Enriched transcription factor signatures in triple negative breast cancer indicates possible targeted therapies with existing drugs

Meta Gene

Volumn 4, Issue , 2015, Pages 129-141

  Willis, Scooter ^a   De, Pradip ^a   Dey, Nandini ^a   Long, Bradley ^b   Young, Brandon ^a   Sparano, Joseph A ^c   Wang, Victoria ^d   Davidson, Nancy E ^e   Leyland Jones, Brian R ^a  

^a Avera Health   (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

^c MONTEFIORE MEDICAL CENTER   (United States)

^d DANA FARBER CANCER INSTITUTE   (United States)

^e UNIVERSITY OF PITTSBURGH CANCER INSTITUTE   (United States)

Author keywords

Breast cancer; ER+; GSEA; NR6A1; Triple negative

Indexed keywords

N [4 (3 BROMOANILINO) 6 QUINAZOLINYL] 2 BUTYNAMIDE; NUCLEAR RECEPTOR NR6A1; PROTEIN C JUN; SALIRASIB; STAT1 PROTEIN; TOSEDOSTAT; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR 7; TRANSCRIPTION FACTOR E2F1; TRANSCRIPTION FACTOR HIF1A; TRANSCRIPTION FACTOR HMGA1; TRANSCRIPTION FACTOR SOX9; UNCLASSIFIED DRUG;

ARTICLE; CELL PROLIFERATION; DOWN REGULATION; FOLLOW UP; GENE EXPRESSION REGULATION; GENE MUTATION; GENETIC ASSOCIATION; IMMUNOHISTOCHEMISTRY; MOLECULARLY TARGETED THERAPY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN MOTIF; TRANSCRIPTION REGULATION; TRIPLE NEGATIVE BREAST CANCER;

EID: 84929299585     PISSN: 22145400     EISSN: 22145400     Source Type: Journal    
DOI: 10.1016/j.mgene.2015.04.002     Document Type: Article

References (59)

1. Alexopoulou A., Leao M., Caballero O., Da S., Reid L., Lakhani S., et al. Dissecting the transcriptional networks underlying breast cancer: NR4A1 reduces the migration of normal and breast cancer cell lines. Breast Cancer Res. 2010, 12(4):10.
2. Ben-Porath I., Thomson M.W., Carey V.J., Ge R., Bell G.W., Regev A., et al. An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors. Nat. Genet. 2008, 40(5):499-507.
3. Blum R., Elkon R., Yaari S., Zundelevich A., Jacob-Hirsch J., Rechavi G., et al. Gene expression signature of human cancer cell lines treated with the ras inhibitor salirasib (S-farnesylthiosalicylic acid). Cancer Res. 2007, 67(7):3320-3328.
4. Cancer G. Comprehensive molecular portraits of human breast tumours. Nature 2012, 490(7418):61-70.
5. Carey L.A., Perou C.M., Livasy C.A., Dressler L.G., Cowan D., Conway K., et al. Race, breast cancer subtypes, and survival in the Carolina Breast Cancer Study. JAMA 2006, 295(21):2492-2502.
6. Chen F., Cooney A., Wang Y., Law S., O'Malley B. Cloning of a novel orphan receptor (GCNF) expressed during germ cell development. Mol. Endocrinol. 1994, 8(10):1434-1444.
7. Chin K., DeVries S., Fridlyand J., Spellman P., Roydasgupta R., Kuo W., et al. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 2006, 10(6):529-541.
8. Cornwall G., Hann S. Specialized gene expression in the epididymis. J. Androl. 1995, 16(5):379-383.
9. Dey N., Barwick B., Moreno C., Ordanic-Kodani M., Chen Z., Oprea-Ilies G., et al. Wnt signaling in triple negative breast cancer is associated with metastasis. BMC Cancer 2013, 13(1):537.
10. Dey N., Young B., Abramovitz M., Bouzyk M., Barwick B., De P., et al. Differential activation of Wnt-β-catenin pathway in triple negative breast cancer increases MMP7 in a PTEN dependent manner. PLoS One 2013, 8(10):10.
11. Ding L., Ellis M., Li S., Larson D., Chen K., Wallis J., et al. Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature 2010, 464(7291):999-1005.
12. Fisher R.A. Statistical Methods for Research Workers 1958, (356pp.).
13. Foulkes W., Smith I., Reis-Filho J. Triple-negative breast cancer. N. Engl. J. Med. 2010, 363(20):1938-1948.
14. Fridlyand J., Snijders A., Ylstra B., Li H., Olshen A., Segraves R., et al. Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer 2006, 6:96.
15. Goldstein L.J., O'Neill A., Sparano J.A., Perez E.A., Shulman L.N., Martino S., et al. Concurrent doxorubicin plus docetaxel is not more effective than concurrent doxorubicin plus cyclophosphamide in operable breast cancer with 0 to 3 positive axillary nodes: North American breast cancer intergroup trial E 2197. J. Clin. Oncol. 2008, 26(25):4092-4099.
16. Grigoriadis A., Mackay A., Noel E., Wu P., Natrajan R., Frankum J., et al. Molecular characterisation of cell line models for triple-negative breast cancers. BMC Genomics 2012, 13:619.
17. Hatzis C., Pusztai L., Valero V., Booser D., Esserman L., Lluch A., et al. A genomic predictor of response and survival following taxane-anthracycline chemotherapy for invasive breast cancer. JAMA 2011, 305(18):1873-1881.
18. Hirose T., O'Brien D., Jetten A. RTR: a new member of the nuclear receptor superfamily that is highly expressed in murine testis. Gene 1995, 152(2):247-251.
19. Honeth G., Bendahl P.O., Ringnér M., Saal L.H., Gruvberger-Saal S.K., Lövgren K., et al. The CD44+/CD24- phenotype is enriched in basal-like breast tumors. Breast Cancer Res. 2008, 10(3):R53.
20. Hu Y., Zhou Z., Xu C., Shang Q., Zhang Y., Zhang Y., et al. Androgen down-regulated and region-specific expression of germ cell nuclear factor in mouse epididymis. Endocrinology 2003, 144(4):1612-1619.
21. Ingle J., Twito D., Schaid D., Cullinan S., Krook J., Mailliard J., et al. Randomized clinical trial of tamoxifen alone or combined with fluoxymesterone in postmenopausal women with metastatic breast cancer. J. Clin. Oncol. 1988, 6(5):825-831.
22. Jordan V. Antiestrogens and selective estrogen receptor modulators as multifunctional medicines. 2. Clinical considerations and new agents. J. Med. Chem. 2003, 46(7):1081-1111.
23. Jordan V. Antiestrogens and selective estrogen receptor modulators as multifunctional medicines. 1. Receptor interactions. J. Med. Chem. 2003, 46(6):883-908.
24. Jordan V. SERMs: meeting the promise of multifunctional medicines. J. Natl. Cancer Inst. 2007, 99(5):350-356.
25. Jordan V., O'Malley B. Selective estrogen-receptor modulators and antihormonal resistance in breast cancer. J. Clin. Oncol. 2007, 25(36):5815-5824.
26. Kobayashi S., Shimamura T., Monti S., Steidl U., Hetherington C., Lowell A., et al. Transcriptional profiling identifies cyclin D1 as a critical downstream effector of mutant epidermal growth factor receptor signaling. Cancer Res. 2006, 66(23):11389-11398.
27. Krige D., Needham L., Bawden L., Flores N., Farmer H., Miles L., et al. CHR-2797: an antiproliferative aminopeptidase inhibitor that leads to amino acid deprivation in human leukemic cells. Cancer Res. 2008, 68(16):6669-6679.
28. Kuhn M., Szklarczyk D., Pletscher-Frankild S., Blicher T., von M., Jensen L., et al. STITCH 4: integration of protein-chemical interactions with user data. Nucleic Acids Res. 2014, 42(Database issue):D401-D407.
29. Lee K., Jeong J., Wang J., Ma L., Martin J., Tsai S., et al. Bmp2 is critical for the murine uterine decidual response. Mol. Cell. Biol. 2007, 27(15):5468-5478.
30. Lee S., Li X., Khan S., Safe S. Targeting NR4A1 (TR3) in cancer cells and tumors. Expert Opin. Ther. Targets 2011, 15(2):195-206.
31. Lee S., Andey T., Jin U., Kim K., Singh M., Safe S., et al. The nuclear receptor TR3 regulates mTORC1 signaling in lung cancer cells expressing wild-type p53. Oncogene 2012, 31(27):3265-3276.
32. Lien H.C., Hsiao Y.H., Lin Y.S., Yao Y.T., Juan H.F., Kuo W.H., et al. Molecular signatures of metaplastic carcinoma of the breast by large-scale transcriptional profiling: identification of genes potentially related to epithelial-mesenchymal transition. Oncogene 2007, 26(57):7859-7871.
33. Loo L., Wang Y., Flynn E., Lund M., Bowles E., Buist D., et al. Genome-wide copy number alterations in subtypes of invasive breast cancers in young white and African American women. Breast Cancer Res. Treat. 2011, 127(1):297-308.
34. Mathieu R., Evrard B., Fromont G., Rioux-Leclercq N., Godet J., Cathelineau X., et al. Expression screening of cancer/testis genes in prostate cancer identifies NR6A1 as a novel marker of disease progression and aggressiveness. Prostate 2013, 73(10):1103-1114.
35. Mayer I., Abramson V., Lehmann B., Pietenpol J. New strategies for triple-negative breast cancer-deciphering the heterogeneity. Clin. Cancer Res. 2014, 20(4):782-790.
36. McCall M., Uppal K., Jaffee H., Zilliox M., Irizarry R. The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes. Nucleic Acids Res. 2011, 39(Database issue):D1011-D1015.
37. Miller K., Wang M., Gralow J., Dickler M., Cobleigh M., Perez E., et al. Paclitaxel plus bevacizumab versus paclitaxel alone for metastatic breast cancer. N. Engl. J. Med. 2007, 357(26):2666-2676.
38. Mootha V., Lindgren C., Eriksson K., Subramanian A., Sihag S., Lehar J., et al. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet. 2003, 34(3):267-273.
39. Muscat G., Eriksson N., Byth K., Loi S., Graham D., Jindal S., et al. Research resource: nuclear receptors as transcriptome: discriminant and prognostic value in breast cancer. Mol. Endocrinol. 2013, 27(2):350-365.
40. Neve R., Chin K., Fridlyand J., Yeh J., Baehner F., Fevr T., et al. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell 2006, 10(6):515-527.
41. Rastelli F., Biancanelli S., Falzetta A., Martignetti A., Casi C., Bascioni R., et al. Triple-negative breast cancer: current state of the art. Tumori 2010, 96(6):875-888.
42. Safe S., Kim K., Li X., Lee S.O. NR4A orphan receptors and cancer. Nucl. Recept. Signal. 2011, 9(2011).
43. Safe S., Jin U., Hedrick E., Reeder A., Lee S. Minireview: role of orphan nuclear receptors in cancer and potential as drug targets. Mol. Endocrinol. 2014, 28(2):157-172.
44. Shah S., Roth A., Goya R., Oloumi A., Ha G., Zhao Y., et al. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature 2012, 486(7403):395-399.
45. Shi Y. Orphan nuclear receptors in drug discovery. Drug Discov. Today 2007, 12(11-12):440-445.
46. Siegel R., Naishadham D., Jemal A. Cancer statistics, 2012. CA Cancer J. Clin. 2012, 62(1):10-29.
47. Sørlie T., Perou C., 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(19):10869-10874.
48. Subramanian A., Tamayo P., Mootha V.K., Mukherjee S., Ebert B.L., Gillette M.A., et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. U. S. A. 2005, 102(43):15545-15550.
49. Tobin J., Freedman L. Nuclear receptors as drug targets in metabolic diseases: new approaches to therapy. Trends Endocrinol. Metab. 2006, 17(7):284-290.
50. Toh Y., Li T. Mitoxantrone inhibits HIF-1α expression in a topoisomerase II-independent pathway. Clin. Cancer Res. 2011, 17(15):5026-5037.
51. Wang Q., Cooney A. Revisiting the role of GCNF in embryonic development. Semin. Cell Dev. Biol. 2013, 24(10-12):679-686.
52. Wang W., Jia W., Xu G., Wang Z., Li J., Ma J., et al. Antitumoral activity of rapamycin mediated through inhibition of HIF-1alpha and VEGF in hepatocellular carcinoma. Dig. Dis. Sci. 2009, 54(10):2128-2136.
53. Wang Z., Iwasaki M., Ficara F., Lin C., Matheny C., Wong S.H.K., et al. GSK-3 promotes conditional association of CREB and its co-activators with MEIS1 to facilitate HOX-mediated transcription and oncogenesis. Cancer Cell 2010, 17(6):597-608.
54. Weigman V., Chao H., Shabalin A., He X., Parker J., Nordgard S., et al. Basal-like Breast cancer DNA copy number losses identify genes involved in genomic instability, response to therapy, and patient survival. Breast Cancer Res. Treat. 2012, 133(3):865-880.
55. Whitlock M. Combining probability from independent tests: the weighted Z-method is superior to Fisher's approach. J. Evol. Biol. 2005, 18(5):1368-1373.
56. Willson T., Brown P., Sternbach D., Henke B. The PPARs: from orphan receptors to drug discovery. J. Med. Chem. 2000, 43(4):527-550.
57. Zaykin D. Optimally weighted Z-test is a powerful method for combining probabilities in meta-analysis. J. Evol. Biol. 2011, 24(8):1836-1841.
58. Zhang C., Zou Y., He W., Gage F., Evans R. A role for adult TLX-positive neural stem cells in learning and behaviour. Nature 2008, 451(7181):1004-1007.
59. Zheng Q., Banaszak L., Fracci S., Basali D., Dunlap S., Hursting S., et al. Leptin receptor maintains cancer stem-like properties in triple negative breast cancer cells. Endocr. Relat. Cancer 2013, 20(6):797-808.