductal carcinoma in situ (DCIS) and early invasive breast cancer. Mol. Oncol. 2010, 4:357-368.
35. Murphy C.G., Fornier M. HER2-positive breast cancer: beyond trastuzumab. Oncol. (Williston Park) 2010, 24:410-415.
36. Myhre S., Mohammed H., Tramm T., Alsner J., Finak G., Park M., et al. In silico ascription of gene expression differences to tumor and stromal cells in a model to study impact on breast cancer outcome. PLoS One 2010, 5:e14002.
37. Naume B., Zhao X., Synnestvedt M., Borgen E., Russnes H.G., Lingjaerde O.C., et al. Presence of bone marrow micrometastasis is associated with different recurrence risk within molecular subtypes of breast cancer. Mol. Oncol. 2007, 1:160-171.
38. Nielsen H.M., Overgaard M., Grau C., Jensen A.R., Overgaard J. Study of failure pattern among high-risk breast cancer patients with or without postmastectomy radiotherapy in addition to adjuvant systemic therapy: long-term results from the Danish Breast Cancer Cooperative Group DBCG 82 b and c randomized studies. J.Clin. Oncol. 2006, 24:2268-2275.
39. Nimeus-Malmstrom E., Koliadi A., Ahlin C., Holmqvist M., Holmberg L., Amini R.M., et al. Cyclin B1 is a prognostic proliferation marker with a high reproducibility in a population-based lymph node negative breast cancer cohort. Int. J. Cancer 2010, 127:961-967.
40. Pass H.I., Goparaju C., Ivanov S., Donington J., Carbone M., Hoshen M., et al. hsa-miR-29c is linked to the prognosis of malignant pleural mesothelioma. Cancer Res. 2010, 70:1916-1924.
41. Pauletti G., Godolphin W., Press M.F., Slamon D.J. Detection and quantitation of HER-2/neu gene amplification in human breast cancer archival material using fluorescence in situ hybridization. Oncogene 1996, 13:63-72.
42. Pollack J.R., Sorlie T., Perou C.M., Rees C.A., Jeffrey S.S., Lonning P.E., et al. Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc. Natl. Acad. Sci. U. S. A. 2002, 99:12963-12968.
43. Reis-Filho J.S., Savage K., Lambros M.B., James M., Steele D., Jones R.L., Dowsett M. Cyclin D1 protein overexpression and CCND1 amplification in breast carcinomas: an immunohistochemical and chromogenic in situ hybridisation analysis. Mod. Pathol. 2006, 19:999-1009.
44. Rojo F., Najera L., Lirola J., Jimenez J., Guzman M., Sabadell M.D., et al. 4E-binding protein 1, a cell signaling hallmark in breast cancer that correlates with pathologic grade and prognosis. Clin. Cancer Res. 2007, 13:81-89.
45. Roy P.G., Pratt N., Purdie C.A., Baker L., Ashfield A., Quinlan P., Thompson A.M. High CCND1 amplification identifies a group of poor prognosis women with estrogen receptor positive breast cancer. Int. J. Cancer 2010, 127:355-360.
46. Russnes H.G., Vollan H.K., Lingjaerde O.C., Krasnitz A., Lundin P., Naume B., et al. Genomic architecture characterizes tumor progression paths and fate in breast cancer patients. Sci. Transl. Med. 2010, 2:38ra47.
47. Shi L., Reid L.H., Jones W.D., Shippy R., Warrington J.A., Baker S.C., et al. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat. Biotechnol. 2006, 24:1151-1161.
48. Sorlie T., Perou C.M., Tibshirani R., Aas T., Geisler S., Johnsen H., et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc. Natl. Acad. Sci. U. S. A. 2001, 98:10869-10874.
49. Sorlie T., Tibshirani R., Parker J., Hastie T., Marron J.S., Nobel A., et al. Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc. Natl. Acad. Sci. U. S. A. 2003, 100:8418-8423.
50. Spearman C. The proof and measurement of association between two things. Int. J. Epidemiol. 2010, 39:1137-1150.
51. Stingele S., Stoehr G., Peplowska K., Cox J., Mann M., Storchova Z. Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells. Mol. Syst. Biol. 2012, 8:608.
52. Stranger B.E., Forrest M.S., Dunning M., Ingle C.E., Beazley C., Thorne N., et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 2007, 315:848-853.
53. Tibes R., Qiu Y., Lu Y., Hennessy B., Andreeff M., Mills G.B., Kornblau S.M. Reverse phase protein array: validation of a novel proteomic technology and utility for analysis of primary leukemia specimens and hematopoietic stem cells. Mol. Cancer Ther. 2006, 5:2512-2521.
54. 2012a. http://tcga-data.nci.nih.gov/tcga/.
55. 2012b. http://www.targetscan.org/.
56. Varley J.M., Swallow J.E., Brammar W.J., Whittaker J.L., Walker R.A. Alterations to either c-erbB-2(neu) or c-myc proto-oncogenes in breast carcinomas correlate with poor short-term prognosis. Oncogene 1987, 1:423-430.
57. Wiedswang G., Borgen E., Karesen R., Kvalheim G., Nesland J.M., Qvist H., et al. Detection of isolated tumor cells in bone marrow is an independent prognostic factor in breast cancer. J.Clin. Oncol. 2003, 21:3469-3478.
58. Wilusz J.E., Sunwoo H., Spector D.L. Long noncoding RNAs: functional surprises from the RNA world. Genes Dev. 2009, 23:1494-1504.
59. Zhao Y., Jensen O.N. Modification-specific proteomics: strategies for characterization of post-translational modifications using enrichment techniques. Proteomics 2009, 9:4632-4641.